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NFU1
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pnrobinson committed Jan 8, 2025
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289 changes: 289 additions & 0 deletions notebooks/NFU1/NFU1_SPG93_individuals.ipynb
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340 changes: 340 additions & 0 deletions notebooks/NFU1/phenopackets/PMID_25758857_Clinicaldata.json
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{
"id": "PMID_25758857_Clinical_data",
"subject": {
"id": "Clinical data",
"timeAtLastEncounter": {
"age": {
"iso8601duration": "P30Y"
}
},
"vitalStatus": {
"status": "ALIVE"
},
"sex": "MALE"
},
"phenotypicFeatures": [
{
"type": {
"id": "HP:0002376",
"label": "Developmental regression"
},
"onset": {
"age": {
"iso8601duration": "P1Y6M"
}
}
},
{
"type": {
"id": "HP:0002510",
"label": "Spastic tetraplegia"
},
"onset": {
"age": {
"iso8601duration": "P1Y6M"
}
}
},
{
"type": {
"id": "HP:0007371",
"label": "Corpus callosum atrophy"
},
"onset": {
"age": {
"iso8601duration": "P30Y"
}
}
},
{
"type": {
"id": "HP:0012708",
"label": "Reduced brain N-acetyl aspartate level by MRS"
},
"onset": {
"age": {
"iso8601duration": "P30Y"
}
}
},
{
"type": {
"id": "HP:0012706",
"label": "Elevated brain choline level by MRS"
},
"onset": {
"age": {
"iso8601duration": "P30Y"
}
}
},
{
"type": {
"id": "HP:0012707",
"label": "Elevated brain lactate level by MRS"
},
"onset": {
"age": {
"iso8601duration": "P30Y"
}
}
},
{
"type": {
"id": "HP:0001263",
"label": "Global developmental delay"
}
},
{
"type": {
"id": "HP:0001258",
"label": "Spastic paraplegia"
}
},
{
"type": {
"id": "HP:0001348",
"label": "Brisk reflexes"
}
},
{
"type": {
"id": "HP:0009830",
"label": "Peripheral neuropathy"
}
},
{
"type": {
"id": "HP:0002650",
"label": "Scoliosis"
}
},
{
"type": {
"id": "HP:0033748",
"label": "Hