diff --git a/docs/collections.md b/docs/collections.md index 0d1ef271e..66ae89a85 100644 --- a/docs/collections.md +++ b/docs/collections.md @@ -8,12 +8,14 @@ were mainly created using the Python library [pyphetools](https://github.com/mon | Cohort | Comments |:----------- |:-------------------- | | [ANKH](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/ANKH/ANKH_Summary.ipynb){:target="_blank"} | 7 Phenopackets; [Craniometaphyseal dysplasia](https://omim.org/entry/123000){:target="_blank"}; [Chondrocalcinosis 2](https://omim.org/entry/118600){:target="_blank"} | +| ANKRD11 | 328 phenopackets; [KBG syndrome](https://omim.org/entry/ 148050){:target="_blank"} | | [COL3A1](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/COL3A1/COL3A1_Summary.ipynb){:target="_blank"} | 39 Phenopackets; [Polymicrogyria with or without vascular-type EDS](https://omim.org/entry/618343){:target="_blank"}; [Ehlers-Danlos syndrome, vascular type](https://omim.org/entry/130050){:target="_blank"} | | [ERI1](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/ERI1/ERI1_Guo_2013_PMID_37352860.ipynb){:target="_blank"} | 10 Phenopackets; [ERI1](https://omim.org/entry/608739){:target="_blank"} | | [EZH1](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/EZH1/GraciaDiaz_EZH1_PMID_37433783.ipynb){:target="_blank"} | 19 Phenopackets; [EZH1](https://omim.org/entry/601674) | -| [FBN1](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/FBN1){:target="_blank"} | 103 phenopackets ;[Ectopia lentis, familial](https://omim.org/entry/129600){:target="_blank"}, [Marfan lipodystrophy syndrome](https://omim.org/entry/616914){:target="_blank"}, [Marfan syndrome](https://omim.org/entry/154700){:target="_blank"}, [Geleophysic dysplasia 2](https://omim.org/entry/614185){:target="_blank"},[Acromicric dysplasia](https://omim.org/entry/102370){:target="_blank"}, | -| [FLXB4](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/FBXL4){:target="_blank"}| todo | +| [FBN1](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/FBN1){:target="_blank"} | 103 phenopackets ;[Ectopia lentis, familial](https://omim.org/entry/129600){:target="_blank"}, [Marfan lipodystrophy syndrome](https://omim.org/entry/616914){:target="_blank"}, [Marfan syndrome](https://omim.org/entry/154700){:target="_blank"}, [Geleophysic dysplasia 2](https://omim.org/entry/614185){:target="_blank"},[Acromicric dysplasia](https://omim.org/entry/102370){:target="_blank"} | +| [FLXB4](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/FBXL4){:target="_blank"|todo | | [GLI3](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/GLI3){:target="_blank"} | 77 phenopackets; [Greig cephalopolysyndactyly syndrome](https://omim.org/entry/175700){:target="_blank"}, [Pallister-Hall syndrome](https://omim.org/entry/146510){:target="_blank"}, [Polydactyly, postaxial, types A1 and B](https://omim.org/entry/174200){:target="_blank"} | +| [KDM6B](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/KDM6B/KDM6B_PMID_37196654.ipynb){:target="_blank"} |73 phenopackets; [Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities](https://omim.org/entry/ 618505){:target="_blank"} | diff --git a/docs/developers.md b/docs/developers.md index b0c81178d..20d9dcf74 100644 --- a/docs/developers.md +++ b/docs/developers.md @@ -15,5 +15,5 @@ other software, and then we present a notebook that summarizes the phenopackets. All phenopackets are stored in subfolders of the notebooks folder, which is organized according to cohort. phenopacket-store has a small python package that facilitates exporting all available phenopackets. See -[](https://github.com/monarch-initiative/phenopacket-store/blob/main/GetPhenopackets.ipynb){:target="_blank"} for details. +[GetPhenopackets](https://github.com/monarch-initiative/phenopacket-store/blob/main/GetPhenopackets.ipynb){:target="_blank"} for details. diff --git a/notebooks/ANKRD11/Martinez-Cayuelas-KBG-2022.ipynb b/notebooks/ANKRD11/Martinez-Cayuelas-KBG-2022.ipynb index 1ef5a0fcc..96a9da1d6 100644 --- a/notebooks/ANKRD11/Martinez-Cayuelas-KBG-2022.ipynb +++ b/notebooks/ANKRD11/Martinez-Cayuelas-KBG-2022.ipynb @@ -957,31 +957,362 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 13, "id": "78e49976-d007-4819-9010-fb6756424773", "metadata": {}, "outputs": [ { - "ename": "TypeError", - "evalue": "PhenopacketTable.__init__() got an unexpected keyword argument 'phenopacket_list'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[12], line 2\u001b[0m\n\u001b[1;32m 1\u001b[0m phenopackets \u001b[38;5;241m=\u001b[39m [i\u001b[38;5;241m.\u001b[39mto_ga4gh_phenopacket(metadata\u001b[38;5;241m=\u001b[39mmetadata\u001b[38;5;241m.\u001b[39mto_ga4gh()) \u001b[38;5;28;01mfor\u001b[39;00m i \u001b[38;5;129;01min\u001b[39;00m individuals]\n\u001b[0;32m----> 2\u001b[0m table \u001b[38;5;241m=\u001b[39m \u001b[43mPhenopacketTable\u001b[49m\u001b[43m(\u001b[49m\u001b[43mphenopacket_list\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mphenopackets\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 3\u001b[0m display(HTML(table\u001b[38;5;241m.\u001b[39mto_html()))\n", - "\u001b[0;31mTypeError\u001b[0m: PhenopacketTable.__init__() got an unexpected keyword argument 'phenopacket_list'" - ] + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
328 phenopackets - PMID:36446582 (n=328)
IndividualDiseaseGenotypePhenotypic features
KBG1 (MALE; P1Y)KBG syndrome (OMIM:148050)16q24.3(89336307_89354085)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Abnormality of the outer ear (HP:0000356)
KBG2 (MALE; P1Y)KBG syndrome (OMIM:148050)16q24.3(89256478_89506223)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); excluded: Global developmental delay (HP:0001263); excluded: Long philtrum (HP:0000343)
KBG3 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2398_2401del (heterozygous)Global developmental delay (HP:0001263); Thick eyebrow (HP:0000574); Hearing impairment (HP:0000365); excluded: Long philtrum (HP:0000343)
KBG4 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7083del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Abnormal external nose morphology (HP:0010938); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG5 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)excluded: Long philtrum (HP:0000343)
KBG64 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7407C>G (heterozygous)Intellectual disability (HP:0001249); Short stature (HP:0004322); Hearing impairment (HP:0000365)
KBG6 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6691dup (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729)
KBG10A (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3590_3594del (heterozygous)Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Hearing impairment (HP:0000365); excluded: Short stature (HP:0004322)
KBG10B (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3590_3594del (heterozygous)Macrodontia (HP:0001572); Triangular face (HP:0000325); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Abnormal external nose morphology (HP:0010938); excluded: Thick eyebrow (HP:0000574); excluded: Long philtrum (HP:0000343); excluded: Short stature (HP:0004322)
KBG8A (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6792dup (heterozygous)Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Autistic behavior (HP:0000729); excluded: Thick eyebrow (HP:0000574); excluded: Long philtrum (HP:0000343); excluded: Hearing impairment (HP:0000365)
KBG8B (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6792dup (heterozygous)Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Thick eyebrow (HP:0000574); excluded: Long philtrum (HP:0000343)
KBG9 (FEMALE; P1Y)KBG syndrome (OMIM:148050)16q24.3(88854757_89520963)x1 (hg19): chromosomal_deletion (SO:1000029)excluded: Intellectual disability (HP:0001249); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Global developmental delay (HP:0001263); excluded: Abnormal external nose morphology (HP:0010938); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Long philtrum (HP:0000343); excluded: Abnormality of the outer ear (HP:0000356); excluded: Abnormality of the hand (HP:0001155); excluded: Hearing impairment (HP:0000365)
KBG39 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3193A>T (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG40 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3309dup (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263)
KBG41 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1381_1384del (heterozygous)Hearing impairment (HP:0000365)
KBG32 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2765_2766del (heterozygous)Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); excluded: Intellectual disability (HP:0001249); excluded: Long philtrum (HP:0000343); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG33 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.548_551del (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Triangular face (HP:0000325); excluded: Long philtrum (HP:0000343); excluded: Short stature (HP:0004322)
KBG34 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.831del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Hearing impairment (HP:0000365); excluded: Abnormality of the outer ear (HP:0000356); excluded: Short stature (HP:0004322)
KBG35 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Attention deficit hyperactivity disorder (HP:0007018); Abnormal external nose morphology (HP:0010938); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Long philtrum (HP:0000343); excluded: Short stature (HP:0004322)
KBG36 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2408_2412del (heterozygous)Intellectual disability (HP:0001249); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Global developmental delay (HP:0001263); excluded: Long philtrum (HP:0000343); excluded: Abnormality of the hand (HP:0001155)
KBG37 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3046del (heterozygous)Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Thick eyebrow (HP:0000574)
KBG38 (FEMALE; P1Y)KBG syndrome (OMIM:148050)16q24.3(89349711_89607741)x1 (hg19): chromosomal_deletion (SO:1000029)Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Hearing impairment (HP:0000365); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Abnormality of the outer ear (HP:0000356); excluded: Short stature (HP:0004322)
KBG65 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3905_3906del (heterozygous)Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Intellectual disability (HP:0001249); excluded: Autistic behavior (HP:0000729); excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG66 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4384dup (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); excluded: Abnormality of the outer ear (HP:0000356); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
KBG59 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1731dup (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Hearing impairment (HP:0000365); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Abnormality of the outer ear (HP:0000356); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
KBG7 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1940_1941delinsT (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Macrodontia (HP:0001572); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574)
KBG49 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7180C>T (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Long philtrum (HP:0000343)
KBG50 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7570_7572del (heterozygous)Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Intellectual disability (HP:0001249); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG63 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6682del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Long philtrum (HP:0000343); excluded: Abnormality of the hand (HP:0001155)
KBG48 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249); excluded: Autistic behavior (HP:0000729); excluded: Global developmental delay (HP:0001263)
KBG43 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1367_1370del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); excluded: Global developmental delay (HP:0001263)
KBG51 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5790C>A (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Thick eyebrow (HP:0000574); excluded: Long philtrum (HP:0000343); excluded: Abnormality of the hand (HP:0001155)
KBG52 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2593dup (heterozygous)Intellectual disability (HP:0001249); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Macrodontia (HP:0001572); excluded: Long philtrum (HP:0000343); excluded: Hearing impairment (HP:0000365)
KBG53 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1846G>T (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Abnormal external nose morphology (HP:0010938); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Autistic behavior (HP:0000729); excluded: Macrodontia (HP:0001572); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Long philtrum (HP:0000343); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG54 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.520C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Macrodontia (HP:0001572); excluded: Long philtrum (HP:0000343); excluded: Short stature (HP:0004322)
KBG55 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6701del (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Abnormal external nose morphology (HP:0010938); excluded: Triangular face (HP:0000325); excluded: Long philtrum (HP:0000343); excluded: Hearing impairment (HP:0000365)
KBG56 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2367del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Abnormal external nose morphology (HP:0010938); excluded: Long philtrum (HP:0000343)
KBG57 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2197C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Macrodontia (HP:0001572); excluded: Abnormal external nose morphology (HP:0010938); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Long philtrum (HP:0000343); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG58 (MALE; P1Y)KBG syndrome (OMIM:148050)16q24.3(89283689-89579130)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Autistic behavior (HP:0000729); excluded: Global developmental delay (HP:0001263); excluded: Triangular face (HP:0000325); excluded: Long philtrum (HP:0000343); excluded: Hearing impairment (HP:0000365)
KBG31A (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7834G>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Macrodontia (HP:0001572)
KBG47 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3448C>T (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Hearing impairment (HP:0000365); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Short stature (HP:0004322)
KBG19 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4171C>T (heterozygous)Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249); excluded: Autistic behavior (HP:0000729); excluded: Hearing impairment (HP:0000365)
KBG20 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249); excluded: Long philtrum (HP:0000343); excluded: Hearing impairment (HP:0000365)
KBG21 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3931C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Abnormality of the outer ear (HP:0000356); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG22 (FEMALE; P1Y)KBG syndrome (OMIM:148050)16q24.3(89359701_89379306)x1 (hg19): chromosomal_deletion (SO:1000029)Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Intellectual disability (HP:0001249); excluded: Autistic behavior (HP:0000729); excluded: Triangular face (HP:0000325); excluded: Short stature (HP:0004322)
KBG44 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Abnormal external nose morphology (HP:0010938)
KBG45 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Abnormal external nose morphology (HP:0010938); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Long philtrum (HP:0000343); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG62 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4384dup (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Triangular face (HP:0000325); excluded: Autistic behavior (HP:0000729); excluded: Abnormal external nose morphology (HP:0010938); excluded: Thick eyebrow (HP:0000574); excluded: Long philtrum (HP:0000343); excluded: Abnormality of the outer ear (HP:0000356); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG46 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7534C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Macrodontia (HP:0001572); excluded: Abnormal external nose morphology (HP:0010938); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Abnormality of the hand (HP:0001155)
KBG11 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3334del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Global developmental delay (HP:0001263); excluded: Macrodontia (HP:0001572)
KBG12 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6792dup (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Autistic behavior (HP:0000729); excluded: Triangular face (HP:0000325); excluded: Long philtrum (HP:0000343)
KBG13 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2329_2332del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Abnormality of the hand (HP:0001155)
KBG14 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5790C>A (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG15 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6968_6975del (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Hearing impairment (HP:0000365); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Abnormality of the outer ear (HP:0000356); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
KBG16 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2329_2332del (heterozygous)Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Intellectual disability (HP:0001249); excluded: Abnormality of the hand (HP:0001155)
KBG17 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6628G>T (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Abnormality of the hand (HP:0001155)
KBG18 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7753C>T (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Thick eyebrow (HP:0000574); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG23 (FEMALE; P1Y)KBG syndrome (OMIM:148050)16q24.3(89325387_89409147)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Thick eyebrow (HP:0000574); excluded: Abnormality of the hand (HP:0001155)
KBG24 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6792dup (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Abnormality of the outer ear (HP:0000356); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
KBG25 (MALE; P1Y)KBG syndrome (OMIM:148050)16q24.3(89556618_89557004)x1 (hg19): chromosomal_deletion (SO:1000029)Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Abnormal external nose morphology (HP:0010938); excluded: Triangular face (HP:0000325); excluded: Long philtrum (HP:0000343); excluded: Hearing impairment (HP:0000365)
KBG26 (MALE; P1Y)KBG syndrome (OMIM:148050)16q24.3(89261399_89419131)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Long philtrum (HP:0000343); excluded: Abnormality of the outer ear (HP:0000356); excluded: Abnormality of the hand (HP:0001155)
KBG27 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Thick eyebrow (HP:0000574); excluded: Abnormality of the hand (HP:0001155); excluded: Hearing impairment (HP:0000365)
KBG28 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4529dup (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Abnormality of the outer ear (HP:0000356); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
KBG29 (MALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3704_3707del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Autistic behavior (HP:0000729); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Abnormality of the hand (HP:0001155); excluded: Hearing impairment (HP:0000365)
KBG30 (FEMALE; P1Y)KBG syndrome (OMIM:148050)NM_013275.6:c.866dup (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
Alves, 2019 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5145C>G (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Behnert, 2018 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(88854757_89577705)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018)
Bianchi, 2018 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2408_2412del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Hearing impairment (HP:0000365); excluded: Abnormality of the outer ear (HP:0000356); excluded: Short stature (HP:0004322)
Bucerzan2020 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89542695_89656251)x3 (hg19): chromosomal_duplication (SO:1000037)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Crippa2015_P1 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89350931_89439639)x3 (hg19): chromosomal_duplication (SO:1000037)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Crippa2015_P2 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89350931_89439639)x3 (hg19): chromosomal_duplication (SO:1000037)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Crippa2015_P3 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89350931_89439639)x3 (hg19): chromosomal_duplication (SO:1000037)Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155)
Cucco, 2020 (Patient B) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3224_3227del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Hearing impairment (HP:0000365); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
DeBernardi2018 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4528_4529del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Gnazzo, 2020_P1 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1285_1286del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P10 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2398_2401del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P11 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2408_2412del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P12 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2412del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P13 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3019C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P14 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3180dup (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P15 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3309dup (heterozygous)Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249); excluded: Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P16 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3770_3771del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P17 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4107_4108del (heterozygous)Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P18 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4374_4375del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P19 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4389_4390del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P2 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1385_1388del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P20 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4498C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P21 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5146G>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P22 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5205del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P23 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5712_5713insT (heterozygous)Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249); excluded: Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P24 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6513dup (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P25 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7000C>T (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P26 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7192C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P27 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7216C>T (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P28 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7416C>G (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Macrodontia (HP:0001572)
Gnazzo, 2020_P29 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89283689_89572450)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P3 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1457C>G (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Macrodontia (HP:0001572)
Gnazzo, 2020_P30 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89273092_89577046)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P31 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.2q24.3(87652026_89507330)x1 (hg19): chromosomal_deletion (SO:1000029)Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Short stature (HP:0004322); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P4 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P5 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1977C>G (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P6 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1977C>G (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Macrodontia (HP:0001572)
Gnazzo, 2020_P7 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2175_2178del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Gnazzo, 2020_P8 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2175_2178del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155)
Gnazzo, 2020_P9 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2197C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P1 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89249149_89376186)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P10 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89199607_89472627)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Goldenberg2016_P11 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Goldenberg2016_P12 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89315698_89548093)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P13 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(88809983_89472627)x1 (hg19): chromosomal_deletion (SO:1000029)Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Goldenberg2016_P14 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1120G>T (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Goldenberg2016_P15 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3198_3199del (heterozygous)Global developmental delay (HP:0001263); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Goldenberg2016_P16 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1381_1384del (heterozygous)Global developmental delay (HP:0001263); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Goldenberg2016_P17 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1381_1384del (heterozygous)Global developmental delay (HP:0001263); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Macrodontia (HP:0001572)
Goldenberg2016_P18 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3(88621654_89383486)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P19 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89328477_89477051)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Goldenberg2016_P2 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89249149_89376186)x1 (hg19): chromosomal_deletion (SO:1000029)Macrodontia (HP:0001572); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P20 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89328477_89477051)x1 (hg19): chromosomal_deletion (SO:1000029)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Goldenberg2016_P21 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89161684-89505106)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P22 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3(88230961_89383486)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Short stature (HP:0004322)
Goldenberg2016_P23 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3774_3775del (heterozygous)Global developmental delay (HP:0001263); Short stature (HP:0004322); excluded: Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P24 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89435258-89553707)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Short stature (HP:0004322)
Goldenberg2016_P25 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2647G>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Short stature (HP:0004322); excluded: Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P26 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3(87925812_89521860)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P27 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6792dup (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P28 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(88763460_89344049)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Goldenberg2016_P29 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89461583_89559189)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Short stature (HP:0004322); excluded: Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P3 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89249149_89376186)x1 (hg19): chromosomal_deletion (SO:1000029)Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Goldenberg2016_P30 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6766C>T (heterozygous)Global developmental delay (HP:0001263); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Intellectual disability (HP:0001249); excluded: Short stature (HP:0004322)
Goldenberg2016_P31 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1367_1370del (heterozygous)Global developmental delay (HP:0001263); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Goldenberg2016_P32 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(87800226-89559330)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P33 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89507776_89565656)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Macrodontia (HP:0001572)
Goldenberg2016_P34 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4087C>T (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Goldenberg2016_P35 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4786G>T (heterozygous)Global developmental delay (HP:0001263); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Short stature (HP:0004322)
Goldenberg2016_P36 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89295307_89559189)x1 (hg19): chromosomal_deletion (SO:1000029)Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Short stature (HP:0004322)
Goldenberg2016_P38 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.867C>G (heterozygous)Macrodontia (HP:0001572); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Goldenberg2016_P39 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1893dup (heterozygous)Abnormality of the hand (HP:0001155); excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Goldenberg2016_P4 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89249149_89376186)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Goldenberg2016_P5 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1381_1384del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Goldenberg2016_P6 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3153del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Goldenberg2016_P7 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3045del (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Intellectual disability (HP:0001249); excluded: Short stature (HP:0004322)
Goldenberg2016_P8 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2398_2401del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Goldenberg2016_P9 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Global developmental delay (HP:0001263); Abnormality of the hand (HP:0001155); excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Isrie, 2012_P1 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89343893_89565656)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Isrie, 2012_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89335228-89472768)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Abnormality of the hand (HP:0001155)
Jin Kim, 2020_P1 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5889del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Jin Kim, 2020_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3310dup (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Macrodontia (HP:0001572); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Khalifa, 2013_P1A (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89388113_89541926)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Triangular face (HP:0000325)
Khalifa, 2013_P1B (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89388113_89541926)x1 (hg19): chromosomal_deletion (SO:1000029)Macrodontia (HP:0001572); Long philtrum (HP:0000343); excluded: Autistic behavior (HP:0000729); excluded: Triangular face (HP:0000325); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
Kim, 2015_P1 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2398_2401del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Kim, 2015_P2 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2398_2401del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Kim, 2015_P3 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2398_2401del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Kleyner, 2016 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6015dup (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Triangular face (HP:0000325)
Kutkowska-Kazmierczak2021_P1 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Triangular face (HP:0000325); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249)
Kutkowska-Kazmierczak2021_P10 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3295_3296del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Triangular face (HP:0000325); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P11 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3771dup (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P12 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1385_1388del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P13 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6053_6057del (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Triangular face (HP:0000325); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P14 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.2-24.3(87954851-89484166)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P15 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.3(89238120-89341161)x1 (hg19): chromosomal_deletion (SO:1000029)excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P16 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.3(89343893-89584394)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P17 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.3(89261814-89556020)x3 (hg19): chromosomal_duplication (SO:1000037)Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); excluded: Intellectual disability (HP:0001249); excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P18 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.3(89332453-89371851)x1 (hg19): chromosomal_deletion (SO:1000029)excluded: Intellectual disability (HP:0001249); excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P19 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.3(89343893-89497947)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P2 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); excluded: Intellectual disability (HP:0001249); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P20 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.3(89525403-89553574)x1 (hg19): chromosomal_deletion (SO:1000029)Short stature (HP:0004322); excluded: Macrodontia (HP:0001572)
Kutkowska-Kazmierczak2021_P21 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.3(89547555-89556020)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P22 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.3(89476167-89484721)x1 (hg19): chromosomal_deletion (SO:1000029)Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P23 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.3(89343893-89555548)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P3 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7607G>A (heterozygous)Triangular face (HP:0000325); excluded: Intellectual disability (HP:0001249); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P4 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4558del (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Triangular face (HP:0000325); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249)
Kutkowska-Kazmierczak2021_P5 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2395A>T (heterozygous)Global developmental delay (HP:0001263); Triangular face (HP:0000325); excluded: Intellectual disability (HP:0001249); excluded: Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P6 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1389dup (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Triangular face (HP:0000325); Short stature (HP:0004322); excluded: Macrodontia (HP:0001572)
Kutkowska-Kazmierczak2021_P7 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7552C>T (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P8 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2828_2829del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Triangular face (HP:0000325); excluded: Short stature (HP:0004322)
Kutkowska-Kazmierczak2021_P9 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6340C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); excluded: Short stature (HP:0004322)
Libianto2019 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3045del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Triangular face (HP:0000325); excluded: Long philtrum (HP:0000343)
Lim2014 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89349966-89593853)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_30 (28) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4408A>T (heterozygous)Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Low, 2016_31 (29) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2182_2183del (heterozygous)Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_32 (30) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2182_2183del (heterozygous)Macrodontia (HP:0001572); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_33 (31) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2182_2183del (heterozygous)Macrodontia (HP:0001572); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_34 (32) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2512C>T (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P1 (19) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Macrodontia (HP:0001572); Short stature (HP:0004322); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P10 (18) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2408_2412del (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P11 (20) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2408_2412del (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155)
Low, 2016_P12 (13) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2408_2412del (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P13 (27) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2408_2412del (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P14 (2) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2398_2401del (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P15 (3) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5426_5430del (heterozygous)Macrodontia (HP:0001572); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P16 (9) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5274dup (heterozygous)Autistic behavior (HP:0000729); Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P17 (10) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3437_3461del (heterozygous)Macrodontia (HP:0001572); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P18 (12) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1381_1384del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Hearing impairment (HP:0000365); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P2 (26) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Abnormality of the hand (HP:0001155); excluded: Abnormality of mental function (HP:0011446); excluded: Macrodontia (HP:0001572)
Low, 2016_P20 (14) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4103_4104del (heterozygous)Macrodontia (HP:0001572); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P21 (15) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7363del (heterozygous)Macrodontia (HP:0001572); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P22 (16) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3208_3209del (heterozygous)Macrodontia (HP:0001572); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P23 (17) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4177_4189del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155)
Low, 2016_P24 (21) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3582del (heterozygous)Macrodontia (HP:0001572); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P25 (22) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3704_3707del (heterozygous)excluded: Abnormality of mental function (HP:0011446); excluded: Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P26 (23) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4206C>G (heterozygous)Autistic behavior (HP:0000729); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365)
Low, 2016_P27 (24) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5199_5227del (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P28 (25) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6364_6367del (heterozygous)Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Hearing impairment (HP:0000365); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P29 (27) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1801C>T (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P3 (4) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Macrodontia (HP:0001572); excluded: Abnormality of mental function (HP:0011446); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P4 (5) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P5 (6) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P6 (7) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P7 (8) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); excluded: Abnormality of mental function (HP:0011446)
Low, 2016_P8 (33) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)excluded: Abnormality of mental function (HP:0011446); excluded: Macrodontia (HP:0001572); excluded: Abnormality of the hand (HP:0001155)
Low, 2016_P9 (1) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2408_2412del (heterozygous)Autistic behavior (HP:0000729); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Macrodontia (HP:0001572)
Low2017 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7471-1G>C (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
Mattei2021 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Hearing impairment (HP:0000365); excluded: Abnormality of the outer ear (HP:0000356); excluded: Short stature (HP:0004322)
Miyatake, 2013 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3(88641808-89332049)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Triangular face (HP:0000325); excluded: Short stature (HP:0004322)
Miyatake, 2017_P1 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Macrodontia (HP:0001572); excluded: Abnormal external nose morphology (HP:0010938)
Miyatake, 2017_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3224_3227del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); excluded: Triangular face (HP:0000325)
Miyatake, 2017_P3 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6187G>T (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); excluded: Abnormal external nose morphology (HP:0010938); excluded: Abnormality of the hand (HP:0001155)
Murray, 2017_P1 (1.1) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Triangular face (HP:0000325); Long philtrum (HP:0000343); Hearing impairment (HP:0000365); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Murray, 2017_P10 (7.1.) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7471A>C (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Murray, 2017_P11 (8.1.) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6409_6410del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Murray, 2017_P12 (9.1) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3224_3227del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Murray, 2017_P13 (11.1) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7216C>T (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Murray, 2017_P16 (13.1) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6472G>T (heterozygous)Intellectual disability (HP:0001249); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Murray, 2017_P2 (1.2) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Murray, 2017_P3 (1.3) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); excluded: Abnormality of the outer ear (HP:0000356); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Murray, 2017_P4 (2.1) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.505G>T (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Murray, 2017_P5 (3.1) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4406G>A (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); excluded: Long philtrum (HP:0000343); excluded: Short stature (HP:0004322)
Murray, 2017_P6 (3.2) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4406G>A (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Triangular face (HP:0000325); excluded: Long philtrum (HP:0000343)
Murray, 2017_P7 (3.3) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4406G>A (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Long philtrum (HP:0000343)
Murray, 2017_P8 (4.1) (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Murray, 2017_P9 (5.1.) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1173C>G (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Abnormality of the outer ear (HP:0000356); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Novara, 2017_P1 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3 (88635000_89628950)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Triangular face (HP:0000325)
Novara, 2017_P11 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3 (89161684_89505106)x1 (hg19): chromosomal_deletion (SO:1000029)Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Novara, 2017_P12 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3(88666177_89472627)x1 (hg19): chromosomal_deletion (SO:1000029)Long philtrum (HP:0000343); Hearing impairment (HP:0000365); excluded: Triangular face (HP:0000325); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Novara, 2017_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3 (87340135_89335428)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Abnormality of the hand (HP:0001155); excluded: Macrodontia (HP:0001572); excluded: Triangular face (HP:0000325); excluded: Short stature (HP:0004322)
Novara, 2017_P3 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3 (88230961_89363602)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Hearing impairment (HP:0000365); excluded: Triangular face (HP:0000325); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Novara, 2017_P4 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3 (88755312_89584412)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Abnormality of the hand (HP:0001155)
Novara, 2017_P5 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3 (88556191_89557911)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Hearing impairment (HP:0000365); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Abnormality of the outer ear (HP:0000356); excluded: Short stature (HP:0004322)
Novara, 2017_P7 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3 (88230760-89363742)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); excluded: Triangular face (HP:0000325); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Novara, 2017_P8 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3 (88630607_89607742)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729)
Novara, 2017_P9 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3 (87183661_89520803)x1 (hg19): chromosomal_deletion (SO:1000029)Short stature (HP:0004322)
Ockeloen2015_P1 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7481dup (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Ockeloen2015_P10 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Ockeloen2015_P11 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3832A>T (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Ockeloen2015_P12 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3832A>T (heterozygous)Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Ockeloen2015_P13 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3832A>T (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Ockeloen2015_P14 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2751dup (heterozygous)Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249); excluded: Abnormality of the hand (HP:0001155)
Ockeloen2015_P15 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3382_3383del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Ockeloen2015_P16 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Ockeloen2015_P17 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6513dup (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Ockeloen2015_P18 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1318C>T (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Ockeloen2015_P19 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1318C>T (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Ockeloen2015_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7481dup (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Ockeloen2015_P20 (UNKNOWN; P2Y)KBG syndrome (OMIM:148050)16q24.3(88231090-89388103)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Short stature (HP:0004322); excluded: Triangular face (HP:0000325); excluded: Abnormality of the hand (HP:0001155)
Ockeloen2015_P3 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7481dup (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Short stature (HP:0004322)
Ockeloen2015_P4 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7481dup (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Triangular face (HP:0000325)
Ockeloen2015_P5 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7481dup (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Ockeloen2015_P6 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4391_4392del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Ockeloen2015_P7 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6184del (heterozygous)Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Ockeloen2015_P8 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3123_3126del (heterozygous)Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Intellectual disability (HP:0001249)
Ockeloen2015_P9 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1460_1463del (heterozygous)Intellectual disability (HP:0001249); Triangular face (HP:0000325); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Macrodontia (HP:0001572)
Palumbo 2016 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2q24.3 (87502161_89688617)x3 (hg19): chromosomal_duplication (SO:1000037)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Abnormality of the hand (HP:0001155); excluded: Autistic behavior (HP:0000729); excluded: Short stature (HP:0004322); excluded: Hearing impairment (HP:0000365)
Parenti2016_P1 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5483C>A (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Macrodontia (HP:0001572); excluded: Triangular face (HP:0000325); excluded: Short stature (HP:0004322)
Parenti2016_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2297_2300del (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); excluded: Triangular face (HP:0000325); excluded: Short stature (HP:0004322)
Parenti2021_P1 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.915del (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Hearing impairment (HP:0000365); excluded: Triangular face (HP:0000325); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Parenti2021_P10 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4218C>A (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Short stature (HP:0004322)
Parenti2021_P11 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4087C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Macrodontia (HP:0001572); excluded: Triangular face (HP:0000325); excluded: Short stature (HP:0004322)
Parenti2021_P12 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7470+2T>C (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Parenti2021_P13 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1381_1384del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Parenti2021_P14 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Thick eyebrow (HP:0000574); excluded: Short stature (HP:0004322)
Parenti2021_P15 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3888dup (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Thick eyebrow (HP:0000574); excluded: Short stature (HP:0004322)
Parenti2021_P16 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3591_3594del (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Short stature (HP:0004322)
Parenti2021_P17 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1381_1384del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Autistic behavior (HP:0000729); excluded: Global developmental delay (HP:0001263); excluded: Short stature (HP:0004322)
Parenti2021_P18 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Short stature (HP:0004322)
Parenti2021_P19 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Thick eyebrow (HP:0000574); excluded: Short stature (HP:0004322)
Parenti2021_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1711_1723del (heterozygous)Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Intellectual disability (HP:0001249); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Short stature (HP:0004322)
Parenti2021_P20 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2408_2412del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Thick eyebrow (HP:0000574); excluded: Short stature (HP:0004322)
Parenti2021_P21 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5123C>A (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Parenti2021_P22 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1381_1384del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Autistic behavior (HP:0000729); excluded: Attention deficit hyperactivity disorder (HP:0007018)
Parenti2021_P23 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89335426-89371803)x1 (hg19): chromosomal_deletion (SO:1000029)Autistic behavior (HP:0000729); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365)
Parenti2021_P3 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1977C>G (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Triangular face (HP:0000325)
Parenti2021_P4 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2398_2401del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Triangular face (HP:0000325)
Parenti2021_P5 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2408_2412del (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249); excluded: Triangular face (HP:0000325)
Parenti2021_P6 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2692C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Triangular face (HP:0000325); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Parenti2021_P7 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7356dup (heterozygous)Global developmental delay (HP:0001263); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); excluded: Intellectual disability (HP:0001249); excluded: Macrodontia (HP:0001572); excluded: Triangular face (HP:0000325); excluded: Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Parenti2021_P8 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7411_7422del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Triangular face (HP:0000325); excluded: Thick eyebrow (HP:0000574); excluded: Short stature (HP:0004322)
Parenti2021_P9 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155); excluded: Triangular face (HP:0000325); excluded: Short stature (HP:0004322)
Rentas2021_P1 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.211_226+1del (heterozygous)Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); excluded: Short stature (HP:0004322)
Sacharow, 2012_P1 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89283689_89603390)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Triangular face (HP:0000325); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365); excluded: Short stature (HP:0004322)
Sacharow, 2012_P2 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89295307-89660379)x1 (hg19): chromosomal_deletion (SO:1000029)Macrodontia (HP:0001572); Triangular face (HP:0000325); Abnormality of the hand (HP:0001155)
Sayed, 2020_P1 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5488G>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Sayed, 2020_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5488G>T (heterozygous)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Short stature (HP:0004322); excluded: Thick eyebrow (HP:0000574); excluded: Abnormality of the hand (HP:0001155)
Scarano, 2013_P1 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2197C>T (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Scarano, 2013_P10 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-q24.3 (89283689_89429735)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Scarano, 2013_P11 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3 (89335428_89559189)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Scarano, 2013_P12 (FEMALE; P2Y)KBG syndrome (OMIM:148050)16q24.3 (89429676_89559189)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Scarano, 2013_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3221_3222del (heterozygous)Macrodontia (HP:0001572); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Scarano, 2013_P3 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5957_5958del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Scarano, 2013_P4 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3974del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Scarano, 2013_P5 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3222dup (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Scarano, 2013_P6 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2866G>T (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Scarano, 2013_P7 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7534C>T (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Scarano, 2013_P8 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2650del (heterozygous)Macrodontia (HP:0001572); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249)
Scarano, 2013_P9 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3339G>A (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); Hearing impairment (HP:0000365)
Sirmaci2011_P1/F1? (previously published Tekin, 2004) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7570-1G>C (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155)
Sirmaci2011_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2305del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155)
Sirmaci2011_P2/F1? (previously published Tekin, 2004) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7570-1G>C (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Hearing impairment (HP:0000365)
Sirmaci2011_P3 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7189C>T (heterozygous)Intellectual disability (HP:0001249); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the hand (HP:0001155)
Sirmaci2011_P3/F1? (previously published Tekin, 2004) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7570-1G>C (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155)
Sirmaci2011_P4 (previously published Brancati, 2004) (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.5953_5954del (heterozygous)Intellectual disability (HP:0001249); Attention deficit hyperactivity disorder (HP:0007018); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155)
Sirmaci2011_P5 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6071_6084del (heterozygous)Intellectual disability (HP:0001249); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155)
Spengler, 2013 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89371838_89607414)x1 (hg19): chromosomal_deletion (SO:1000029)Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Abnormality of the outer ear (HP:0000356); Abnormality of the hand (HP:0001155); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249)
Srivastava, 2017_P1 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.1q24.3 (86680657_89578069)x1 (hg19): chromosomal_deletion (SO:1000029)Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Thick eyebrow (HP:0000574); Long philtrum (HP:0000343); Short stature (HP:0004322); Hearing impairment (HP:0000365); excluded: Abnormality of the hand (HP:0001155)
VanDongen2019_P1 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1763C>A (heterozygous)Hearing impairment (HP:0000365)
VanDongen2019_P10 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.3460G>T (heterozygous)Hearing impairment (HP:0000365)
VanDongen2019_P3 (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4964_4965del (heterozygous)Hearing impairment (HP:0000365)
VanDongen2019_P6 (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2175_2178del (heterozygous)Hearing impairment (HP:0000365)
Walz2015_PA (FEMALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1785_1786delinsTT (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Walz2015_PB (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.1903_1907del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); Short stature (HP:0004322)
Walz2015_PC (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.2130del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Walz2015_PD (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.4283_4286del (heterozygous)Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Short stature (HP:0004322); excluded: Intellectual disability (HP:0001249)
Walz2015_PE (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.6817_6833del (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Short stature (HP:0004322)
Walz2015_Pf (MALE; P2Y)KBG syndrome (OMIM:148050)NM_013275.6:c.7535G>A (heterozygous)Intellectual disability (HP:0001249); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Thick eyebrow (HP:0000574); Abnormality of the hand (HP:0001155); excluded: Short stature (HP:0004322)
Willemsen2010_P1 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89122739_89501030)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Abnormality of the outer ear (HP:0000356); Short stature (HP:0004322); excluded: Triangular face (HP:0000325)
Willemsen2010_P2 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(89273092_89538759)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); excluded: Abnormality of the outer ear (HP:0000356); excluded: Short stature (HP:0004322)
Willemsen2010_P3 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-24.3(87498264_89596942)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Global developmental delay (HP:0001263); Hearing impairment (HP:0000365); excluded: Thick eyebrow (HP:0000574); excluded: Abnormality of the outer ear (HP:0000356)
Willemsen2010_P4 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.2-24.3(88230961_89363602)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); excluded: Abnormality of the outer ear (HP:0000356); excluded: Short stature (HP:0004322)
Youngs2011 (MALE; P2Y)KBG syndrome (OMIM:148050)16q24.3(87920000-88100000)x1 (hg19): chromosomal_deletion (SO:1000029)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Global developmental delay (HP:0001263); Macrodontia (HP:0001572); Abnormal external nose morphology (HP:0010938); Triangular face (HP:0000325); Short stature (HP:0004322); Hearing impairment (HP:0000365)
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" } ], "source": [ - "phenopackets = [i.to_ga4gh_phenopacket(metadata=metadata.to_ga4gh()) for i in individuals]\n", - "table = PhenopacketTable(individual_list==phenopackets)\n", + "table = PhenopacketTable(individual_list=individuals, metadata=metadata)\n", "display(HTML(table.to_html()))" ] }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 14, "id": "059f0438-697c-4a64-a2eb-37eaaaabafe9", "metadata": {}, "outputs": [ diff --git a/notebooks/EZH1/GraciaDiaz_EZH1_PMID_37433783.ipynb b/notebooks/EZH1/GraciaDiaz_EZH1_PMID_37433783.ipynb index f6430f968..3dccbc8e1 100644 --- a/notebooks/EZH1/GraciaDiaz_EZH1_PMID_37433783.ipynb +++ b/notebooks/EZH1/GraciaDiaz_EZH1_PMID_37433783.ipynb @@ -20,7 +20,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "pyphetools version 0.8.23\n" + "pyphetools version 0.8.25\n" ] } ], @@ -1754,7 +1754,7 @@ }, { "cell_type": "code", - "execution_count": 53, + "execution_count": null, "id": "cb47bcdf", "metadata": {}, "outputs": [], diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P1.json b/notebooks/EZH1/phenopackets/PMID_37433783_P1.json index 9d4d8485c..5cd2411f1 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P1.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P1.json @@ -198,7 +198,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_NEbMnBilEFCMojheDNlrMruYw", + "id": "var_prvDFILOPxkMRZLzsRJsNGqYu", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -233,7 +233,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.603188037Z", + "created": "2023-11-25T07:14:09.439437150Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P10.json b/notebooks/EZH1/phenopackets/PMID_37433783_P10.json index 7d454d6df..ecbf943e7 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P10.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P10.json @@ -187,7 +187,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_ymDUYYHdgWFZDPfydNDYRNjkj", + "id": "var_vZnmVYitTIxtswOmndqBKqymO", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -222,7 +222,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.652964115Z", + "created": "2023-11-25T07:14:09.500533103Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P11.json b/notebooks/EZH1/phenopackets/PMID_37433783_P11.json index 7f7a2b6c7..349c8d298 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P11.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P11.json @@ -182,7 +182,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_ymDUYYHdgWFZDPfydNDYRNjkj", + "id": "var_vZnmVYitTIxtswOmndqBKqymO", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -217,7 +217,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.655633926Z", + "created": "2023-11-25T07:14:09.511334896Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P12.json b/notebooks/EZH1/phenopackets/PMID_37433783_P12.json index 9ca71d2db..eab796c15 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P12.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P12.json @@ -168,7 +168,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_FfABaTfmVRhindhltqlfVdUAz", + "id": "var_FcKVcCTYYTKgTxbxTpQkelchP", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -203,7 +203,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_rQhmfKMAuhjgEnngJWSpedgel", + "id": "var_vVIUmLxzLKqXTEgdiRReSimlE", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -238,7 +238,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.658720016Z", + "created": "2023-11-25T07:14:09.516778945Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P13.json b/notebooks/EZH1/phenopackets/PMID_37433783_P13.json index cfa951cb2..5ba1d1412 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P13.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P13.json @@ -127,7 +127,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_NfNmEmsihWFkJxtROwnchhVoR", + "id": "var_vsIMzDKCOoGzWolllJFVzbYTz", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -162,7 +162,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.669409990Z", + "created": "2023-11-25T07:14:09.523674011Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P14.json b/notebooks/EZH1/phenopackets/PMID_37433783_P14.json index e1938ba27..21c4c19b4 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P14.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P14.json @@ -85,7 +85,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_NfNmEmsihWFkJxtROwnchhVoR", + "id": "var_vsIMzDKCOoGzWolllJFVzbYTz", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -120,7 +120,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.672555923Z", + "created": "2023-11-25T07:14:09.535418987Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P15.json b/notebooks/EZH1/phenopackets/PMID_37433783_P15.json index 2b22cb348..65ac0c1ef 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P15.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P15.json @@ -114,7 +114,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_NfNmEmsihWFkJxtROwnchhVoR", + "id": "var_vsIMzDKCOoGzWolllJFVzbYTz", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -149,7 +149,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.675185918Z", + "created": "2023-11-25T07:14:09.550678968Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P16.json b/notebooks/EZH1/phenopackets/PMID_37433783_P16.json index 1fae7a006..a6a9f598e 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P16.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P16.json @@ -73,7 +73,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_NfNmEmsihWFkJxtROwnchhVoR", + "id": "var_vsIMzDKCOoGzWolllJFVzbYTz", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -108,7 +108,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.677797079Z", + "created": "2023-11-25T07:14:09.556304931Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P17newbranchofP13-14.json b/notebooks/EZH1/phenopackets/PMID_37433783_P17newbranchofP13-14.json index f35cab5e5..ee874be49 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P17newbranchofP13-14.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P17newbranchofP13-14.json @@ -193,7 +193,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_NfNmEmsihWFkJxtROwnchhVoR", + "id": "var_vsIMzDKCOoGzWolllJFVzbYTz", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -228,7 +228,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.680325031Z", + "created": "2023-11-25T07:14:09.570159196Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P18.json b/notebooks/EZH1/phenopackets/PMID_37433783_P18.json index 2179a920b..7c73760f4 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P18.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P18.json @@ -178,7 +178,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_NfNmEmsihWFkJxtROwnchhVoR", + "id": "var_vsIMzDKCOoGzWolllJFVzbYTz", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -213,7 +213,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.683145999Z", + "created": "2023-11-25T07:14:09.578144073Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P19Newpatient.json b/notebooks/EZH1/phenopackets/PMID_37433783_P19Newpatient.json index 35fb15131..e761f2b7f 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P19Newpatient.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P19Newpatient.json @@ -144,7 +144,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_YPDmLmHFlfkeWEudgGckcacns", + "id": "var_VWADFtgIMOamuqojvzVPHZdjg", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -179,7 +179,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.685951948Z", + "created": "2023-11-25T07:14:09.584033012Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P2.json b/notebooks/EZH1/phenopackets/PMID_37433783_P2.json index c134df11c..a579e95d0 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P2.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P2.json @@ -56,7 +56,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_jDNkOwyuWRszGGjLwuIFuvfkJ", + "id": "var_xLjrJhIjbpAztrfoOGJZNkOwk", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -91,7 +91,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.612631082Z", + "created": "2023-11-25T07:14:09.447468042Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P3.json b/notebooks/EZH1/phenopackets/PMID_37433783_P3.json index 7b58ab587..ff5aca4e7 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P3.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P3.json @@ -229,7 +229,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_wRuapXfUhbMbXCdyBONtXnkGu", + "id": "var_euZzpscQQFpVichIAQYLrFJcb", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -264,7 +264,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.625082015Z", + "created": "2023-11-25T07:14:09.452582836Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P4.json b/notebooks/EZH1/phenopackets/PMID_37433783_P4.json index ea403cbe2..c470b62f3 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P4.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P4.json @@ -221,7 +221,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_daYIlnIKDvtkjEdjkRFQJZCUB", + "id": "var_uqzXjbEECcGxCPHcoUQUhXPUs", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -256,7 +256,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.632848978Z", + "created": "2023-11-25T07:14:09.460997104Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P5.json b/notebooks/EZH1/phenopackets/PMID_37433783_P5.json index d4e177344..28aa03126 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P5.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P5.json @@ -236,7 +236,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_nOxqLfvKPKIBbDBCeuFXHsRjK", + "id": "var_LNmiRngqDSyjrHwEyAGhnoNnC", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -271,7 +271,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.638660192Z", + "created": "2023-11-25T07:14:09.467932939Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P6.json b/notebooks/EZH1/phenopackets/PMID_37433783_P6.json index ba50687e5..fd7877dfe 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P6.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P6.json @@ -184,7 +184,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_nOxqLfvKPKIBbDBCeuFXHsRjK", + "id": "var_LNmiRngqDSyjrHwEyAGhnoNnC", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -219,7 +219,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.642032861Z", + "created": "2023-11-25T07:14:09.475063085Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P7.json b/notebooks/EZH1/phenopackets/PMID_37433783_P7.json index a1717a668..632217cb0 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P7.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P7.json @@ -179,7 +179,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_DzwtwntgmSVvrXgJqFnGptdGG", + "id": "var_nZTKoTbQPBqooKLHpkwyOJBeO", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -214,7 +214,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.644890785Z", + "created": "2023-11-25T07:14:09.480892896Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P8.json b/notebooks/EZH1/phenopackets/PMID_37433783_P8.json index 4de4d4fd7..dc8d1d6f8 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P8.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P8.json @@ -203,7 +203,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_oUuiOGkxsjzJOVKqAczvXSaJf", + "id": "var_JgioiTzaCZUBTQHDteGcprXUF", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -238,7 +238,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.647516965Z", + "created": "2023-11-25T07:14:09.486885070Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/EZH1/phenopackets/PMID_37433783_P9.json b/notebooks/EZH1/phenopackets/PMID_37433783_P9.json index 4497ab15e..370b207a0 100644 --- a/notebooks/EZH1/phenopackets/PMID_37433783_P9.json +++ b/notebooks/EZH1/phenopackets/PMID_37433783_P9.json @@ -232,7 +232,7 @@ "interpretationStatus": "CAUSATIVE", "variantInterpretation": { "variationDescriptor": { - "id": "var_oUuiOGkxsjzJOVKqAczvXSaJf", + "id": "var_JgioiTzaCZUBTQHDteGcprXUF", "geneContext": { "valueId": "HGNC:3526", "symbol": "EZH1" @@ -267,7 +267,7 @@ } ], "metaData": { - "created": "2023-11-24T10:01:37.650235891Z", + "created": "2023-11-25T07:14:09.493402957Z", "createdBy": "ORCID:0000-0002-0736-9199", "resources": [ { diff --git a/notebooks/KDM6B/KDM6B_PMID_37196654.ipynb b/notebooks/KDM6B/KDM6B_PMID_37196654.ipynb index 08d7e3c3a..89791c6ca 100644 --- a/notebooks/KDM6B/KDM6B_PMID_37196654.ipynb +++ b/notebooks/KDM6B/KDM6B_PMID_37196654.ipynb @@ -13,7 +13,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 1, "id": "afa4ac8e-bd70-4590-9107-8640c4d0119b", "metadata": {}, "outputs": [ @@ -21,44 +21,53 @@ "name": "stdout", "output_type": "stream", "text": [ - "Using pyphetools version 0.8.3\n" + "Using pyphetools version 0.8.28\n" ] } ], "source": [ - "import phenopackets as PPkt\n", - "from google.protobuf.json_format import MessageToDict, MessageToJson\n", - "from google.protobuf.json_format import Parse, ParseDict\n", + "import phenopackets as PPKt\n", + "from google.protobuf.json_format import MessageToDict, MessageToJson, Parse, ParseDict\n", "import pandas as pd\n", "pd.set_option('display.max_colwidth', None) # show entire column contents, important!\n", "from collections import defaultdict\n", + "from IPython.display import HTML, display\n", "from pyphetools.creation import *\n", + "from pyphetools.validation import *\n", "from pyphetools.visualization import *\n", - "import importlib.metadata\n", - "from IPython.display import HTML, display\n", - "__version__ = importlib.metadata.version(\"pyphetools\")\n", - "print(f\"Using pyphetools version {__version__}\")" + "import pyphetools\n", + "print(f\"Using pyphetools version {pyphetools.__version__}\")" ] }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 2, "id": "88f3a65a-fef2-4cbe-bdd1-01ccef7f9a90", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2023-10-09\n" + ] + } + ], "source": [ "parser = HpoParser()\n", "hpo_cr = parser.get_hpo_concept_recognizer()\n", "hpo_version = parser.get_version()\n", + "hpo_ontology = parser.get_ontology()\n", "PMID = \"PMID:37196654\"\n", "title = \"The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder\"\n", "metadata = MetaData(created_by=\"ORCID:0000-0002-0736-9199\", pmid=PMID, pubmed_title=title)\n", - "metadata.default_versions_with_hpo(version=hpo_version)" + "metadata.default_versions_with_hpo(version=hpo_version)\n", + "print(f\"HPO version {hpo_version}\")" ] }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 3, "id": "e0439b7e-6d67-4191-96b1-c4b90f9635c1", "metadata": {}, "outputs": [], @@ -68,7 +77,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 4, "id": "6c6dfb2e-90f7-453b-ae98-a7127c4fece1", "metadata": {}, "outputs": [ @@ -302,7 +311,7 @@ "[5 rows x 74 columns]" ] }, - "execution_count": 13, + "execution_count": 4, "metadata": {}, "output_type": "execute_result" } @@ -313,7 +322,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 5, "id": "b41a3774-6832-41db-b9c4-f6bcfeddbfdd", "metadata": {}, "outputs": [ @@ -349,8 +358,8 @@ " Heterozygous/Homozygous\n", " Additional findings of genetic testing\n", " ...\n", - " Other\n", - " Other\n", + " Constipation\n", + " Other_gi\n", " Skin hyperlaxity\n", " Genitourinary abnormalities\n", " Cryptorchidism\n", @@ -375,7 +384,7 @@ " Heterozygous\n", " No\n", " ...\n", - " NaN\n", + " No\n", " NaN\n", " No\n", " No\n", @@ -399,7 +408,7 @@ " Heterozygous\n", " No\n", " ...\n", - " NaN\n", + " No\n", " NaN\n", " No\n", " No\n", @@ -423,7 +432,7 @@ " Heterozygous\n", " Beta-thalasemia carrier\n", " ...\n", - " NaN\n", + " Yes\n", " NaN\n", " No\n", " No\n", @@ -447,8 +456,8 @@ " Heterozygous\n", " No\n", " ...\n", + " No\n", " Eats/drinks no cow's milk, no gluten and little soya. No allergy but seems sensitive to these products\n", - " NaN\n", " No\n", " No\n", " No\n", @@ -471,7 +480,7 @@ " Heterozygous\n", " No\n", " ...\n", - " NaN\n", + " No\n", " NaN\n", " No\n", " phimosis\n", @@ -484,7 +493,7 @@ " \n", " \n", "\n", - "

5 rows × 77 columns

\n", + "

5 rows × 76 columns

\n", "" ], "text/plain": [ @@ -516,33 +525,26 @@ "Individual 5 Heterozygous No \n", "Individual 6 Heterozygous No \n", "\n", - "Field ... \\\n", - "Individual 1 ... \n", - "Individual 2 ... \n", - "Individual 3 ... \n", - "Individual 5 ... \n", - "Individual 6 ... \n", + "Field ... Constipation \\\n", + "Individual 1 ... No \n", + "Individual 2 ... No \n", + "Individual 3 ... Yes \n", + "Individual 5 ... No \n", + "Individual 6 ... No \n", "\n", - "Field Other \\\n", + "Field Other_gi \\\n", "Individual 1 NaN \n", "Individual 2 NaN \n", "Individual 3 NaN \n", "Individual 5 Eats/drinks no cow's milk, no gluten and little soya. No allergy but seems sensitive to these products \n", "Individual 6 NaN \n", "\n", - "Field Other Skin hyperlaxity Genitourinary abnormalities \\\n", - "Individual 1 NaN No No \n", - "Individual 2 NaN No No \n", - "Individual 3 NaN No No \n", - "Individual 5 NaN No No \n", - "Individual 6 NaN No phimosis \n", - "\n", - "Field Cryptorchidism \\\n", - "Individual 1 NaN \n", - "Individual 2 NaN \n", - "Individual 3 No \n", - "Individual 5 No \n", - "Individual 6 No \n", + "Field Skin hyperlaxity Genitourinary abnormalities Cryptorchidism \\\n", + "Individual 1 No No NaN \n", + "Individual 2 No No NaN \n", + "Individual 3 No No No \n", + "Individual 5 No No No \n", + "Individual 6 No phimosis No \n", "\n", "Field Other medication received \\\n", "Individual 1 Not reported \n", @@ -572,10 +574,10 @@ "Individual 5 NaN NaN \n", "Individual 6 NaN NaN \n", "\n", - "[5 rows x 77 columns]" + "[5 rows x 76 columns]" ] }, - "execution_count": 14, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } @@ -589,7 +591,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 6, "id": "ca522a2e-b23c-42ae-80dd-9300864d3821", "metadata": {}, "outputs": [ @@ -625,7 +627,7 @@ " Heterozygous/Homozygous\n", " Additional findings of genetic testing\n", " ...\n", - " Other\n", + " Other_gi\n", " Skin hyperlaxity\n", " Genitourinary abnormalities\n", " Cryptorchidism\n", @@ -723,7 +725,7 @@ " Heterozygous\n", " No\n", " ...\n", - " NaN\n", + " Eats/drinks no cow's milk, no gluten and little soya. No allergy but seems sensitive to these products\n", " No\n", " No\n", " No\n", @@ -760,7 +762,7 @@ " \n", " \n", "\n", - "

5 rows × 78 columns

\n", + "

5 rows × 77 columns

\n", "" ], "text/plain": [ @@ -792,19 +794,26 @@ "Individual 5 Heterozygous No \n", "Individual 6 Heterozygous No \n", "\n", - "Field ... Other Skin hyperlaxity Genitourinary abnormalities \\\n", - "Individual 1 ... NaN No No \n", - "Individual 2 ... NaN No No \n", - "Individual 3 ... NaN No No \n", - "Individual 5 ... NaN No No \n", - "Individual 6 ... NaN No phimosis \n", + "Field ... \\\n", + "Individual 1 ... \n", + "Individual 2 ... \n", + "Individual 3 ... \n", + "Individual 5 ... \n", + "Individual 6 ... \n", + "\n", + "Field Other_gi \\\n", + "Individual 1 NaN \n", + "Individual 2 NaN \n", + "Individual 3 NaN \n", + "Individual 5 Eats/drinks no cow's milk, no gluten and little soya. No allergy but seems sensitive to these products \n", + "Individual 6 NaN \n", "\n", - "Field Cryptorchidism \\\n", - "Individual 1 NaN \n", - "Individual 2 NaN \n", - "Individual 3 No \n", - "Individual 5 No \n", - "Individual 6 No \n", + "Field Skin hyperlaxity Genitourinary abnormalities Cryptorchidism \\\n", + "Individual 1 No No NaN \n", + "Individual 2 No No NaN \n", + "Individual 3 No No No \n", + "Individual 5 No No No \n", + "Individual 6 No phimosis No \n", "\n", "Field Other medication received \\\n", "Individual 1 Not reported \n", @@ -841,10 +850,10 @@ "Individual 5 NaN Individual 5 \n", "Individual 6 NaN Individual 6 \n", "\n", - "[5 rows x 78 columns]" + "[5 rows x 77 columns]" ] }, - "execution_count": 16, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } @@ -856,7 +865,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 7, "id": "16a36bc8-1ad8-421a-ba39-8d1e45dcd9c5", "metadata": {}, "outputs": [], @@ -866,17 +875,17 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 8, "id": "a6c7acc5-9486-4272-9f34-6df9190e38a8", "metadata": {}, "outputs": [], "source": [ - "column_d = generator.try_mapping_columns()" + "column_mapper_d = generator.try_mapping_columns()" ] }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 9, "id": "235ca20f-294d-4506-9af2-a319d77d89c2", "metadata": {}, "outputs": [ @@ -891,7 +900,7 @@ " \n", " \n", "MappedMotor delay; Intellectual disability; Autism spectrum disorder; Sleep disturbances; Hypotonia; Spasticity; Joint hypermobility; Syndactyly; Pectus excavatum; Strabismus; Recurrent ear infections; Constipation; Cryptorchidism\n", - "UnmappedSex; Age, years; Cohort type; Mutation (NM_); cDNA change (ENST00000254846.9 or NM_001080424.2); Amino acid change; Variant Type (PTV or PAV); Inheritance; Heterozygous/Homozygous; Additional findings of genetic testing; Other affected relatives; Pregnancy/delivery; Complications of Pregnancy/Delivery; Gestational age, weeks; Birth weight, g (SD); Growth; Height, cm (SD); Weight, kg(SD); Head circumference, cm(SD); Age at folow-up/measurements, years; Neurodevelopment; Language/speech delay; First words, months; First steps, months; IQ profile; nan; nan; Behavior problems; Psychosis / Schizophrenia; Use of psychiatric drugs; Other; Neurological; Seizures / Epilepsy; Dystonia, if present - type and age of onset; Other neurological/movement issues; Brain MRI findings; Musculoskeletal/extremities; Vertebral abnormalities (Scoliosis, kyphosis etc).; Hand /foot/ finger abnormalities; Other; Dysmorphism; Dysmorphic features; Lip/palate cleft; Eyes/visual problems; Hypermetropia/myopia; Other; Ear/ hearing problems; Hearing; Other; Cardiovascular; Congenital heart disease; Other; Gastrointestinal; Neonatal feeding difficulties; Yes; Other; Other; Skin hyperlaxity; Genitourinary abnormalities; Other medication received; Other; nan; nan; nan; patient_id\n", + "UnmappedSex; Age, years; Cohort type; Mutation (NM_); cDNA change (ENST00000254846.9 or NM_001080424.2); Amino acid change; Variant Type (PTV or PAV); Inheritance; Heterozygous/Homozygous; Additional findings of genetic testing; Other affected relatives; Pregnancy/delivery; Complications of Pregnancy/Delivery; Gestational age, weeks; Birth weight, g (SD); Growth; Height, cm (SD); Weight, kg(SD); Head circumference, cm(SD); Age at folow-up/measurements, years; Neurodevelopment; Language/speech delay; First words, months; First steps, months; IQ profile; nan; nan; Behavior problems; Psychosis / Schizophrenia; Use of psychiatric drugs; Other_neurodev; Neurological; Seizures / Epilepsy; Dystonia, if present - type and age of onset; Other neurological/movement issues; Brain MRI findings; Musculoskeletal/extremities; Vertebral abnormalities (Scoliosis, kyphosis etc).; Hand /foot/ finger abnormalities; Other_musculoskel; Dysmorphism; Dysmorphic features; Lip/palate cleft; Eyes/visual problems; Hypermetropia/myopia; Other_eye; Ear/ hearing problems; Hearing; Other_ear; Cardiovascular; Congenital heart disease; Other_cv; Gastrointestinal; Neonatal feeding difficulties; Yes; Other_gi; Skin hyperlaxity; Genitourinary abnormalities; Other medication received; Other; nan; nan; nan; patient_id\n", "\n" ], "text/plain": [ @@ -908,394 +917,1215 @@ }, { "cell_type": "code", - "execution_count": 24, - "id": "8ad7183c-4200-462c-8c5d-2629c1f99b3e", - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "array(['Bossy, Agressive (verbally)', 'No',\n", - " 'Irritability, Anger, anxiety (associated with obstipation periods); No contact except parents and physician',\n", - " 'Yes', 'ADHD', 'AHDS; Aggression, problems in social interaction ',\n", - " 'Tantrums and inattention',\n", - " 'ADHD, aggression, problems in social interaction ',\n", - " 'AHDS, aggressive, impulsive behaivior ', 'Anxiety, aggression',\n", - " 'probable ADHD', 'Stubborn, \"lazy\"', 'Agitation,agressivity',\n", - " 'Aggressive behavior, noncompliance, physical aggression, poor play skills ',\n", - " 'Anxiety',\n", - " 'Early and atypical depression, attention deficit, anxiety, atypical sensory',\n", - " 'Yes, Aggression', 'ADHD, anxiety',\n", - " 'Poor social skills, stereotypic behaviour.',\n", - " 'stubborn, aggressive, tantrums', 'Short attention span',\n", - " 'Rigid behaviour', 'ADHD, aggressive behavior', nan,\n", - " 'hyperactivity', 'attention deficit', ' impulsive', 'ADHD ',\n", - " 'Hyperactivity'], dtype=object)" - ] - }, - "execution_count": 24, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "dft[\"Behavior problems\"].unique()" - ] - }, - { - "cell_type": "code", - "execution_count": 27, + "execution_count": 10, "id": "efcc72f2-9e4f-491e-ac0f-027c430a29fa", "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
\n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
terms
0HP:0000718 (Aggressive behavior/observed)
1HP:0000708 (Atypical behavior/excluded)
2n/a
3HP:0000708 (Atypical behavior/observed)
4n/a
......
68HP:0000708 (Atypical behavior/excluded)
69n/a
70n/a
71n/a
72n/a
\n", - "

73 rows × 1 columns

\n", - "
" - ], - "text/plain": [ - " terms\n", - "0 HP:0000718 (Aggressive behavior/observed)\n", - "1 HP:0000708 (Atypical behavior/excluded)\n", - "2 n/a\n", - "3 HP:0000708 (Atypical behavior/observed)\n", - "4 n/a\n", - ".. ...\n", - "68 HP:0000708 (Atypical behavior/excluded)\n", - "69 n/a\n", - "70 n/a\n", - "71 n/a\n", - "72 n/a\n", - "\n", - "[73 rows x 1 columns]" - ] - }, - "execution_count": 27, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "option_d = {'Bossy, Agressive (verbally)':'Aggressive behavior',\n", " 'Yes': 'Atypical behavior'}\n", "excluded_d = {'No':'Atypical behavior'}\n", "behaviorMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=option_d, excluded_d=excluded_d)\n", - "behaviorMapper.preview_column(dft[\"Behavior problems\"])" + "# behaviorMapper.preview_column(dft[\"Behavior problems\"])\n", + "column_mapper_d[\"Behavior problems\"] = behaviorMapper" ] }, { "cell_type": "code", - "execution_count": 32, + "execution_count": 11, "id": "61a187af-1f91-4408-a5eb-76d8822e966f", "metadata": {}, "outputs": [], "source": [ - "result = OptionColumnMapper.autoformat(df=dft, concept_recognizer=hpo_cr, delimiter=\";,\")" + "# only needed to generate suggestions for mappers\n", + "#result = OptionColumnMapper.autoformat(df=dft, concept_recognizer=hpo_cr, delimiter=\";,\")" ] }, { "cell_type": "code", - "execution_count": 40, - "id": "48393b10-b4cb-499f-80e0-ccf28028d525", + "execution_count": 12, + "id": "9b73918a-72db-40b3-a44d-24f32e31d20e", "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "array(['F', 'M'], dtype=object)" - ] - }, - "execution_count": 40, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ - "dft['Sex'].unique()" + "complications_of_pregnancy_d = {\n", + " 'Gestational diabetes. Requiring insulin in 3rd term': 'Maternal diabetes',\n", + " 'Premature rupture of amnion': 'Premature rupture of membranes',\n", + " 'No; cesarian section for breech presentation': 'Breech presentation',\n", + " 'Pregnancy uncomplicate; Prolonged delivery and vacuum extraction': 'Ventouse delivery',\n", + " 'Small for gestational age, c-section': 'Small for gestational age',\n", + " 'Failed induction, fetal distress': 'Fetal distress',\n", + " 'Vacuum extraction': 'Ventouse delivery',\n", + " 'Intrauterine growth restriction': 'Intrauterine growth retardation',\n", + " 'Gestational diabetes': 'Maternal diabetes',\n", + " 'Shoulder dystocia': 'Shoulder dystocia',\n", + " #'Maternal alcohol abuse': 'Fetal alcohol exposure',\n", + " 'Moderate IUGR': 'Moderate intrauterine growth retardation',\n", + " 'Polyhydramnios, elective c-section': 'Polyhydramnios',\n", + " 'Ventouse; Induced': 'Ventouse delivery',\n", + " 'induction of labor at 40^ wg for reduced fetal movements': 'Decreased fetal movement',\n", + " 'induction of labor at 37/40 for reduced fetal movements; born in good condition (Apgar scores 7 & 8). Deteriorated in first day of life - severe pulmonary HTn (see cardiac)': 'Decreased fetal movement'\n", + " }\n", + "complications_of_pregnancyMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=complications_of_pregnancy_d)\n", + "complications_of_pregnancyMapper.preview_column(dft['Complications of Pregnancy/Delivery'])\n", + "column_mapper_d['Complications of Pregnancy/Delivery'] = complications_of_pregnancyMapper" ] }, { "cell_type": "code", - "execution_count": 41, - "id": "519d5fb5-55bb-4d4b-bcfe-b9062342ac34", + "execution_count": 13, + "id": "a6d9f478-1bf4-4b3f-bc2a-2c234a4b2123", "metadata": {}, "outputs": [], "source": [ - "sexMapper = SexColumnMapper(male_symbol=\"M\", female_symbol=\"F\", column_name=\"Sex\")" + "birth_weight_g_d = {'4370 (>2)': 'Large for gestational age',\n", + " '4490 (>2)': 'Large for gestational age',\n", + " '3595 (>2)': 'Large for gestational age',\n", + " '1814 (<-2)': 'Small for gestational age',\n", + " '2414 (>2)': 'Large for gestational age',\n", + " '3814 (>2)': 'Large for gestational age',\n", + " '4000 (>2)': 'Large for gestational age',\n", + " '4140 (>2)': 'Large for gestational age',\n", + " '4150 (>2)': 'Large for gestational age',\n", + " '1644 (-2.60)': 'Small for gestational age',\n", + " '2100 (< -2)': 'Small for gestational age',\n", + " '2270 (<-2)': 'Small for gestational age',\n", + " '3800 (>2)': 'Large for gestational age',}\n", + "birth_weight_g_Mapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=birth_weight_g_d)\n", + "birth_weight_g_Mapper.preview_column(dft['Birth weight, g (SD)'])\n", + "column_mapper_d['Birth weight, g (SD)'] = birth_weight_g_Mapper" ] }, { "cell_type": "code", - "execution_count": 42, - "id": "b4c395e7-c599-4879-923a-e908a29550f1", + "execution_count": 14, + "id": "b68f254f-2117-444c-8751-5314a61e5df2", "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
\n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
original column contentssex
0FFEMALE
1FFEMALE
2MMALE
3MMALE
4MMALE
.........
68MMALE
69MMALE
70MMALE
71MMALE
72MMALE
\n", - "

73 rows × 2 columns

\n", - "
" - ], - "text/plain": [ - " original column contents sex\n", - "0 F FEMALE\n", - "1 F FEMALE\n", - "2 M MALE\n", - "3 M MALE\n", - "4 M MALE\n", - ".. ... ...\n", - "68 M MALE\n", - "69 M MALE\n", - "70 M MALE\n", - "71 M MALE\n", - "72 M MALE\n", - "\n", - "[73 rows x 2 columns]" - ] - }, - "execution_count": 42, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ - "sexMapper.preview_column(dft['Sex'])" + "height_cm_d = {\n", + " '149.5 (+3)': 'Tall stature',\n", + " '130 (+2.6)': 'Tall stature',\n", + " '149 (+3.5)': 'Tall stature',\n", + " }\n", + "height_cm_Mapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=height_cm_d)\n", + "height_cm_Mapper.preview_column(dft['Height, cm (SD)'])\n", + "column_mapper_d['Height, cm (SD)'] = height_cm_Mapper" ] }, { "cell_type": "code", - "execution_count": 44, - "id": "5cf19ef8-a24c-4d4a-bd8a-aa1ee8dd086d", + "execution_count": 15, + "id": "9c32d6d1-d3d0-404f-bd0b-5b9470287e33", "metadata": {}, "outputs": [], "source": [ - "var_list = dft[\"cDNA change (ENST00000254846.9 or NM_001080424.2)\"].unique()" + "weight_kg_d = {'60 (>+2 weight to length)': 'Obesity',\n", + " '70 (+4.1)': 'Obesity',\n", + " '83.1 (+2.5)': 'Obesity',\n", + " '31 (+2.4)': 'Obesity',\n", + " '22.1 (+2.4)': 'Obesity',\n", + " '149.6 (>3)': 'Obesity'}\n", + "weight_kgMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=weight_kg_d)\n", + "weight_kgMapper.preview_column(dft['Weight, kg(SD)'])\n", + "column_mapper_d['Weight, kg(SD)'] = weight_kgMapper" ] }, { "cell_type": "code", - "execution_count": 46, - "id": "88ea5b74-24f2-4b93-b25d-b9222832f5cf", + "execution_count": 16, + "id": "b9f8a982-3a02-4518-9eb8-05301bce4ed4", "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1014delC/NM_001080424.2?content-type=application%2Fjson\n" - ] - }, - { - "ename": "ConnectionError", - "evalue": "HTTPSConnectionPool(host='rest.variantvalidator.org', port=443): Max retries exceeded with url: /VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1014delC/NM_001080424.2?content-type=application%2Fjson (Caused by NameResolutionError(\": Failed to resolve 'rest.variantvalidator.org' ([Errno -3] Temporary failure in name resolution)\"))", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mgaierror\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/urllib3/connection.py:203\u001b[0m, in \u001b[0;36mHTTPConnection._new_conn\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 202\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 203\u001b[0m sock \u001b[38;5;241m=\u001b[39m \u001b[43mconnection\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_connection\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 204\u001b[0m \u001b[43m \u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_dns_host\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mport\u001b[49m\u001b[43m)\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 205\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 206\u001b[0m \u001b[43m \u001b[49m\u001b[43msource_address\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msource_address\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 207\u001b[0m \u001b[43m \u001b[49m\u001b[43msocket_options\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msocket_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 208\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 209\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m socket\u001b[38;5;241m.\u001b[39mgaierror \u001b[38;5;28;01mas\u001b[39;00m e:\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/urllib3/util/connection.py:60\u001b[0m, in \u001b[0;36mcreate_connection\u001b[0;34m(address, timeout, source_address, socket_options)\u001b[0m\n\u001b[1;32m 58\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m LocationParseError(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mhost\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m, label empty or too long\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[0;32m---> 60\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m res \u001b[38;5;129;01min\u001b[39;00m \u001b[43msocket\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgetaddrinfo\u001b[49m\u001b[43m(\u001b[49m\u001b[43mhost\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mport\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfamily\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msocket\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mSOCK_STREAM\u001b[49m\u001b[43m)\u001b[49m:\n\u001b[1;32m 61\u001b[0m af, socktype, proto, canonname, sa \u001b[38;5;241m=\u001b[39m res\n", - "File \u001b[0;32m/usr/lib/python3.10/socket.py:955\u001b[0m, in \u001b[0;36mgetaddrinfo\u001b[0;34m(host, port, family, type, proto, flags)\u001b[0m\n\u001b[1;32m 954\u001b[0m addrlist \u001b[38;5;241m=\u001b[39m []\n\u001b[0;32m--> 955\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m res \u001b[38;5;129;01min\u001b[39;00m \u001b[43m_socket\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgetaddrinfo\u001b[49m\u001b[43m(\u001b[49m\u001b[43mhost\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mport\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfamily\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mtype\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mproto\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mflags\u001b[49m\u001b[43m)\u001b[49m:\n\u001b[1;32m 956\u001b[0m af, socktype, proto, canonname, sa \u001b[38;5;241m=\u001b[39m res\n", - "\u001b[0;31mgaierror\u001b[0m: [Errno -3] Temporary failure in name resolution", - "\nThe above exception was the direct cause of the following exception:\n", - "\u001b[0;31mNameResolutionError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/urllib3/connectionpool.py:790\u001b[0m, in \u001b[0;36mHTTPConnectionPool.urlopen\u001b[0;34m(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)\u001b[0m\n\u001b[1;32m 789\u001b[0m \u001b[38;5;66;03m# Make the request on the HTTPConnection object\u001b[39;00m\n\u001b[0;32m--> 790\u001b[0m response \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_make_request\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 791\u001b[0m \u001b[43m \u001b[49m\u001b[43mconn\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 792\u001b[0m \u001b[43m \u001b[49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 793\u001b[0m \u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 794\u001b[0m \u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout_obj\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 795\u001b[0m \u001b[43m \u001b[49m\u001b[43mbody\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbody\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 796\u001b[0m \u001b[43m \u001b[49m\u001b[43mheaders\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mheaders\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 797\u001b[0m \u001b[43m \u001b[49m\u001b[43mchunked\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mchunked\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 798\u001b[0m \u001b[43m \u001b[49m\u001b[43mretries\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mretries\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 799\u001b[0m \u001b[43m \u001b[49m\u001b[43mresponse_conn\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mresponse_conn\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 800\u001b[0m \u001b[43m \u001b[49m\u001b[43mpreload_content\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mpreload_content\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 801\u001b[0m \u001b[43m \u001b[49m\u001b[43mdecode_content\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdecode_content\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 802\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mresponse_kw\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 803\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 805\u001b[0m \u001b[38;5;66;03m# Everything went great!\u001b[39;00m\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/urllib3/connectionpool.py:491\u001b[0m, in \u001b[0;36mHTTPConnectionPool._make_request\u001b[0;34m(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)\u001b[0m\n\u001b[1;32m 490\u001b[0m new_e \u001b[38;5;241m=\u001b[39m _wrap_proxy_error(new_e, conn\u001b[38;5;241m.\u001b[39mproxy\u001b[38;5;241m.\u001b[39mscheme)\n\u001b[0;32m--> 491\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m new_e\n\u001b[1;32m 493\u001b[0m \u001b[38;5;66;03m# conn.request() calls http.client.*.request, not the method in\u001b[39;00m\n\u001b[1;32m 494\u001b[0m \u001b[38;5;66;03m# urllib3.request. It also calls makefile (recv) on the socket.\u001b[39;00m\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/urllib3/connectionpool.py:467\u001b[0m, in \u001b[0;36mHTTPConnectionPool._make_request\u001b[0;34m(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)\u001b[0m\n\u001b[1;32m 466\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 467\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_validate_conn\u001b[49m\u001b[43m(\u001b[49m\u001b[43mconn\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 468\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (SocketTimeout, BaseSSLError) \u001b[38;5;28;01mas\u001b[39;00m e:\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1092\u001b[0m, in \u001b[0;36mHTTPSConnectionPool._validate_conn\u001b[0;34m(self, conn)\u001b[0m\n\u001b[1;32m 1091\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m conn\u001b[38;5;241m.\u001b[39mis_closed:\n\u001b[0;32m-> 1092\u001b[0m \u001b[43mconn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconnect\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1094\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m conn\u001b[38;5;241m.\u001b[39mis_verified:\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/urllib3/connection.py:611\u001b[0m, in \u001b[0;36mHTTPSConnection.connect\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 610\u001b[0m sock: socket\u001b[38;5;241m.\u001b[39msocket \u001b[38;5;241m|\u001b[39m ssl\u001b[38;5;241m.\u001b[39mSSLSocket\n\u001b[0;32m--> 611\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msock \u001b[38;5;241m=\u001b[39m sock \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_new_conn\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 612\u001b[0m server_hostname: \u001b[38;5;28mstr\u001b[39m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhost\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/urllib3/connection.py:210\u001b[0m, in \u001b[0;36mHTTPConnection._new_conn\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 209\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m socket\u001b[38;5;241m.\u001b[39mgaierror \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[0;32m--> 210\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m NameResolutionError(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mhost, \u001b[38;5;28mself\u001b[39m, e) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01me\u001b[39;00m\n\u001b[1;32m 211\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m SocketTimeout \u001b[38;5;28;01mas\u001b[39;00m e:\n", - "\u001b[0;31mNameResolutionError\u001b[0m: : Failed to resolve 'rest.variantvalidator.org' ([Errno -3] Temporary failure in name resolution)", - "\nThe above exception was the direct cause of the following exception:\n", - "\u001b[0;31mMaxRetryError\u001b[0m Traceback (most recent call last)", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/requests/adapters.py:486\u001b[0m, in \u001b[0;36mHTTPAdapter.send\u001b[0;34m(self, request, stream, timeout, verify, cert, proxies)\u001b[0m\n\u001b[1;32m 485\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 486\u001b[0m resp \u001b[38;5;241m=\u001b[39m \u001b[43mconn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43murlopen\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 487\u001b[0m \u001b[43m \u001b[49m\u001b[43mmethod\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 488\u001b[0m \u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 489\u001b[0m \u001b[43m \u001b[49m\u001b[43mbody\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mbody\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 490\u001b[0m \u001b[43m \u001b[49m\u001b[43mheaders\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mheaders\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 491\u001b[0m \u001b[43m \u001b[49m\u001b[43mredirect\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 492\u001b[0m \u001b[43m \u001b[49m\u001b[43massert_same_host\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 493\u001b[0m \u001b[43m \u001b[49m\u001b[43mpreload_content\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 494\u001b[0m \u001b[43m \u001b[49m\u001b[43mdecode_content\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mFalse\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 495\u001b[0m \u001b[43m \u001b[49m\u001b[43mretries\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmax_retries\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 496\u001b[0m \u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 497\u001b[0m \u001b[43m \u001b[49m\u001b[43mchunked\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mchunked\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 498\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 500\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (ProtocolError, \u001b[38;5;167;01mOSError\u001b[39;00m) \u001b[38;5;28;01mas\u001b[39;00m err:\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/urllib3/connectionpool.py:844\u001b[0m, in \u001b[0;36mHTTPConnectionPool.urlopen\u001b[0;34m(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)\u001b[0m\n\u001b[1;32m 842\u001b[0m new_e \u001b[38;5;241m=\u001b[39m ProtocolError(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mConnection aborted.\u001b[39m\u001b[38;5;124m\"\u001b[39m, new_e)\n\u001b[0;32m--> 844\u001b[0m retries \u001b[38;5;241m=\u001b[39m \u001b[43mretries\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mincrement\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 845\u001b[0m \u001b[43m \u001b[49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43merror\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnew_e\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m_pool\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m_stacktrace\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msys\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexc_info\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m2\u001b[39;49m\u001b[43m]\u001b[49m\n\u001b[1;32m 846\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 847\u001b[0m retries\u001b[38;5;241m.\u001b[39msleep()\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/urllib3/util/retry.py:515\u001b[0m, in \u001b[0;36mRetry.increment\u001b[0;34m(self, method, url, response, error, _pool, _stacktrace)\u001b[0m\n\u001b[1;32m 514\u001b[0m reason \u001b[38;5;241m=\u001b[39m error \u001b[38;5;129;01mor\u001b[39;00m ResponseError(cause)\n\u001b[0;32m--> 515\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m MaxRetryError(_pool, url, reason) \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mreason\u001b[39;00m \u001b[38;5;66;03m# type: ignore[arg-type]\u001b[39;00m\n\u001b[1;32m 517\u001b[0m log\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mIncremented Retry for (url=\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m): \u001b[39m\u001b[38;5;132;01m%r\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, url, new_retry)\n", - "\u001b[0;31mMaxRetryError\u001b[0m: HTTPSConnectionPool(host='rest.variantvalidator.org', port=443): Max retries exceeded with url: /VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1014delC/NM_001080424.2?content-type=application%2Fjson (Caused by NameResolutionError(\": Failed to resolve 'rest.variantvalidator.org' ([Errno -3] Temporary failure in name resolution)\"))", - "\nDuring handling of the above exception, another exception occurred:\n", - "\u001b[0;31mConnectionError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[46], line 4\u001b[0m\n\u001b[1;32m 2\u001b[0m variant_d \u001b[38;5;241m=\u001b[39m {}\n\u001b[1;32m 3\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m v \u001b[38;5;129;01min\u001b[39;00m var_list:\n\u001b[0;32m----> 4\u001b[0m vvar \u001b[38;5;241m=\u001b[39m \u001b[43mvvalidator\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mencode_hgvs\u001b[49m\u001b[43m(\u001b[49m\u001b[43mv\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 5\u001b[0m \u001b[38;5;28mprint\u001b[39m(v)\n\u001b[1;32m 6\u001b[0m \u001b[38;5;28mprint\u001b[39m(vvar)\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/pyphetools/creation/variant_validator.py:53\u001b[0m, in \u001b[0;36mVariantValidator.encode_hgvs\u001b[0;34m(self, hgvs, custom_transcript)\u001b[0m\n\u001b[1;32m 50\u001b[0m \u001b[38;5;66;03m#f\"https://rest.variantvalidator.org/VariantValidator/variantvalidator/{self._genome_assembly}/{transcript}%3A{hgvs}/{transcript}\"\u001b[39;00m\n\u001b[1;32m 51\u001b[0m \u001b[38;5;66;03m#\u001b[39;00m\n\u001b[1;32m 52\u001b[0m \u001b[38;5;28mprint\u001b[39m(api_url)\n\u001b[0;32m---> 53\u001b[0m response \u001b[38;5;241m=\u001b[39m \u001b[43mrequests\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43mapi_url\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 54\u001b[0m \u001b[38;5;66;03m# We expect to get a dictionary with three keys. The first is the name of the variant, e.g., ACC:HGVS, then we\u001b[39;00m\n\u001b[1;32m 55\u001b[0m \u001b[38;5;66;03m# get flag and metadata\u001b[39;00m\n\u001b[1;32m 56\u001b[0m vv_dict \u001b[38;5;241m=\u001b[39m response\u001b[38;5;241m.\u001b[39mjson() \n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/requests/api.py:73\u001b[0m, in \u001b[0;36mget\u001b[0;34m(url, params, **kwargs)\u001b[0m\n\u001b[1;32m 62\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mget\u001b[39m(url, params\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs):\n\u001b[1;32m 63\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124mr\u001b[39m\u001b[38;5;124;03m\"\"\"Sends a GET request.\u001b[39;00m\n\u001b[1;32m 64\u001b[0m \n\u001b[1;32m 65\u001b[0m \u001b[38;5;124;03m :param url: URL for the new :class:`Request` object.\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 70\u001b[0m \u001b[38;5;124;03m :rtype: requests.Response\u001b[39;00m\n\u001b[1;32m 71\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m---> 73\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mrequest\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mget\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparams\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mparams\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/requests/api.py:59\u001b[0m, in \u001b[0;36mrequest\u001b[0;34m(method, url, **kwargs)\u001b[0m\n\u001b[1;32m 55\u001b[0m \u001b[38;5;66;03m# By using the 'with' statement we are sure the session is closed, thus we\u001b[39;00m\n\u001b[1;32m 56\u001b[0m \u001b[38;5;66;03m# avoid leaving sockets open which can trigger a ResourceWarning in some\u001b[39;00m\n\u001b[1;32m 57\u001b[0m \u001b[38;5;66;03m# cases, and look like a memory leak in others.\u001b[39;00m\n\u001b[1;32m 58\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m sessions\u001b[38;5;241m.\u001b[39mSession() \u001b[38;5;28;01mas\u001b[39;00m session:\n\u001b[0;32m---> 59\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43msession\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmethod\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/requests/sessions.py:589\u001b[0m, in \u001b[0;36mSession.request\u001b[0;34m(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)\u001b[0m\n\u001b[1;32m 584\u001b[0m send_kwargs \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m 585\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mtimeout\u001b[39m\u001b[38;5;124m\"\u001b[39m: timeout,\n\u001b[1;32m 586\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mallow_redirects\u001b[39m\u001b[38;5;124m\"\u001b[39m: allow_redirects,\n\u001b[1;32m 587\u001b[0m }\n\u001b[1;32m 588\u001b[0m send_kwargs\u001b[38;5;241m.\u001b[39mupdate(settings)\n\u001b[0;32m--> 589\u001b[0m resp \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msend\u001b[49m\u001b[43m(\u001b[49m\u001b[43mprep\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43msend_kwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 591\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m resp\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/requests/sessions.py:703\u001b[0m, in \u001b[0;36mSession.send\u001b[0;34m(self, request, **kwargs)\u001b[0m\n\u001b[1;32m 700\u001b[0m start \u001b[38;5;241m=\u001b[39m preferred_clock()\n\u001b[1;32m 702\u001b[0m \u001b[38;5;66;03m# Send the request\u001b[39;00m\n\u001b[0;32m--> 703\u001b[0m r \u001b[38;5;241m=\u001b[39m \u001b[43madapter\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43msend\u001b[49m\u001b[43m(\u001b[49m\u001b[43mrequest\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 705\u001b[0m \u001b[38;5;66;03m# Total elapsed time of the request (approximately)\u001b[39;00m\n\u001b[1;32m 706\u001b[0m elapsed \u001b[38;5;241m=\u001b[39m preferred_clock() \u001b[38;5;241m-\u001b[39m start\n", - "File \u001b[0;32m~/GIT/phenopacket-store/ps_venv/lib/python3.10/site-packages/requests/adapters.py:519\u001b[0m, in \u001b[0;36mHTTPAdapter.send\u001b[0;34m(self, request, stream, timeout, verify, cert, proxies)\u001b[0m\n\u001b[1;32m 515\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(e\u001b[38;5;241m.\u001b[39mreason, _SSLError):\n\u001b[1;32m 516\u001b[0m \u001b[38;5;66;03m# This branch is for urllib3 v1.22 and later.\u001b[39;00m\n\u001b[1;32m 517\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m SSLError(e, request\u001b[38;5;241m=\u001b[39mrequest)\n\u001b[0;32m--> 519\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mConnectionError\u001b[39;00m(e, request\u001b[38;5;241m=\u001b[39mrequest)\n\u001b[1;32m 521\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m ClosedPoolError \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 522\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mConnectionError\u001b[39;00m(e, request\u001b[38;5;241m=\u001b[39mrequest)\n", - "\u001b[0;31mConnectionError\u001b[0m: HTTPSConnectionPool(host='rest.variantvalidator.org', port=443): Max retries exceeded with url: /VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1014delC/NM_001080424.2?content-type=application%2Fjson (Caused by NameResolutionError(\": Failed to resolve 'rest.variantvalidator.org' ([Errno -3] Temporary failure in name resolution)\"))" - ] - } - ], + "outputs": [], "source": [ - "vvalidator = VariantValidator(genome_build=\"hg38\", transcript=\"NM_001080424.2\" )\n", + "head_circumference_cm_d = {\n", + " '58 (>+2.5)': 'Macrocephaly',\n", + " '60.5 (>+2)': 'Macrocephaly',\n", + " '57 (>+2.5)': 'Macrocephaly',\n", + " '55.3 (>2.5)': 'Macrocephaly',\n", + " '55.5 (+2.3)': 'Macrocephaly',\n", + " '56 (>+2)': 'Macrocephaly',\n", + " '55 (+3.4)': 'Macrocephaly',\n", + " '56.5 (+3.3)': 'Macrocephaly',\n", + " '54.5 (>+2)': 'Macrocephaly',\n", + " '59 (+2.7)': 'Macrocephaly',\n", + " '55 (+2.2)': 'Macrocephaly',\n", + " '59.4 (+3)': 'Macrocephaly'}\n", + "head_circumference_cmMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=head_circumference_cm_d)\n", + "head_circumference_cmMapper.preview_column(dft['Head circumference, cm(SD)'])\n", + "column_mapper_d['Head circumference, cm(SD)'] = head_circumference_cmMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "b352466c-3bfb-4e23-95b9-2ebdfeeb0739", + "metadata": {}, + "outputs": [], + "source": [ + "language_speech_delay_d = {'Yes': 'Delayed speech and language development',\n", + " 'Yes, mild': 'Delayed speech and language development',\n", + " 'Yes, Mild': 'Delayed speech and language development'}\n", + "excluded = { 'No': 'Delayed speech and language development'}\n", + "language_speech_delayMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=language_speech_delay_d, excluded_d=excluded)\n", + "language_speech_delayMapper.preview_column(dft['Language/speech delay'])\n", + "column_mapper_d['Language/speech delay'] = language_speech_delayMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "fab29355-8cc8-4ef9-8a47-314fb891254c", + "metadata": {}, + "outputs": [], + "source": [ + "motor_delay_d = {'Yes': 'Motor delay',\n", + " 'Yes, mild': 'Motor delay'}\n", + "excluded = { 'No': 'Motor delay'}\n", + "\n", + "motor_delayMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=motor_delay_d, excluded_d=excluded)\n", + "motor_delayMapper.preview_column(dft['Motor delay'])\n", + "column_mapper_d['Motor delay'] = motor_delayMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "id": "fcb4f326-d7b3-4e58-bb46-56a768335175", + "metadata": {}, + "outputs": [], + "source": [ + "intellectual_disability_d = {'No; learning problems': 'Specific learning disability',\n", + " \"Yes, Mild\": 'Intellectual disability, mild',\n", + " 'Yes, moderate': 'Intellectual disability, moderate',\n", + " 'Yes': 'Intellectual disability',\n", + " 'learning difficulties': 'Specific learning disability',\n", + " 'Yes, mild': 'Intellectual disability, mild',\n", + " 'Yes, severe (contributed by Pathogenic HNRNPU variant)': 'Intellectual disability, severe',\n", + " 'No, learning difficulties': 'Specific learning disability',\n", + " 'Yes, severe': 'Intellectual disability, severe',\n", + " 'Yes, mild/borderline; learning difficulties': 'Intellectual disability, borderline',\n", + " 'learning difficulty': 'Specific learning disability',\n", + " 'Learning disability in special education classes in school': 'Specific learning disability',\n", + " 'Yes, Moderate': 'Intellectual disability, moderate'}\n", + "excluded = { 'No': 'Intellectual disability',}\n", + "intellectual_disabilityMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=intellectual_disability_d)\n", + "intellectual_disabilityMapper.preview_column(dft['Intellectual disability'])\n", + "column_mapper_d['Intellectual disability'] = intellectual_disabilityMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "0d5f3937-42d1-4f41-a298-69401d1eea08", + "metadata": {}, + "outputs": [], + "source": [ + "autism_spectrum_disorder_d = {'Yes': 'Autistic behavior',\n", + " 'Autistic-like features - hand flapping, mouthing and repetitive mannerisms. Difficulties with language and socialising but also some features not in keeping with ASD - desire to include other people in her experiences and demonstration of empathy': 'Autistic behavior',\n", + " 'Yes, moderate-severe': 'Autistic behavior'}\n", + "excluded = {'No': 'Autistic behavior'}\n", + "autism_spectrum_disorderMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=autism_spectrum_disorder_d, excluded_d=excluded)\n", + "autism_spectrum_disorderMapper.preview_column(dft['Autism spectrum disorder'])\n", + "column_mapper_d['Autism spectrum disorder'] = autism_spectrum_disorderMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "id": "e3929bbd-a196-45dc-8510-f514f5e3711b", + "metadata": {}, + "outputs": [], + "source": [ + "behavior_problems_d = {'Bossy, Agressive (verbally)': 'Aggressive behavior',\n", + " 'Irritability, Anger, anxiety (associated with obstipation periods); No contact except parents and physician': ['Irritability', \"Anxiety\"],\n", + " 'Yes': 'Atypical behavior',\n", + " 'ADHD': 'Attention deficit hyperactivity disorder',\n", + " 'AHDS; Aggression, problems in social interaction': ['Aggressive behavior', 'Attention deficit hyperactivity disorder'],\n", + " 'Tantrums and inattention': 'Severe temper tantrums',\n", + " 'ADHD, aggression, problems in social interaction': ['Aggressive behavior', 'Attention deficit hyperactivity disorder'],\n", + " 'AHDS, aggressive, impulsive behaivior': ['Impulsivity', 'Aggressive behavior', 'Attention deficit hyperactivity disorder'],\n", + " 'Anxiety, aggression': ['Anxiety','Aggressive behavior'],\n", + " 'probable ADHD': 'Attention deficit hyperactivity disorder',\n", + " 'Agitation, agressivity': ['Agitation','Aggressive behavior'],\n", + " 'Aggressive behavior, noncompliance, physical aggression, poor play skills': ['Aggressive behavior','Delay in the acquisition of play skills'],\n", + " 'Anxiety': 'Anxiety',\n", + " 'Early and atypical depression, attention deficit, anxiety, atypical sensory': ['Depression', 'Attention deficit hyperactivity disorder'],\n", + " 'Yes, Aggression': 'Aggressive behavior',\n", + " 'ADHD, anxiety': ['Aggressive behavior','Anxiety'],\n", + " 'Poor social skills, stereotypic behaviour.': 'Abnormal repetitive mannerisms',\n", + " 'stubborn, aggressive, tantrums': 'Aggressive behavior',\n", + " 'Short attention span': 'Short attention span',\n", + " 'ADHD, aggressive behavior':['Aggressive behavior', 'Attention deficit hyperactivity disorder'],\n", + " 'hyperactivity': 'Hyperactivity',\n", + " 'attention deficit': 'Attention deficit hyperactivity disorder',\n", + " 'impulsive': 'Impulsivity',\n", + " 'Hyperactivity': 'Hyperactivity'}\n", + "excluded = {'No': 'Aggressive behavior'}\n", + "behavior_problemsMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=behavior_problems_d, excluded_d=excluded)\n", + "behavior_problemsMapper.preview_column(dft['Behavior problems'])\n", + "column_mapper_d['Behavior problems'] = behavior_problemsMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "id": "9fc4be91-b167-4a52-afcd-2afe1ca6b483", + "metadata": {}, + "outputs": [], + "source": [ + "psychosis_schizophrenia_d = {'No': 'PLACEHOLDER',\n", + " 'Yes': 'Psychosis'}\n", + "psychosis_schizophreniaMapper = SimpleColumnMapper(hpo_id=\"HP:0000709\", hpo_label=\"Psychosis\", observed=\"Yes\", excluded=\"No\")\n", + "psychosis_schizophreniaMapper.preview_column(dft['Psychosis / Schizophrenia'])\n", + "column_mapper_d['Psychosis / Schizophrenia'] = psychosis_schizophreniaMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 23, + "id": "364296a4-c21f-49fd-8312-b02f8edec950", + "metadata": {}, + "outputs": [], + "source": [ + "sleep_disturbances_d = {\n", + " 'Yes': 'Sleep abnormality',\n", + " 'History of obstructive sleep apnea': 'Obstructive sleep apnea',\n", + " 'Yes, sleep apnea': 'Sleep apnea',\n", + " 'Yes, delayed sleep initiation and maintenance': 'Sleep abnormality',\n", + " 'Yes (previously)': 'Sleep abnormality',\n", + " 'Yes, in the first year': 'Sleep abnormality',\n", + " 'Yes, in the first year of life': 'Sleep abnormality',\n", + " 'Yes, uses melatonine':'Sleep abnormality',\n", + " 'obstructive and central sleep apnea': 'Central sleep apnea',\n", + " 'Yes, poor sleep, frequent waking for prolonged periods of time': 'Sleep abnormality',\n", + " 'Yes, uses melatonin': 'Sleep abnormality',}\n", + "excluded = {'No': 'Sleep abnormality',}\n", + "sleep_disturbancesMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=sleep_disturbances_d, excluded_d=excluded)\n", + "sleep_disturbancesMapper.preview_column(dft['Sleep disturbances'])\n", + "column_mapper_d['Sleep disturbances'] = sleep_disturbancesMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "id": "d29009be-4485-415e-9556-8047b92b5758", + "metadata": {}, + "outputs": [], + "source": [ + "other_d = {\n", + " 'Social developmental delay': 'Global developmental delay',\n", + " 'GDD': 'Global developmental delay',\n", + " 'hyperphagia, problems in social interaction': 'Polyphagia',\n", + " 'Regression - loss of words at 8m': 'Developmental regression',\n", + " 'DD': 'Global developmental delay',\n", + " 'Bruxism': 'Bruxism',\n", + " 'drooling': 'Drooling',\n", + " 'Moderate GDD': 'Moderate global developmental delay',\n", + " 'Moderate GDD, short attention span': ['Moderate global developmental delay','Short attention span'],\n", + " 'Developmental regression': 'Developmental regression',\n", + " 'problems in social interaction': 'Abnormal social behavior',\n", + " 'Depression ; abnormal eating behaviour; no eye contact at age of 3 years; no interest in socializing with others; echolalia; OCD': 'Depression',\n", + " 'stereotypic behaviors (flapping, rubbing ears, hitting his thighs)': 'Recurrent hand flapping',\n", + " 'inconsistently responds to own name at 17 months (normal audiology). Sensory seeking. Mostly happy baby.': 'Sensory seeking',\n", + " 'GDD; Bruxism': ['Global developmental delay','Bruxism'],\n", + " 'enuresis': 'Enuresis',\n", + " 'Mild GDD': 'Mild global developmental delay'}\n", + "otherMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=other_d)\n", + "otherMapper.preview_column(dft['Other_neurodev'])\n", + "column_mapper_d['Other_neurodev'] = otherMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 25, + "id": "80728107-2b78-4646-9201-943d019146c2", + "metadata": {}, + "outputs": [], + "source": [ + "seizures_epilepsy_d = {\n", + " 'Febrile seizure after BMR vaccination (around 14 months), thereafter stagnation of social emotional and speech development': 'Seizure',\n", + " 'Yes': 'Seizure',\n", + " 'Yes (absence seizures and GTC)': ['Generalized non-motor (absence) seizure', 'Bilateral tonic-clonic seizure'],\n", + " 'Yes, At 5y 6 m onset. Long lasting complex partial seizures with hospitalization in the intensive care unit, partial seizures during sleep, focal epilepsy with opercular seizures; Current therapy: Ethosuximide, Clobazam': 'Focal impaired awareness seizure',\n", + " 'Yes; myoclonic onset 12m': 'Myoclonic seizure',\n", + "\n", + " 'Yes, drug resistant epilepsy: general and focal seizures; with currently 1 event per month on oxacarbazepine + clobazam': 'Seizure',\n", + " 'Yes. In newborn period after neurological insult from hypoperfusion. Has been off AEDs for > 1 year and remains seizure free.': 'Seizure'}\n", + "excluded = {'No; normal EEG': 'Seizure', 'No': 'Seizure'}\n", + "seizures_epilepsyMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=seizures_epilepsy_d, excluded_d=excluded)\n", + "seizures_epilepsyMapper.preview_column(dft['Seizures / Epilepsy'])\n", + "column_mapper_d['Seizures / Epilepsy'] = seizures_epilepsyMapper\n" + ] + }, + { + "cell_type": "code", + "execution_count": 26, + "id": "d843f47a-679d-4784-a9f0-d4b908aa430f", + "metadata": {}, + "outputs": [], + "source": [ + "hypotonia_d = {\n", + " 'Yes': 'Hypotonia',\n", + " 'Yes, neonatal': 'Hypotonia',\n", + " 'Yes, core': 'Hypotonia',\n", + " 'Yes, muscle issues in core and hands': 'Hypotonia',}\n", + "excluded = {'No': 'Hypotonia',}\n", + "hypotoniaMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=hypotonia_d, excluded_d=excluded)\n", + "hypotoniaMapper.preview_column(dft['Hypotonia'])\n", + "column_mapper_d['Hypotonia'] = hypotoniaMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 27, + "id": "d32f5912-9671-4415-bfd1-94788d7b2ca9", + "metadata": {}, + "outputs": [], + "source": [ + "dystonia_d = {\n", + " 'Dystonic type episodes': 'Dystonia',\n", + " 'Yes - dystonic posture of the upper limbs': 'Dystonia',}\n", + "excluded = {'No': 'Dystonia',}\n", + "dystoniaMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=dystonia_d, excluded_d=excluded)\n", + "dystoniaMapper.preview_column(dft['Dystonia, if present - type and age of onset'])\n", + "column_mapper_d['Dystonia, if present - type and age of onset'] = dystoniaMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 28, + "id": "6d5e959c-0750-40e8-af1c-e31dde3efd40", + "metadata": {}, + "outputs": [], + "source": [ + "spasticity_d = {\n", + " 'No but always tendency tip-toe walking. botulinum toxin type A (BTX-A) injections ere performed at the calfs - Triceps surae muscle': 'Tip-toe gait',\n", + " 'Increased tonus in legs. Tip-toe walking': 'Tip-toe gait'}\n", + "excluded = {'No': 'Spasticity'}\n", + "spasticityMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=spasticity_d, excluded_d=excluded)\n", + "spasticityMapper.preview_column(dft['Spasticity'])\n", + "column_mapper_d['Spasticity'] = spasticityMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 29, + "id": "9067112e-f86e-41e8-a6fc-d3f79dc8fff8", + "metadata": {}, + "outputs": [], + "source": [ + "other_neurological_d = {\n", + " 'Mild intention tremor; \"wooden\" motoric skills; poor fine motoric skills': 'Intention tremor',\n", + " 'Tics in stressfull situation': 'Tics',\n", + " 'Ataxia': 'Ataxia',\n", + " 'Neurogenic bladder; tethered cord': ['Neurogenic bladder',\"Tethered cord\"],\n", + " 'Tics': 'Tics',\n", + " 'mild dysartria. Neurological evaluation Jun 2020 (10y5m): cerebellar and extrapriamidal involvement with dystonic postures. Slight piramidal signs.': 'Dysarthria',\n", + " 'tethered spinal cord s/p 1/2019': \"Tethered cord\",\n", + " 'Getting tired quickly': 'Fatigue',\n", + " 'Getting tired quickly; hyporeflexia': 'Fatigue',\n", + " 'Occasional enuresis': 'Enuresis',\n", + " 'Poor coordination skills': 'Poor coordination',\n", + " 'still unsteady at 9 years': 'Unsteady gait',\n", + " 'PVL - due to prematurity (born at 32 6/7)': 'Periventricular leukomalacia',\n", + " 'Coordination issues': 'Poor coordination',\n", + " 'gross motor impairment, slight balance disturbance': 'Poor gross motor coordination',\n", + " 'initial very broad based gait': 'Broad-based gait',\n", + " 'Brachycephaly': 'Brachycephaly',\n", + " 'Dolichocephaly, unsteady gait': ['Dolichocephaly', \"Unsteady gait\"]}\n", + "other_neurologicalMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=other_neurological_d)\n", + "other_neurologicalMapper.preview_column(dft['Other neurological/movement issues'])\n", + "column_mapper_d['Other neurological/movement issues'] = other_neurologicalMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 30, + "id": "323efc3b-48fc-4191-93dc-0f51aedd3828", + "metadata": {}, + "outputs": [], + "source": [ + "brain_mri_findings_d = {\n", + " 'cerebellar mild cortical atrophy': 'Cerebellar cortical atrophy',\n", + " 'Cerebral atrophy, multiple lesions including glial lesions, atrophy of the cerebellar vermis, corpus callosum agenesis': ['Cerebral atrophy',\"Agenesis of corpus callosum\"],\n", + " 'platybasia, small foramen magnum': ['Platybasia',\"Small foramen magnum\"],\n", + " 'multiple focal areas of altered signal, mostly subcortical, especially in the bilateral frontal area. Thinning of corpus callosum. Dilation of the Virchow-Robin perivascular spaces': 'Dilation of Virchow-Robin spaces',\n", + " 'external hydrocephalus': 'Hydrocephalus',\n", + " 'Assymetric hyppocampus; lightly delayed myelinisation': 'Delayed CNS myelination',\n", + " }\n", + "brain_mri_findingsMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=brain_mri_findings_d)\n", + "brain_mri_findingsMapper.preview_column(dft['Brain MRI findings'])\n", + "column_mapper_d['Brain MRI findings'] = brain_mri_findingsMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 31, + "id": "c03a0828-f464-459b-9c16-411ec85261a2", + "metadata": {}, + "outputs": [], + "source": [ + "joint_hypermobility_d = {\n", + " 'Yes (Breighton score 6/8)': 'Joint hypermobility',\n", + " 'Yes': 'Joint hypermobility',\n", + " 'Yes, at knees': 'Knee joint hypermobility',\n", + " 'Yes, mild': 'Joint hypermobility',\n", + " 'Yes, Mild hypermobility in hands': 'Hyperextensible hand joints',\n", + " 'Yes (distal)': 'Joint hypermobility',\n", + " 'Yes (recurvatum knees and elbows)': 'Joint hypermobility'}\n", + "excluded = {'No': 'Joint hypermobility',}\n", + "joint_hypermobilityMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=joint_hypermobility_d)\n", + "joint_hypermobilityMapper.preview_column(dft['Joint hypermobility'])\n", + "column_mapper_d['Joint hypermobility'] = joint_hypermobilityMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 32, + "id": "1f696d82-8d1d-426b-a3ad-c06be8e5c37d", + "metadata": {}, + "outputs": [], + "source": [ + "syndactyly_d = {\n", + " 'Yes, slight bilateral II, III, IV toe syndactyly;': '2-4 toe syndactyly',\n", + " '2-3 toe syndactyly': '2-3 toe syndactyly'}\n", + "excluded = {'No': 'Syndactyly',}\n", + "syndactylyMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=syndactyly_d, excluded_d=excluded)\n", + "syndactylyMapper.preview_column(dft['Syndactyly'])\n", + "column_mapper_d['Syndactyly'] = syndactylyMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 33, + "id": "90c667ff-4fcf-44df-9135-30b8817ee89f", + "metadata": {}, + "outputs": [], + "source": [ + "vertebral_abnormalities_d = {\n", + " 'Kyphosis': 'Kyphosis',\n", + " 'Scoliosis': 'Scoliosis',\n", + " 'Scoliosis, dorsolumbar': 'Scoliosis',\n", + " 'Hyperlordosis': 'Hyperlordosis',\n", + " 'thoracic kyphosis without vertebral defect': 'Thoracic kyphosis',\n", + " 'kyphosis': 'Kyphosis'}\n", + "excluded = {'No': 'Scoliosis',}\n", + "vertebral_abnormalitiesMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=vertebral_abnormalities_d, excluded_d=excluded)\n", + "vertebral_abnormalitiesMapper.preview_column(dft['Vertebral abnormalities (Scoliosis, kyphosis etc).'])\n", + "column_mapper_d['Vertebral abnormalities (Scoliosis, kyphosis etc).'] = vertebral_abnormalitiesMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 34, + "id": "d0aaa64e-6a7d-4f16-ab22-a77c972ebdf9", + "metadata": {}, + "outputs": [], + "source": [ + "hand_foot_finger_abnormalities_d = {\n", + " 'finger clubbing; clinodactyly IV and V bilateral': 'Clubbing of fingers',\n", + " 'clinodactyly IV and V bilateral;short and broad feet;': 'Clinodactyly',\n", + " 'Flat feet, broad finger tips, curls up toes in shoes.': 'Pes planus',\n", + " 'unilateral varus foot; clinodactyly 5th finger, short hands': 'Clinodactyly',\n", + " 'PIP joints prominent': 'Prominent interphalangeal joints',\n", + " 'Broad fingertips': 'Broad fingertip',\n", + " 'pes planus': 'Pes planus',\n", + " 'Brachydactyly; broad toes': 'Brachydactyly',\n", + " 'Hands: broad. Feet: broad feet, short toes, sandal gap, mild clinodactyly dig 3-4.': 'Broad foot',\n", + " 'Prominent fingertip pads': 'Prominent fingertip pads',\n", + " 'flat feet with a broad base but otherwise normal gait': 'Pes planus',\n", + " 'yes - one hand very enlarged; pes planus': 'Pes planus',\n", + " 'Flat feet': 'Pes planus',\n", + " 'flat feet': 'Pes planus',\n", + " 'simian crease, short thumbs, fetal pads, pes planovalgus': 'Single transverse palmar crease',\n", + " 'Genu valgum, short toe nails, Pes planus et valgus': ['Genu valgum', 'Pes planus'],\n", + " 'Talipes': 'Talipes'}\n", + "hand_foot_finger_abnormalitiesMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=hand_foot_finger_abnormalities_d)\n", + "hand_foot_finger_abnormalitiesMapper.preview_column(dft['Hand /foot/ finger abnormalities'])\n", + "column_mapper_d['Hand /foot/ finger abnormalities'] = hand_foot_finger_abnormalitiesMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 35, + "id": "e800d63c-b0b0-40c0-9dfc-7c8bc95b8ff2", + "metadata": {}, + "outputs": [], + "source": [ + "other_musculoskel_d = {\n", + " 'Hip dysplasia': 'Hip dysplasia',\n", + " 'bilateral external tibial torsion': 'External tibial torsion',\n", + " 'extra rib on each side; cervical vertebral fusion suspected': 'Fused cervical vertebrae',\n", + " 'Downward sloping shoulders, proportionate tall stature, talipes': ['Down-sloping shoulders', \"Tall stature\", \"Talipes\"],\n", + " 'Proportionate tall stature': 'Proportionate tall stature',\n", + " 'A strawberry neavus was present at the back of his neck with no other skin lesions or freckling.': 'Freckling',\n", + " 'coccygeal dimple': 'Sacral dimple',\n", + " 'hip dysplasia': 'Hip dysplasia',\n", + " 'recurrent patella luxation, temporary hemiepiphysiodesis distal femur medial left': 'Patellar subluxation',\n", + " 'torticollis, lingual frenulum': 'Torticollis',\n", + " 'Soft skin': 'Soft skin'}\n", + "otherMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=other_musculoskel_d)\n", + "otherMapper.preview_column(dft['Other_musculoskel'])\n", + "column_mapper_d['Other_musculoskel'] = otherMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 36, + "id": "ad9cc2f5-a312-4255-9cf8-1fa20e74ff0f", + "metadata": {}, + "outputs": [], + "source": [ + "dysmorphic_featuresMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d={})\n", + "dysmorphic_featuresMapper.preview_column(dft['Dysmorphic features'])\n", + "column_mapper_d['Dysmorphic features'] = dysmorphic_featuresMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 37, + "id": "e6b02138-923b-4bd6-8076-4ba1af83abc7", + "metadata": {}, + "outputs": [], + "source": [ + "cleft_d = {\n", + " 'Cleft palate': 'Cleft palate'}\n", + "excluded = {\"No\": 'Cleft palate'}\n", + "cleftMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=cleft_d, excluded_d=excluded)\n", + "cleftMapper.preview_column(dft['Lip/palate cleft'])\n", + "column_mapper_d['Lip/palate cleft'] = cleftMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 38, + "id": "6a583074-eecc-4ab4-85f3-ec9c0c07c57c", + "metadata": {}, + "outputs": [], + "source": [ + "hypermetropia_myopia_d = {'Hypermetropia, mild': 'Mild hypermetropia',\n", + " 'Hypermetropia': 'Hypermetropia',\n", + " 'Yes': 'Abnormality of refraction',\n", + " 'Myopia': 'Myopia',\n", + " 'Myopia + astigmatism': 'Myopia',\n", + " 'Unilateral myopia causing right esotropia': 'Myopia',\n", + " 'Hypermetropia and astigmatism': 'Hypermetropia',\n", + " 'Myopia, mild': 'Mild myopia',\n", + " 'Mild hypermetropic astigmatism': 'Astigmatism'}\n", + "excluded = {\"No\": \"Abnormality of refraction\"}\n", + "hypermetropiamyopiaMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=hypermetropia_myopia_d, excluded_d=excluded)\n", + "hypermetropiamyopiaMapper.preview_column(dft['Hypermetropia/myopia'])\n", + "column_mapper_d['Hypermetropia/myopia'] = hypermetropiamyopiaMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 39, + "id": "46daf256-6251-4ad1-bec5-117d9dae2fc7", + "metadata": {}, + "outputs": [], + "source": [ + "strabismus_d = {\n", + " 'Yes (exotropia)': 'Exotropia',\n", + " 'Yes': 'Strabismus'}\n", + "excluded = {'No':\"Strabismus\"}\n", + "strabismusMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=strabismus_d, excluded_d=excluded)\n", + "strabismusMapper.preview_column(dft['Strabismus'])\n", + "column_mapper_d['Strabismus'] = strabismusMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 40, + "id": "a4dc28df-24c9-4261-b4e3-79f9535c0c8c", + "metadata": {}, + "outputs": [], + "source": [ + "other_eye_d = {\n", + " 'astigmatism (R=-2, 00;10º; L=-2, 00;0º)': 'Astigmatism',\n", + " 'persistent nystagmus': 'Nystagmus',\n", + " \"vision20/400 right eye and 20/30 causing amblyopia and right esotropia-doesn't use righ eye\": 'Esotropia',\n", + " 'Astigmatism.': 'Astigmatism',\n", + " 'left ptosis': 'Ptosis',\n", + " 'horizontal nystagmus': 'Horizontal nystagmus',\n", + " 'astigmatism': 'Astigmatism'}\n", + "otherMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=other_d)\n", + "otherMapper.preview_column(dft['Other_eye'])\n", + "column_mapper_d['Other_eye'] = otherMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 41, + "id": "b272bea8-ceea-4983-bbb0-fee48644047d", + "metadata": {}, + "outputs": [], + "source": [ + "hearing_d = {\n", + " 'Hearing loss': 'Hearing impairment',}\n", + "excluded = {'Hearing impairment': 'PLACEHOLDER'}\n", + "hearingMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=hearing_d, excluded_d=excluded)\n", + "hearingMapper.preview_column(dft['Hearing'])\n", + "column_mapper_d['Hearing'] = hearingMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 42, + "id": "eae9510b-8703-4b26-b43e-1a7cf237890f", + "metadata": {}, + "outputs": [], + "source": [ + "recurrent_ear_infections_d = {'Yes, Ear tubes': 'Recurrent otitis media',\n", + " 'Yes': 'Recurrent otitis media',\n", + " }\n", + "excluded = {'No': 'Recurrent otitis media'}\n", + "recurrent_ear_infectionsMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=recurrent_ear_infections_d, excluded_d=excluded)\n", + "recurrent_ear_infectionsMapper.preview_column(dft['Recurrent ear infections'])\n", + "column_mapper_d['Recurrent ear infections'] = recurrent_ear_infectionsMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 43, + "id": "8243b5e2-e7b9-4ff6-a906-f279366094cf", + "metadata": {}, + "outputs": [], + "source": [ + "other_ear_d = {\n", + " 'vestibular aqueduct dilation': 'Enlarged vestibular aqueduct',\n", + " 'Rhinitis sicca': 'Rhinitis',\n", + " 'grommets/Ts and As removed, bilateral preauricular pits': 'Preauricular pit',\n", + " 'Tinnitus': 'Tinnitus'}\n", + "otherEarMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=other_ear_d)\n", + "otherEarMapper.preview_column(dft['Other_ear'])\n", + "column_mapper_d['Other_ear'] = otherEarMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 44, + "id": "773acd29-1c71-4245-95a9-308e693953e9", + "metadata": {}, + "outputs": [], + "source": [ + "congenital_heart_disease_d = {\n", + " 'PDA': 'Patent ductus arteriosus',\n", + " 'ASD II': 'Secundum atrial septal defect',\n", + " 'pulmonary stenosis that resolved by age 3': 'Pulmonic stenosis',\n", + " }\n", + "congenital_heart_diseaseMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=congenital_heart_disease_d)\n", + "congenital_heart_diseaseMapper.preview_column(dft['Congenital heart disease'])\n", + "column_mapper_d['Congenital heart disease'] = congenital_heart_diseaseMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 45, + "id": "e79aa552-8b88-42d7-970b-ac50e602ca68", + "metadata": {}, + "outputs": [], + "source": [ + "neonatal_feeding_difficulties_d = {'slow weight gain in first month due to the breastfeeding problems. Resolved after switching to bottle feeding.': 'Feeding difficulties',\n", + " 'Yes': 'Feeding difficulties',\n", + " 'Yes, G-tube': 'Feeding difficulties',\n", + " 'Yes, admitted to NICU for 8d for feeding difficulties': 'Feeding difficulties',\n", + " 'Yes-lethargy interfered with taking a bottle well': 'Feeding difficulties',\n", + " 'Yes NG fed 3 days': 'Feeding difficulties',\n", + " 'Yes NG fed 5 days': 'Feeding difficulties',\n", + " 'Yes NG fed for 5 days': 'Feeding difficulties',\n", + " 'Difficulties with breast feeding': 'Feeding difficulties',\n", + " 'NG fed for 6 weeks and 84 day SCBU / NICU stay but premature': 'Feeding difficulties'}\n", + "excluded = {\"No\":\"Feeding difficulties\",}\n", + "neonatal_feeding_difficultiesMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=neonatal_feeding_difficulties_d, excluded_d=excluded)\n", + "neonatal_feeding_difficultiesMapper.preview_column(dft['Neonatal feeding difficulties'])\n", + "column_mapper_d['Neonatal feeding difficulties'] = neonatal_feeding_difficultiesMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 46, + "id": "673540b0-791c-4f47-b6d9-cc28c70431f4", + "metadata": {}, + "outputs": [], + "source": [ + "other_gi_d = {\n", + " 'still feeding difficulties': 'Feeding difficulties',\n", + " 'History of vomiting': 'Vomiting',\n", + " 'Failure to thrive, history of frequent vomiting': 'Failure to thrive',\n", + " 'Hyperphagia': 'Polyphagia',\n", + " 'eosinophilic esophagitis': 'Eosinophilic infiltration of the esophagus',\n", + " 'diarrhea': 'Diarrhea',\n", + " 'Feeding difficulties with solid foods': 'Feeding difficulties'}\n", + "otherGiMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=other_gi_d)\n", + "otherGiMapper.preview_column(dft['Other_gi'])\n", + "column_mapper_d['Other_gi'] = otherGiMapper\n" + ] + }, + { + "cell_type": "code", + "execution_count": 47, + "id": "d776722d-aab6-4ebf-af21-164c60626419", + "metadata": {}, + "outputs": [], + "source": [ + "genitourinary_abnormalities_d = {\n", + " 'phimosis': 'Phimosis',\n", + " 'Agenesis of the right kidney': 'Unilateral renal agenesis',\n", + " 'left pyelic duplicity': 'Duplication of renal pelvis',\n", + " 'meatal stenosis': 'Male urethral meatus stenosis',}\n", + "genitourinary_abnormalitiesMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=genitourinary_abnormalities_d)\n", + "genitourinary_abnormalitiesMapper.preview_column(dft['Genitourinary abnormalities'])\n", + "column_mapper_d['Genitourinary abnormalities'] = genitourinary_abnormalitiesMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 48, + "id": "e15e30d1-0f67-40f7-8b06-bcd358205159", + "metadata": {}, + "outputs": [], + "source": [ + "cryptorchidism_d = {\n", + " 'Yes': 'Cryptorchidism',\n", + " 'Yes, bilateral': 'Bilateral cryptorchidism'}\n", + "excluded = {'No': 'Cryptorchidism',}\n", + "cryptorchidismMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=cryptorchidism_d)\n", + "cryptorchidismMapper.preview_column(dft['Cryptorchidism'])\n", + "column_mapper_d['Cryptorchidism'] = cryptorchidismMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 49, + "id": "b0b70fcc-2ea9-43e1-8c3f-34df1ff31fd8", + "metadata": {}, + "outputs": [], + "source": [ + "other_d = {'Nasal speech': 'Hypernasal speech',\n", + " '2 Cafe-au-lait spots': 'Cafe-au-lait spot',\n", + " '1 Cafe-au-lait spot': 'Cafe-au-lait spot',\n", + " 'addidional maxiliar tooth': 'Supernumerary maxillary incisor',\n", + " 'congenital hip dislocation': 'Congenital hip dislocation',\n", + " 'Recurrent skin infections when younger': 'Recurrent skin infections',\n", + " 'Hx of hypercalcemia, carnitine deficiency, and vomiting, urinary and bowel incontinence': 'Hypercalcemia',\n", + " 'Livedo reticularis': 'Livedo reticularis',\n", + " 'Cafe-au-lait spots; - note: he was considered to have overgrowth at some point in childhood': 'Cafe-au-lait spot',\n", + " 'Common infections; fast develops hypothermia (35.5oC)': 'Recurrent infections',\n", + " 'Hypoglycemia and presumed partial adrenal insufficiency': 'Adrenal insufficiency',\n", + " 'Premature adrenarche, advanced bone age, family history of hereditary hemochromatosis': 'Premature adrenarche',\n", + " 'Café-au-lait spot': 'Cafe-au-lait spot',\n", + " 'inguinal lentigines': 'Inguinal freckling',\n", + " 'cafe au lait spots': 'Cafe-au-lait spot',\n", + " 'Telangiectatisia on face and chest': 'Facial telangiectasia',\n", + " 'inguinal hernia (left)': 'Inguinal hernia',\n", + " 'Hypertension': 'Hypertension',\n", + " 'The hypotonia/ hyperlaxity was that severe a muscle panel was performed. CK was normal.': 'Hypotonia',\n", + " 'Ketosis': 'Ketosis'}\n", + "otherMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d=other_d)\n", + "otherMapper.preview_column(dft['Other'])\n", + "column_mapper_d['Other'] = otherMapper" + ] + }, + { + "cell_type": "markdown", + "id": "629d43be-7dc8-462a-9f2f-a0850aa48d0b", + "metadata": {}, + "source": [ + "# Demographics" + ] + }, + { + "cell_type": "code", + "execution_count": 50, + "id": "519d5fb5-55bb-4d4b-bcfe-b9062342ac34", + "metadata": {}, + "outputs": [], + "source": [ + "sexMapper = SexColumnMapper(male_symbol=\"M\", female_symbol=\"F\", column_name=\"Sex\")\n", + "# sexMapper.preview_column(dft['Sex'])\n", + "age_d = {}\n", + "for item in dft[\"Age, years\"].unique():\n", + " item = str(item)\n", + " if \"y\" in item or \"m\" in item:\n", + " age_d[item] = f\"P{item.upper()}\"\n", + " elif item == \"nan\":\n", + " age_d[item] = 'n/a'\n", + " elif item == \"3.9\":\n", + " age_d[item] = \"P3Y10M\"\n", + " elif item == \"6.4\":\n", + " age_d[item] = \"P6Y5M\"\n", + " elif item == \"4.5\":\n", + " age_d[item] = \"P4Y6M\"\n", + " else:\n", + " age_d[item] = f\"P{item}Y\"\n", + "ageMapper = AgeColumnMapper.custom_dictionary(column_name=\"Age, years\", string_to_iso_d=age_d)\n", + "#ageMapper.preview_column(dft[\"Age, years\"])" + ] + }, + { + "cell_type": "markdown", + "id": "25670934-1177-4c9d-ae67-a37715c89c44", + "metadata": {}, + "source": [ + "# Variants" + ] + }, + { + "cell_type": "code", + "execution_count": 51, + "id": "88ea5b74-24f2-4b93-b25d-b9222832f5cf", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1014delC/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1085_1088del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.654_655del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1439dup/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2598delC/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4500C>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.403C>T\n", + "\n", + "/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4737+1G>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3288_3291delTGAG/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.403C>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.138-1G>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.523C>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4733delG/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.445C>T /NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3911_3912delAG /NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2572C>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2699delC /NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1537dup/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3674-2A>G/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.654_655delAG/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3295delC/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3038del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3944+1G>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1258_1268del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.496C>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.419dup/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2985_2988delinsGGGACAGTGCC/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2690_2703del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1229_1233dup/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2923C>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3535dup/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3564_3567del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.685C>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1416_1417del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4794delC/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2134C>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.578del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.138-2A>G/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4468+5G>C/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2125G>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4708G>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.343C>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2011_2012del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4165+2T>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2970dupT/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1769delC/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1044_1047del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2448C>G/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4020_4021delinsAT/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.2865del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4431G>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.1483C>T/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3046dup/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3281C>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4696C>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.3762_3764del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4118T>C/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4193C>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4724G>C/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4174G>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4186T>A/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4187_4189del/NM_001080424.2?content-type=application%2Fjson\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_001080424.2%3Ac.4222T>C/NM_001080424.2?content-type=application%2Fjson\n", + "Extracted 63 unique variants\n" + ] + } + ], + "source": [ + "var_list = dft[\"cDNA change (ENST00000254846.9 or NM_001080424.2)\"].unique()\n", + "vvalidator = VariantValidator(genome_build=\"hg38\", transcript=\"NM_001080424.2\" )\n", "variant_d = {}\n", "for v in var_list:\n", - " vvar = vvalidator.encode_hgvs(v)\n", - " print(v)\n", - " print(vvar)" + " var = vvalidator.encode_hgvs(v)\n", + " variant_d[v] = var\n", + "print(f\"Extracted {len(variant_d)} unique variants\")" ] }, { "cell_type": "code", - "execution_count": null, + "execution_count": 59, "id": "33d8769e-3c46-494e-95fa-5c0adbe60d51", "metadata": {}, "outputs": [], - "source": [] + "source": [ + "varMapper = VariantColumnMapper(variant_d=variant_d,\n", + " variant_column_name=\"cDNA change (ENST00000254846.9 or NM_001080424.2)\",\n", + " default_genotype=\"heterozygous\")" + ] + }, + { + "cell_type": "code", + "execution_count": 60, + "id": "4855bc36-84fe-4257-aa1f-68efd8e42759", + "metadata": {}, + "outputs": [], + "source": [ + "encoder = CohortEncoder(df=dft,\n", + " hpo_cr=hpo_cr,\n", + " column_mapper_d=column_mapper_d,\n", + " individual_column_name='patient_id',\n", + " metadata=metadata,\n", + " agemapper=ageMapper,\n", + " sexmapper=sexMapper,\n", + " variant_mapper=varMapper,\n", + " pmid=PMID\n", + " )\n", + "disease = Disease(disease_id=\"OMIM:618505\", disease_label=\"Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities\")\n", + "encoder.set_disease(disease)" + ] + }, + { + "cell_type": "code", + "execution_count": 61, + "id": "64f78f8a-07d0-4a80-b2bc-6f7b451c5879", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "

Cohort validation

\n", + "

Errors found with 53 of 73 phenopackets.

\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
Error counts
LevelError categoryCount
ERRORCONFLICT6
WARNINGREDUNDANT33
INFORMATIONNOT_MEASURED66
\n", + "

A total of 105 issues were fixed and no individual was removed from the cohort.

" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "individuals = encoder.get_individuals()\n", + "cvalidator = CohortValidator(cohort=individuals, ontology=hpo_ontology, min_hpo=1, allelic_requirement=AllelicRequirement.MONO_ALLELIC)\n", + "qc = QcVisualizer(ontology=hpo_ontology, cohort_validator=cvalidator)\n", + "display(HTML(qc.to_summary_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 65, + "id": "658f5236-f33a-4cb6-9038-e55287267fad", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "

Cohort validation

\n", + "

Errors found with 1 of 73 phenopackets.

\n", + "\n", + "\n", + "\n", + "\n", + "
Error counts
LevelError categoryCount
WARNINGREDUNDANT1
\n", + "

A total of 1 issues were fixed and no individual was removed from the cohort.

" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "individuals = cvalidator.get_error_free_individual_list()\n", + "cvalidator = CohortValidator(cohort=individuals, ontology=hpo_ontology, min_hpo=1, allelic_requirement=AllelicRequirement.MONO_ALLELIC)\n", + "qc = QcVisualizer(ontology=hpo_ontology, cohort_validator=cvalidator)\n", + "display(HTML(qc.to_summary_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 66, + "id": "5a3033a0-9b56-47ba-ba17-25442b18564e", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "

Cohort validation

\n", + "

No errors found for the cohort with 73 individuals

" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "individuals = cvalidator.get_error_free_individual_list()\n", + "cvalidator = CohortValidator(cohort=individuals, ontology=hpo_ontology, min_hpo=1, allelic_requirement=AllelicRequirement.MONO_ALLELIC)\n", + "qc = QcVisualizer(ontology=hpo_ontology, cohort_validator=cvalidator)\n", + "display(HTML(qc.to_summary_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 67, + "id": "70c2cec7-d49b-4953-ba2a-c022b4ffc2cd", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
73 phenopackets - PMID:37196654 (n=73)
IndividualDiseaseGenotypePhenotypic features
Individual 1 (FEMALE; P16Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1018del (heterozygous)Motor delay (HP:0001270); Specific learning disability (HP:0001328); Autistic behavior (HP:0000729); Recurrent otitis media (HP:0000403); Aggressive behavior (HP:0000718); Large for gestational age (HP:0001520); Obesity (HP:0001513); Delayed speech and language development (HP:0000750); Brachydactyly (HP:0001156); Clinodactyly (HP:0030084); Broad foot (HP:0001769); Depressed nasal bridge (HP:0005280); Epicanthus (HP:0000286); Broad chin (HP:0011822); Anteverted nares (HP:0000463); Thin vermilion border (HP:0000233); Coarse facial features (HP:0000280); Square face (HP:0000321); Supernumerary nipple (HP:0002558); Mild hypermetropia (HP:0031728); Feeding difficulties (HP:0011968); Hypernasal speech (HP:0001611); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Constipation (HP:0002019); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175)
Individual 2 (FEMALE; P10Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1085_1088del (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Joint hypermobility (HP:0001382); Delayed speech and language development (HP:0000750); Global developmental delay (HP:0001263); Intention tremor (HP:0002080); Clubbing of fingers (HP:0100759); Hip dysplasia (HP:0001385); Prominent forehead (HP:0011220); Mandibular prognathia (HP:0000303); Hypermetropia (HP:0000540); Feeding difficulties (HP:0011968); Cafe-au-lait spot (HP:0000957); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Hypermetropia (HP:0000540); excluded: Increased body weight (HP:0004324)
Individual 3 (MALE; P9Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.654_655del (heterozygous)Motor delay (HP:0001270); Intellectual disability, moderate (HP:0002342); Autistic behavior (HP:0000729); Sleep abnormality (HP:0002360); Joint hypermobility (HP:0001382); Recurrent otitis media (HP:0000403); Constipation (HP:0002019); Irritability (HP:0000737); Anxiety (HP:0000739); Large for gestational age (HP:0001520); Obesity (HP:0001513); Macrocephaly (HP:0000256); Delayed speech and language development (HP:0000750); Clinodactyly (HP:0030084); Broad foot (HP:0001769); Square face (HP:0000321); Depressed nasal bridge (HP:0005280); Epicanthus (HP:0000286); Protruding ear (HP:0000411); Feeding difficulties (HP:0011968); Cafe-au-lait spot (HP:0000957); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Irritability (HP:0000737); excluded: Anxiety (HP:0000739); excluded: Obstipation (HP:0034782); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 5 (MALE; P25Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1439dup (heterozygous)Motor delay (HP:0001270); Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Recurrent otitis media (HP:0000403); Delayed speech and language development (HP:0000750); Seizure (HP:0001250); Hypertonia (HP:0001276); Involuntary movements (HP:0004305); Pes planus (HP:0001763); Broad finger (HP:0001500); Deeply set eye (HP:0000490); Synophrys (HP:0000664); Thick lower lip vermilion (HP:0000179); Allergy (HP:0012393); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Constipation (HP:0002019); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 6 (MALE; P13Y2M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2598del (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Attention deficit hyperactivity disorder (HP:0007018); Maternal diabetes (HP:0009800); Delayed speech and language development (HP:0000750); Relative macrocephaly (HP:0004482); Synophrys (HP:0000664); Hypermetropia (HP:0000540); Phimosis (HP:0001741); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Hypermetropia (HP:0000540); excluded: Feeding difficulties (HP:0011968)
Individual 7 (FEMALE; P9Y6M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4500C>A (heterozygous)Specific learning disability (HP:0001328); Sleep abnormality (HP:0002360); Aggressive behavior (HP:0000718); Premature rupture of membranes (HP:0001788); Delayed speech and language development (HP:0000750); Seizure (HP:0001250); Tics (HP:0100033); Short nose (HP:0003196); Short philtrum (HP:0000322); Thick vermilion border (HP:0012471); Preauricular pit (HP:0004467); Feeding difficulties (HP:0011968); Supernumerary maxillary incisor (HP:0006332); excluded: Motor delay (HP:0001270); excluded: Autistic behavior (HP:0000729); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 8 (MALE; P10Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.403C>T (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Autistic behavior (HP:0000729); Sleep abnormality (HP:0002360); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Attention deficit hyperactivity disorder (HP:0007018); Breech presentation (HP:0001623); Large for gestational age (HP:0001520); Tall stature (HP:0000098); Delayed speech and language development (HP:0000750); Cerebellar cortical atrophy (HP:0008278); Kyphosis (HP:0002808); Clinodactyly (HP:0030084); Hypotelorism (HP:0000601); Short philtrum (HP:0000322); Prominent nasal bridge (HP:0000426); Brachycephaly (HP:0000248); Congenital hip dislocation (HP:0001374); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Kyphosis (HP:0002808); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 9 (MALE; P6Y6M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4737+1G>A (heterozygous)Motor delay (HP:0001270); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Ventouse delivery (HP:0011412); Delayed speech and language development (HP:0000750); Global developmental delay (HP:0001263); Preauricular skin tag (HP:0000384); Abnormality of refraction (HP:0000539); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Feeding difficulties (HP:0011968)
Individual 11 (FEMALE; P19Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3288_3291del (heterozygous)Motor delay (HP:0001270); Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Hypotonia (HP:0001252); Delayed speech and language development (HP:0000750); Psychosis (HP:0000709); Ataxia (HP:0001251); Hearing impairment (HP:0000365); Enlarged vestibular aqueduct (HP:0011387); Recurrent skin infections (HP:0001581); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Hearing impairment (HP:0000365); excluded: Feeding difficulties (HP:0011968)
Individual 12 (MALE; P17Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3288_3291del (heterozygous)Motor delay (HP:0001270); Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Hypotonia (HP:0001252); Macrocephaly (HP:0000256); Delayed speech and language development (HP:0000750); Psychosis (HP:0000709); Dystonia (HP:0001332); Vomiting (HP:0002013); Hypercalcemia (HP:0003072); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Seizure (HP:0001250); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 13 (FEMALE; P6Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.403C>T (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Obstructive sleep apnea (HP:0002870); Hypotonia (HP:0001252); Severe temper tantrums (HP:0025162); Delayed speech and language development (HP:0000750); Neurogenic bladder (HP:0000011); Tethered cord (HP:0002144); Macrocephaly (HP:0000256); Prominent forehead (HP:0011220); Wide mouth (HP:0000154); Joint hypermobility (HP:0001382); Feeding difficulties (HP:0011968); Failure to thrive (HP:0001508); Livedo reticularis (HP:0033505); excluded: Autistic behavior (HP:0000729); excluded: Obstructive sleep apnea (HP:0002870); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 15 (MALE; P5Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.138-1G>A (heterozygous)Motor delay (HP:0001270); Intellectual disability, moderate (HP:0002342); Autistic behavior (HP:0000729); Sleep apnea (HP:0010535); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Exotropia (HP:0000577); Constipation (HP:0002019); Attention deficit hyperactivity disorder (HP:0007018); Aggressive behavior (HP:0000718); Small for gestational age (HP:0001518); Delayed speech and language development (HP:0000750); Generalized non-motor (absence) seizure (HP:0002121); Bilateral tonic-clonic seizure (HP:0002069); Hypertelorism (HP:0000316); Mandibular prognathia (HP:0000303); Hypodontia (HP:0000668); Microdontia (HP:0000691); Cryptorchidism (HP:0000028); Patent ductus arteriosus (HP:0001643); Feeding difficulties (HP:0011968); Pneumonia (HP:0002090); excluded: Sleep apnea (HP:0010535); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Exotropia (HP:0000577); excluded: Recurrent otitis media (HP:0000403); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Generalized non-motor (absence) seizure (HP:0002121); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 16 (MALE; P12Y 4M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.523C>T (heterozygous)Motor delay (HP:0001270); Specific learning disability (HP:0001328); Autistic behavior (HP:0000729); Sleep abnormality (HP:0002360); Impulsivity (HP:0100710); Delayed speech and language development (HP:0000750); Psychosis (HP:0000709); Tics (HP:0100033); Rhinitis (HP:0012384); Polyphagia (HP:0002591); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Impulsivity (HP:0100710); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 17 (published as Individual 1 in Bramswig et al., 2017) (MALE; P14Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4733del (heterozygous)Motor delay (HP:0001270); Intellectual disability, severe (HP:0010864); Hypotonia (HP:0001252); Delayed speech and language development (HP:0000750); Seizure (HP:0001250); Cerebral atrophy (HP:0002059); Agenesis of corpus callosum (HP:0001274); Scoliosis (HP:0002650); Coarse facial features (HP:0000280); Hypertelorism (HP:0000316); Depressed nasal bridge (HP:0005280); Short nose (HP:0003196); Anteverted nares (HP:0000463); Low-set ears (HP:0000369); Everted lower lip vermilion (HP:0000232); Secundum atrial septal defect (HP:0001684); Feeding difficulties (HP:0011968); Unilateral renal agenesis (HP:0000122); excluded: Autistic behavior (HP:0000729); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 18 (MALE; P19Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1085_1088del (heterozygous)Specific learning disability (HP:0001328); Autistic behavior (HP:0000729); Knee joint hypermobility (HP:0045086); Constipation (HP:0002019); Anxiety (HP:0000739); Aggressive behavior (HP:0000718); Large for gestational age (HP:0001520); Developmental regression (HP:0002376); Prominent interphalangeal joints (HP:0006237); Macrocephaly (HP:0000256); Thin upper lip vermilion (HP:0000219); Myopia (HP:0000545); Asthma (HP:0002099); Pneumonia (HP:0002090); Inguinal hernia (HP:0000023); excluded: Motor delay (HP:0001270); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Anxiety (HP:0000739); excluded: Aggressive behavior (HP:0000718); excluded: Delayed speech and language development (HP:0000750); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Myopia (HP:0000545)
Individual 19 (MALE; P6Y6M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.445C>T (heterozygous)Motor delay (HP:0001270); Specific learning disability (HP:0001328); Autistic behavior (HP:0000729); Fetal distress (HP:0025116); Delayed speech and language development (HP:0000750); Global developmental delay (HP:0001263); Ptosis (HP:0000508); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 20 (FEMALE; P2Y8M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3911_3912del (heterozygous)Motor delay (HP:0001270); Hypotonia (HP:0001252); Ventouse delivery (HP:0011412); Delayed speech and language development (HP:0000750); Coarse facial features (HP:0000280); Prominent forehead (HP:0011220); Depressed nasal bridge (HP:0005280); Plagiocephaly (HP:0001357); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Feeding difficulties (HP:0011968)
Individual 21 (MALE; P10Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2572C>T (heterozygous)Motor delay (HP:0001270); Intellectual disability, severe (HP:0010864); Autistic behavior (HP:0000729); Sleep abnormality (HP:0002360); Hypotonia (HP:0001252); Attention deficit hyperactivity disorder (HP:0007018); Large for gestational age (HP:0001520); Delayed speech and language development (HP:0000750); Broad fingertip (HP:0011300); External tibial torsion (HP:0034373); Infra-orbital crease (HP:0100876); Deep philtrum (HP:0002002); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 22 (MALE; P10Y5M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2699del (heterozygous)Motor delay (HP:0001270); Intellectual disability, borderline (HP:0006889); Tip-toe gait (HP:0030051); Toe syndactyly (HP:0001770); Intrauterine growth retardation (HP:0001511); Delayed speech and language development (HP:0000750); Bruxism (HP:0003763); Dystonia (HP:0001332); Dysarthria (HP:0001260); Fused cervical vertebrae (HP:0002949); Low anterior hairline (HP:0000294); Depressed nasal bridge (HP:0005280); Anteverted nares (HP:0000463); Smooth philtrum (HP:0000319); Thin upper lip vermilion (HP:0000219); Broad face (HP:0000283); Full cheeks (HP:0000293); Hypermetropia (HP:0000540); Astigmatism (HP:0000483); Cafe-au-lait spot (HP:0000957); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Tip-toe gait (HP:0030051); excluded: Toe syndactyly (HP:0001770); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Hypermetropia (HP:0000540); excluded: Feeding difficulties (HP:0011968)
Individual 23 (MALE; P4Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1537dup (heterozygous)Motor delay (HP:0001270); Hypotonia (HP:0001252); Agitation (HP:0000713); Large for gestational age (HP:0001520); Delayed speech and language development (HP:0000750); Prominent nose (HP:0000448); Feeding difficulties (HP:0011968); Duplication of renal pelvis (HP:0005580); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Constipation (HP:0002019); excluded: Agitation (HP:0000713); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175)
Individual 24 (FEMALE; P8Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3674-2A>G (heterozygous)Motor delay (HP:0001270); Hypotonia (HP:0001252); Constipation (HP:0002019); Aggressive behavior (HP:0000718); Tethered cord (HP:0002144); Scoliosis (HP:0002650); Macrocephaly (HP:0000256); Hypertelorism (HP:0000316); Prominent eyelashes (HP:0011231); Overfolded helix (HP:0000396); Diastema (HP:0000699); Mandibular prognathia (HP:0000303); Pulmonic stenosis (HP:0001642); Feeding difficulties (HP:0011968); Eosinophilic infiltration of the esophagus (HP:0410151); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Aggressive behavior (HP:0000718); excluded: Delayed speech and language development (HP:0000750); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175)
Individual 25 (FEMALE; P4Y10M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.654_655del (heterozygous)Motor delay (HP:0001270); Anxiety (HP:0000739); Maternal diabetes (HP:0009800); Delayed speech and language development (HP:0000750); Drooling (HP:0002307); Deeply set eye (HP:0000490); Strabismus (HP:0000486); Full cheeks (HP:0000293); Depressed nasal bridge (HP:0005280); Anteverted nares (HP:0000463); Square face (HP:0000321); Synophrys (HP:0000664); Hypermetropia (HP:0000540); Feeding difficulties (HP:0011968); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Recurrent otitis media (HP:0000403); excluded: Anxiety (HP:0000739); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Hypermetropia (HP:0000540)
Individual 26 (MALE; P26Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3300del (heterozygous)Motor delay (HP:0001270); Sleep abnormality (HP:0002360); Joint hypermobility (HP:0001382); Depression (HP:0000716); Attention deficit hyperactivity disorder (HP:0007018); Hydrocephalus (HP:0000238); Delayed speech and language development (HP:0000750); Psychosis (HP:0000709); Platybasia (HP:0002691); Small foramen magnum (HP:0002677); Pes planus (HP:0001763); Myopia (HP:0000545); Nystagmus (HP:0000639); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Depression (HP:0000716); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Anxiety (HP:0000739); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Cleft palate (HP:0000175); excluded: Astigmatism (HP:0000483); excluded: Myopia (HP:0000545); excluded: Feeding difficulties (HP:0011968)
Individual 27 (MALE; P7Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3038del (heterozygous)Motor delay (HP:0001270); Sleep abnormality (HP:0002360); Hypotonia (HP:0001252); Tip-toe gait (HP:0030051); Recurrent otitis media (HP:0000403); Shoulder dystocia (HP:0011413); Delayed speech and language development (HP:0000750); Fatigue (HP:0012378); Brachydactyly (HP:0001156); Long face (HP:0000276); Depressed nasal bridge (HP:0005280); Anteverted nares (HP:0000463); Downslanted palpebral fissures (HP:0000494); Long philtrum (HP:0000343); Feeding difficulties (HP:0011968); Diarrhea (HP:0002014); excluded: Autistic behavior (HP:0000729); excluded: Tip-toe gait (HP:0030051); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 28 (MALE; P10Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3944+1G>A (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Autistic behavior (HP:0000729); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Aggressive behavior (HP:0000718); Delayed speech and language development (HP:0000750); Fatigue (HP:0012378); Hypermetropia (HP:0000540); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Hypermetropia (HP:0000540); excluded: Feeding difficulties (HP:0011968)
Individual 29 (FEMALE; P13Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1260_1270del (heterozygous)Motor delay (HP:0001270); Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Sleep abnormality (HP:0002360); Hypotonia (HP:0001252); Maternal diabetes (HP:0009800); Delayed speech and language development (HP:0000750); Focal impaired awareness seizure (HP:0002384); Scoliosis (HP:0002650); High forehead (HP:0000348); Horizontal eyebrow (HP:0011228); Prominent nasal bridge (HP:0000426); Wide mouth (HP:0000154); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Focal impaired awareness seizure (HP:0002384); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Feeding difficulties (HP:0011968)
Individual 31 (FEMALE; P12Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.496C>T (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Hypotonia (HP:0001252); Obesity (HP:0001513); Delayed speech and language development (HP:0000750); Small hand (HP:0200055); Clinodactyly (HP:0030084); Prominent nasal bridge (HP:0000426); Ptosis (HP:0000508); Prominent forehead (HP:0011220); Mandibular prognathia (HP:0000303); Myopia (HP:0000545); Esotropia (HP:0000565); Amblyopia (HP:0000646); Feeding difficulties (HP:0011968); Adrenal insufficiency (HP:0000846); excluded: Autistic behavior (HP:0000729); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Myopia (HP:0000545); excluded: Esotropia (HP:0000565); excluded: Lethargy (HP:0001254)
Individual 32 (MALE; P14Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.419dup (heterozygous)Motor delay (HP:0001270); Autistic behavior (HP:0000729); Hypotonia (HP:0001252); Hyperextensible hand joints (HP:0005639); Constipation (HP:0002019); Cryptorchidism (HP:0000028); Aggressive behavior (HP:0000718); Anxiety (HP:0000739); Hypertension (HP:0000822); Delayed speech and language development (HP:0000750); Enuresis (HP:0000805); Brachydactyly (HP:0001156); Macrocephaly (HP:0000256); Anteverted nares (HP:0000463); Bicuspid aortic valve (HP:0001647); Increased body weight (HP:0004324); Premature adrenarche (HP:0012412); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Anxiety (HP:0000739); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 33 (MALE; P7Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2985_2988delinsGGGACAGTGCC (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Autistic behavior (HP:0000729); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Abnormal repetitive mannerisms (HP:0000733); Large for gestational age (HP:0001520); Obesity (HP:0001513); Delayed speech and language development (HP:0000750); Poor coordination (HP:0002370); Hyperlordosis (HP:0003307); Broad foot (HP:0001769); High anterior hairline (HP:0009890); Prominent forehead (HP:0011220); Hypertelorism (HP:0000316); Wide mouth (HP:0000154); Protruding ear (HP:0000411); Hypermetropia (HP:0000540); Astigmatism (HP:0000483); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Abnormal repetitive mannerisms (HP:0000733); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Hyperlordosis (HP:0003307); excluded: Cleft palate (HP:0000175); excluded: Hypermetropia (HP:0000540); excluded: Feeding difficulties (HP:0011968)
Individual 37 (MALE; P4Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2690_2703del (heterozygous)Motor delay (HP:0001270); Intellectual disability (HP:0001249); Hypotonia (HP:0001252); Aggressive behavior (HP:0000718); Delayed speech and language development (HP:0000750); Myoclonic seizure (HP:0032794); Prominent forehead (HP:0011220); Ventricular septal defect (HP:0001629); Subvalvular aortic stenosis (HP:0001682); Interrupted aortic arch (HP:0011611); Atrial septal defect (HP:0001631); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Psychosis (HP:0000709); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 39 (MALE; P4Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1229_1233dup (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Constipation (HP:0002019); Delayed speech and language development (HP:0000750); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 40 (DDD_304502) (MALE; P3Y10M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2923C>T (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Large for gestational age (HP:0001520); Obesity (HP:0001513); Delayed speech and language development (HP:0000750); Moderate global developmental delay (HP:0011343); Prominent fingertip pads (HP:0001212); Down-sloping shoulders (HP:0200021); Tall stature (HP:0000098); Talipes (HP:0001883); Downturned corners of mouth (HP:0002714); Cleft palate (HP:0000175); Feeding difficulties (HP:0011968); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 41 (DDD_274859) (FEMALE; P6Y5M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3535dup (heterozygous)Motor delay (HP:0001270); Moderate intrauterine growth retardation (HP:0011408); Small for gestational age (HP:0001518); Delayed speech and language development (HP:0000750); Moderate global developmental delay (HP:0011343); Short attention span (HP:0000736); Proportionate tall stature (HP:0011407); Feeding difficulties (HP:0011968); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Short attention span (HP:0000736); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 42 (DDD_292095) (MALE; P4Y6M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3564_3567del (heterozygous)Motor delay (HP:0001270); Autistic behavior (HP:0000729); Delayed speech and language development (HP:0000750); Developmental regression (HP:0002376); Feeding difficulties (HP:0011968); Cafe-au-lait spot (HP:0000957); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 45 (DDD_111002863) (MALE; P3Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.685C>T (heterozygous)Motor delay (HP:0001270); Intellectual disability (HP:0001249); Atypical behavior (HP:0000708); Polyhydramnios (HP:0001561); Macrocephaly (HP:0000256); Delayed speech and language development (HP:0000750); Pes planus (HP:0001763); Freckling (HP:0001480); Posteriorly rotated ears (HP:0000358); Deeply set eye (HP:0000490); Frontal bossing (HP:0002007); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 46 (DDD_118000039) (MALE; P4Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2923C>T (heterozygous)Motor delay (HP:0001270); Intellectual disability (HP:0001249); Hypotonia (HP:0001252); Delayed speech and language development (HP:0000750); Unsteady gait (HP:0002317); Pes planus (HP:0001763); Wide mouth (HP:0000154); Macroglossia (HP:0000158); Short nose (HP:0003196); Uplifted earlobe (HP:0009909); Ptosis (HP:0000508); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Aggressive behavior (HP:0000718); excluded: Seizure (HP:0001250); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 47 (DDD_303829) (FEMALE; P8Y8M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1416_1417del (heterozygous)Motor delay (HP:0001270); Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Ventouse delivery (HP:0011412); Macrocephaly (HP:0000256); Delayed speech and language development (HP:0000750); Pes planus (HP:0001763); Macrotia (HP:0000400); Deeply set eye (HP:0000490); High palate (HP:0000218); Widely spaced teeth (HP:0000687); excluded: Autistic behavior (HP:0000729); excluded: Hyperorality (HP:0000710); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 48 (TAS_F3039Y) (MALE; P23Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4795del (heterozygous)Motor delay (HP:0001270); Specific learning disability (HP:0001328); Autistic behavior (HP:0000729); Sleep abnormality (HP:0002360); Aggressive behavior (HP:0000718); Attention deficit hyperactivity disorder (HP:0007018); Delayed speech and language development (HP:0000750); Abnormal social behavior (HP:0012433); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 51 (ASC_80001103038) (MALE; P8 Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2134C>T (heterozygous)Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Delayed speech and language development (HP:0000750); Seizure (HP:0001250); excluded: Motor delay (HP:0001270); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Psychosis (HP:0000709); excluded: Dystonia (HP:0001332)
Individual 52 (SSC_12683.p1) (MALE; n/a)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.578del (heterozygous)Autistic behavior (HP:0000729)
Individual 53 (SSC_11329.p1) (MALE; n/a)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.138-2A>G (heterozygous)Autistic behavior (HP:0000729)
Individual 55 (SSC_13446.p1) (MALE; n/a)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4468+5G>C (heterozygous)Autistic behavior (HP:0000729)
Individual 56 (ASP009) (FEMALE; P25Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2125G>T (heterozygous)Autistic behavior (HP:0000729); Strabismus (HP:0000486); Attention deficit hyperactivity disorder (HP:0007018); Delayed speech and language development (HP:0000750); Depression (HP:0000716); Seizure (HP:0001250); excluded: Motor delay (HP:0001270); excluded: Psychosis (HP:0000709)
Individual 57 (PCGC_1-03321) (MALE; P4Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4708G>T (heterozygous)Strabismus (HP:0000486); Small for gestational age (HP:0001518); Delayed speech and language development (HP:0000750); Periventricular leukomalacia (HP:0006970); Sacral dimple (HP:0000960); Male urethral meatus stenosis (HP:0032077); excluded: Autistic behavior (HP:0000729); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175)
Individual 60 (MSSNG_AU4427301) (MALE; n/a)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.343C>T (heterozygous)Motor delay (HP:0001270); Autistic behavior (HP:0000729); Delayed speech and language development (HP:0000750); Poor coordination (HP:0002370); excluded: Aggressive behavior (HP:0000718)
Individual 61 (MSSNG_MT_48.3) (FEMALE; n/a)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.403C>T (heterozygous)Autistic behavior (HP:0000729)
Individual 62 (MSSNG_AU2168301) (MALE; n/a)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2012_2013del (heterozygous)Motor delay (HP:0001270); Autistic behavior (HP:0000729); Delayed speech and language development (HP:0000750); excluded: Aggressive behavior (HP:0000718); excluded: Scoliosis (HP:0002650)
Individual 63 (MSSNG_2-1764-003) (MALE; n/a)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4165+2T>A (heterozygous)Autistic behavior (HP:0000729); Hypotonia (HP:0001252); Constipation (HP:0002019); Tics (HP:0100033)
Individual 65 (FEMALE; P11Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2970dup (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Sleep abnormality (HP:0002360); Hypotonia (HP:0001252); Macrocephaly (HP:0000256); Delayed speech and language development (HP:0000750); Dilation of Virchow-Robin spaces (HP:0012520); High forehead (HP:0000348); Horizontal eyebrow (HP:0011228); Deeply set eye (HP:0000490); Dimple chin (HP:0010751); Prominent nasal bridge (HP:0000426); Hypermetropia (HP:0000540); Horizontal nystagmus (HP:0000666); excluded: Autistic behavior (HP:0000729); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Hypermetropia (HP:0000540); excluded: Astigmatism (HP:0000483); excluded: Feeding difficulties (HP:0011968)
Individual 67 (MALE; P5Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1769del (heterozygous)Motor delay (HP:0001270); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Macrocephaly (HP:0000256); Delayed speech and language development (HP:0000750); Recurrent hand flapping (HP:0100023); Hydrocephalus (HP:0000238); Thoracic kyphosis (HP:0002942); Pes planus (HP:0001763); High forehead (HP:0000348); Downslanted palpebral fissures (HP:0000494); Deeply set eye (HP:0000490); Dimple chin (HP:0010751); Downturned corners of mouth (HP:0002714); Large earlobe (HP:0009748); Abnormality of refraction (HP:0000539); Inguinal freckling (HP:0030052); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Thoracic kyphosis (HP:0002942); excluded: Cleft palate (HP:0000175); excluded: Feeding difficulties (HP:0011968)
Individual 68 (FEMALE; P35Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1769del (heterozygous)Motor delay (HP:0001270); Joint hypermobility (HP:0001382); Pes planus (HP:0001763); Mild myopia (HP:0025573); Cafe-au-lait spot (HP:0000957); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Delayed speech and language development (HP:0000750); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Feeding difficulties (HP:0011968)
Individual 70 (MALE; P8Y11M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1053_1056del (heterozygous)Sleep abnormality (HP:0002360); Joint hypermobility (HP:0001382); Recurrent otitis media (HP:0000403); Hyperactivity (HP:0000752); Delayed speech and language development (HP:0000750); Midface retrusion (HP:0011800); Short nose (HP:0003196); Short philtrum (HP:0000322); Wide mouth (HP:0000154); Eclabion (HP:0012472); Anteverted nares (HP:0000463); Hypermetropia (HP:0000540); excluded: Motor delay (HP:0001270); excluded: Autistic behavior (HP:0000729); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Constipation (HP:0002019); excluded: Hyperactivity (HP:0000752); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Cleft palate (HP:0000175); excluded: Hypermetropia (HP:0000540); excluded: Feeding difficulties (HP:0011968)
Individual 71 (MALE; P7Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2448C>G (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Autistic behavior (HP:0000729); Sleep abnormality (HP:0002360); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Macrocephaly (HP:0000256); Delayed speech and language development (HP:0000750); Poor gross motor coordination (HP:0007015); Prominent forehead (HP:0011220); Sparse eyebrow (HP:0045075); Uplifted earlobe (HP:0009909); Protruding ear (HP:0000411); Smooth philtrum (HP:0000319); Astigmatism (HP:0000483); Feeding difficulties (HP:0011968); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Astigmatism (HP:0000483)
Individual 72 (MALE; P7Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4020_4021delinsAT (heterozygous)Motor delay (HP:0001270); Strabismus (HP:0000486); Attention deficit hyperactivity disorder (HP:0007018); Small for gestational age (HP:0001518); Delayed speech and language development (HP:0000750); Prominent forehead (HP:0011220); Short nose (HP:0003196); Protruding ear (HP:0000411); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Pectus excavatum (HP:0000767); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175)
Individual 73 (MALE; P10Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1416_1417del (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Autistic behavior (HP:0000729); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Attention deficit hyperactivity disorder (HP:0007018); Delayed speech and language development (HP:0000750); Single transverse palmar crease (HP:0000954); Hip dysplasia (HP:0001385); Hypertelorism (HP:0000316); Microcephaly (HP:0000252); Short chin (HP:0000331); Protruding ear (HP:0000411); Mild hypermetropia (HP:0031728); excluded: Pectus excavatum (HP:0000767); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Cleft palate (HP:0000175)
Individual 74 (MALE; P49Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1416_1417del (heterozygous)Specific learning disability (HP:0001328); excluded: Pectus excavatum (HP:0000767)
Individual 75 (MALE; P9Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.2865del (heterozygous)Motor delay (HP:0001270); Hypotonia (HP:0001252); Impulsivity (HP:0100710); Delayed speech and language development (HP:0000750); Kyphosis (HP:0002808); Pes planus (HP:0001763); Prominent forehead (HP:0011220); Midface retrusion (HP:0011800); Macrocephaly (HP:0000256); excluded: Sleep abnormality (HP:0002360); excluded: Pectus excavatum (HP:0000767); excluded: Impulsivity (HP:0100710); excluded: Kyphosis (HP:0002808); excluded: Cleft palate (HP:0000175)
Individual 76 (FEMALE; P14Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4431G>A (heterozygous)Motor delay (HP:0001270); Central sleep apnea (HP:0010536); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Delayed speech and language development (HP:0000750); Genu valgum (HP:0002857); Short toe (HP:0001831); Pes planus (HP:0001763); Patellar subluxation (HP:0010499); Wide nose (HP:0000445); Full cheeks (HP:0000293); Epicanthus (HP:0000286); Astigmatism (HP:0000483); Feeding difficulties (HP:0011968); Alopecia (HP:0001596); excluded: Autistic behavior (HP:0000729); excluded: Central sleep apnea (HP:0010536); excluded: Syndactyly (HP:0001159); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Cleft palate (HP:0000175)
Individual 77 (MALE; P19Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1483C>T (heterozygous)Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Sleep abnormality (HP:0002360); Strabismus (HP:0000486); Decreased fetal movement (HP:0001558); Macrocephaly (HP:0000256); Delayed speech and language development (HP:0000750); Seizure (HP:0001250); Pes planus (HP:0001763); Prominent forehead (HP:0011220); Synophrys (HP:0000664); Wide nose (HP:0000445); Wide mouth (HP:0000154); Thick vermilion border (HP:0012471); Hypermetropia (HP:0000540); excluded: Motor delay (HP:0001270); excluded: Hypotonia (HP:0001252); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Focal-onset seizure (HP:0007359); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Hypermetropia (HP:0000540); excluded: Feeding difficulties (HP:0011968)
Individual 82 (FEMALE; P1.5Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.1085_1088del (heterozygous)Motor delay (HP:0001270); Sleep abnormality (HP:0002360); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Constipation (HP:0002019); Decreased fetal movement (HP:0001558); Delayed speech and language development (HP:0000750); Sensory seeking (HP:4000079); Seizure (HP:0001250); High forehead (HP:0000348); Short nose (HP:0003196); Full cheeks (HP:0000293); Patent ductus arteriosus (HP:0001643); Feeding difficulties (HP:0011968); Facial telangiectasia (HP:0007380); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 83 (MALE; P8Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3046dup (heterozygous)Motor delay (HP:0001270); Intellectual disability (HP:0001249); Autistic behavior (HP:0000729); Sleep abnormality (HP:0002360); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Recurrent otitis media (HP:0000403); Bilateral cryptorchidism (HP:0008689); Attention deficit hyperactivity disorder (HP:0007018); Tall stature (HP:0000098); Delayed speech and language development (HP:0000750); Broad-based gait (HP:0002136); Pes planus (HP:0001763); Tented upper lip vermilion (HP:0010804); Broad nasal tip (HP:0000455); Preauricular pit (HP:0004467); Feeding difficulties (HP:0011968); Inguinal hernia (HP:0000023); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Constipation (HP:0002019); excluded: Attention deficit hyperactivity disorder (HP:0007018); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 84 (MALE; P1Y2M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3281C>A (heterozygous)Motor delay (HP:0001270); Large for gestational age (HP:0001520); Delayed speech and language development (HP:0000750); Torticollis (HP:0000473); Protruding ear (HP:0000411); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Seizure (HP:0001250); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 85 (MALE; P33Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3281C>A (heterozygous)Specific learning disability (HP:0001328); Obesity (HP:0001513); Delayed speech and language development (HP:0000750); Protruding ear (HP:0000411); Tinnitus (HP:0000360); Hypertension (HP:0000822); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 4 (MALE; P14Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4696C>A (heterozygous)Motor delay (HP:0001270); Intellectual disability, moderate (HP:0002342); Autistic behavior (HP:0000729); Attention deficit hyperactivity disorder (HP:0007018); Delayed speech and language development (HP:0000750); Delayed CNS myelination (HP:0002188); Depressed nasal bridge (HP:0005280); Macrodontia (HP:0001572); Low-set ears (HP:0000369); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 10 (MALE; P4Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.3762_3764del (heterozygous)Motor delay (HP:0001270); Autistic behavior (HP:0000729); Hypotonia (HP:0001252); Joint hypermobility (HP:0001382); Delayed speech and language development (HP:0000750); Global developmental delay (HP:0001263); Bruxism (HP:0003763); Relative macrocephaly (HP:0004482); Micrognathia (HP:0000347); Glossoptosis (HP:0000162); Cleft palate (HP:0000175); Feeding difficulties (HP:0011968); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 34 (MALE; P11Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4118T>C (heterozygous)Motor delay (HP:0001270); Intellectual disability, mild (HP:0001256); Autistic behavior (HP:0000729); Constipation (HP:0002019); Attention deficit hyperactivity disorder (HP:0007018); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Delayed speech and language development (HP:0000750); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539); excluded: Feeding difficulties (HP:0011968)
Individual 38 (MALE; P6Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4193C>A (heterozygous)Motor delay (HP:0001270); Autistic behavior (HP:0000729); Joint hypermobility (HP:0001382); Hypertension (HP:0000822); Delayed speech and language development (HP:0000750); Soft skin (HP:0000977); Synophrys (HP:0000664); Broad forehead (HP:0000337); Long uvula (HP:0010810); Feeding difficulties (HP:0011968); Hypotonia (HP:0001252); Joint laxity (HP:0001388); excluded: Sleep abnormality (HP:0002360); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Aggressive behavior (HP:0000718); excluded: Psychosis (HP:0000709); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 44 (DDD_286674) (FEMALE; P3Y)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4724G>C (heterozygous)Motor delay (HP:0001270); Hyperactivity (HP:0000752); Delayed speech and language development (HP:0000750); Malar flattening (HP:0000272); Prominent forehead (HP:0011220); Upslanted palpebral fissure (HP:0000582); Feeding difficulties (HP:0011968); Ketosis (HP:0001946); excluded: Autistic behavior (HP:0000729); excluded: Sleep abnormality (HP:0002360); excluded: Hypotonia (HP:0001252); excluded: Spasticity (HP:0001257); excluded: Syndactyly (HP:0001159); excluded: Pectus excavatum (HP:0000767); excluded: Strabismus (HP:0000486); excluded: Recurrent otitis media (HP:0000403); excluded: Constipation (HP:0002019); excluded: Hyperactivity (HP:0000752); excluded: Seizure (HP:0001250); excluded: Dystonia (HP:0001332); excluded: Scoliosis (HP:0002650); excluded: Cleft palate (HP:0000175); excluded: Abnormality of refraction (HP:0000539)
Individual 49 (DEASD_0146_001) (MALE; P7Y3M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4174G>A (heterozygous)Motor delay (HP:0001270); Autistic behavior (HP:0000729); Macrocephaly (HP:0000256); Delayed speech and language development (HP:0000750); Enuresis (HP:0000805); excluded: Aggressive behavior (HP:0000718)
Individual 50 (DEASD_0129_001) (MALE; P8Y7M)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4186T>A (heterozygous)Autistic behavior (HP:0000729); excluded: Motor delay (HP:0001270); excluded: Delayed speech and language development (HP:0000750)
Individual 54 (SSC_13675.p1) (MALE; n/a)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4187_4189del (heterozygous)Autistic behavior (HP:0000729); Macrocephaly (HP:0000256)
Individual 58 (DDD_305030) (MALE; n/a)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4187_4189del (heterozygous)Motor delay (HP:0001270); Autistic behavior (HP:0000729); Delayed speech and language development (HP:0000750); Global developmental delay (HP:0001263); Brachycephaly (HP:0000248); Downslanted palpebral fissures (HP:0000494); Low-set ears (HP:0000369)
Individual 59 (DDD_306396) (MALE; n/a)Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities (OMIM:618505)NM_001080424.2:c.4222T>C (heterozygous)Motor delay (HP:0001270); Hypotonia (HP:0001252); 2-3 toe syndactyly (HP:0004691); Delayed speech and language development (HP:0000750); Mild global developmental delay (HP:0011342); Dolichocephaly (HP:0000268); Unsteady gait (HP:0002317); Talipes (HP:0001883); Frontal bossing (HP:0002007); Prominent forehead (HP:0011220); excluded: 2-3 toe syndactyly (HP:0004691)
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "table = PhenopacketTable(individual_list=individuals, metadata=metadata)\n", + "display(HTML(table.to_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 68, + "id": "9a893ecd-f59a-419f-a918-8505aa4eef08", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "We output 73 GA4GH phenopackets to the directory phenopackets\n" + ] + } + ], + "source": [ + "Individual.output_individuals_as_phenopackets(individual_list=individuals,\n", + " metadata=metadata,\n", + " outdir=\"phenopackets\")" + ] + }, + { + "cell_type": "code", + "execution_count": 58, + "id": "e736ef1b-56c8-4cfb-ab12-5a2b854bff7d", + "metadata": {}, + "outputs": [], + "source": [ + "# pxf validate --hpo hp.json *.json\n", + "# no errors" + ] } ], "metadata": { "kernelspec": { - "display_name": "ps_venv", + "display_name": "pstore_env", "language": "python", - "name": "ps_venv" + "name": "pstore_env" }, "language_info": { "codemirror_mode": { @@ -1307,7 +2137,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.10.12" + "version": "3.11.3" } }, "nbformat": 4, diff --git a/notebooks/KDM6B/input/Rots_2023_PMID_37196654.xlsx b/notebooks/KDM6B/input/Rots_2023_PMID_37196654.xlsx index 08d54fdc1..0bd44096d 100644 Binary files a/notebooks/KDM6B/input/Rots_2023_PMID_37196654.xlsx and b/notebooks/KDM6B/input/Rots_2023_PMID_37196654.xlsx differ diff --git a/notebooks/KDM6B/phenopackets/PMID_37196654_Individual1.json b/notebooks/KDM6B/phenopackets/PMID_37196654_Individual1.json new file mode 100644 index 000000000..300ac667e --- /dev/null +++ b/notebooks/KDM6B/phenopackets/PMID_37196654_Individual1.json @@ -0,0 +1,333 @@ +{ + "id": "PMID_37196654_Individual_1", + "subject": { + "id": "Individual 1", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P16Y" + } + }, + "sex": "FEMALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001270", + "label": "Motor delay" + } + }, + { + "type": { + "id": "HP:0001328", + "label": "Specific learning disability" + } + }, + { + "type": { + "id": "HP:0000729", + "label": "Autistic behavior" + } + }, + { + "type": { + "id": "HP:0000403", + "label": "Recurrent otitis media" + } + }, + { + "type": { + "id": "HP:0000718", + "label": "Aggressive behavior" + } + }, + { + "type": { + "id": "HP:0001520", + "label": "Large for gestational age" + } + }, + { + "type": { + "id": "HP:0001513", + "label": "Obesity" + } + }, + { + "type": { + "id": "HP:0000750", + "label": "Delayed speech and language development" + } + }, + { + "type": { + "id": "HP:0001156", + "label": "Brachydactyly" + } + }, + { + "type": { + "id": "HP:0030084", + "label": "Clinodactyly" + } + }, + { + "type": { + "id": "HP:0001769", + "label": "Broad foot" + } + }, + { + "type": { + "id": "HP:0005280", + "label": "Depressed nasal bridge" + } + }, + { + "type": { + "id": "HP:0000286", + "label": "Epicanthus" + } + }, + { + "type": { + "id": "HP:0011822", + "label": "Broad chin" + } + }, + { + "type": { + "id": "HP:0000463", + "label": "Anteverted nares" + } + }, + { + "type": { + "id": "HP:0000233", + "label": "Thin vermilion border" + } + }, + { + "type": { + "id": "HP:0000280", + "label": "Coarse facial features" + } + }, + { + "type": { + "id": "HP:0000321", + "label": "Square face" + } + }, + { + "type": { + "id": "HP:0002558", + "label": "Supernumerary nipple" + } + }, + { + "type": { + "id": "HP:0031728", + "label": "Mild hypermetropia" + } + }, + { + "type": { + "id": "HP:0011968", + "label": "Feeding difficulties" + } + }, + { + "type": { + "id": "HP:0001611", + "label": "Hypernasal speech" + } + }, + { + "type": { + "id": "HP:0002360", + "label": "Sleep abnormality" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001252", + "label": "Hypotonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001257", + "label": "Spasticity" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001159", + "label": "Syndactyly" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000767", + "label": "Pectus excavatum" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000486", + "label": "Strabismus" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002019", + "label": "Constipation" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000709", + "label": "Psychosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001250", + "label": "Seizure" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0001332", + "label": "Dystonia" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0002650", + "label": "Scoliosis" + }, + "excluded": true + }, + { + "type": { + "id": "HP:0000175", + "label": "Cleft palate" + }, + "excluded": true + } + ], + "interpretations": [ + { + "id": "Individual 1", + "progressStatus": "SOLVED", + "diagnosis": { + "disease": { + "id": "OMIM:618505", + "label": "Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities" + }, + "genomicInterpretations": [ + { + "subjectOrBiosampleId": "Individual 1", + "interpretationStatus": "CAUSATIVE", + "variantInterpretation": { + "variationDescriptor": { + "id": "var_tQrOwpepUJZvwdaaYTVqnmsEo", + "geneContext": { + "valueId": "HGNC:29012", + "symbol": "KDM6B" + }, + "expressions": [ + { + "syntax": "hgvs.c", + "value": "NM_001080424.2:c.1018del" + }, + { + "syntax": "hgvs.g", + "value": "NC_000017.11:g.7847213del" + } + ], + "vcfRecord": { + "genomeAssembly": "hg38", + "chrom": "chr17", + "pos": "7847208", + "ref": "GC", + "alt": "G" + }, + "moleculeContext": "genomic", + "allelicState": { + "id": "GENO:0000135", + "label": "heterozygous" + } + } + } + } + ] + } + } + ], + "metaData": { + "created": "2023-11-25T17:06:01.007930994Z", + "createdBy": "ORCID:0000-0002-0736-9199", + "resources": [ + { + "id": "geno", + "name": "Genotype Ontology", + "url": "http://purl.obolibrary.org/obo/geno.owl", + "version": "2022-03-05", + "namespacePrefix": "GENO", + "iriPrefix": "http://purl.obolibrary.org/obo/GENO_" + }, + { + "id": "hgnc", + "name": "HUGO Gene Nomenclature Committee", + "url": "https://www.genenames.org", + "version": "06/01/23", + "namespacePrefix": "HGNC", + "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/" + }, + { + "id": "omim", + "name": "An Online Catalog of Human Genes and Genetic Disorders", + "url": "https://www.omim.org", + "version": "January 4, 2023", + "namespacePrefix": "OMIM", + "iriPrefix": "https://www.omim.org/entry/" + }, + { + "id": "so", + "name": "Sequence types and features ontology", + "url": "http://purl.obolibrary.org/obo/so.obo", + "version": "2021-11-22", + "namespacePrefix": "SO", + "iriPrefix": "http://purl.obolibrary.org/obo/SO_" + }, + { + "id": "hp", + "name": "human phenotype ontology", + "url": "http://purl.obolibrary.org/obo/hp.owl", + "version": "2023-10-09", + "namespacePrefix": "HP", + "iriPrefix": "http://purl.obolibrary.org/obo/HP_" + } + ], + "phenopacketSchemaVersion": "2.0", + "externalReferences": [ + { + "id": "PMID:37196654", + "reference": "https://pubmed.ncbi.nlm.nih.gov/37196654", + "description": "The clinical and molecular spectrum of the KDM6B-related neurodevelopmental disorder" + } + ] + } +} \ No newline at end of file diff --git a/notebooks/KDM6B/phenopackets/PMID_37196654_Individual10.json b/notebooks/KDM6B/phenopackets/PMID_37196654_Individual10.json new file mode 100644 index 000000000..5bc5fee80 --- /dev/null +++ b/notebooks/KDM6B/phenopackets/PMID_37196654_Individual10.json @@ -0,0 +1,280 @@ +{ + "id": "PMID_37196654_Individual_10", + "subject": { + "id": "Individual 10", + "timeAtLastEncounter": { + "age": { + "iso8601duration": "P4Y" + } + }, + "sex": "MALE" + }, + "phenotypicFeatures": [ + { + "type": { + "id": "HP:0001270", + "label": "Motor delay" + } + }, + { + "type": { + "id": "HP:0000729", + "label": 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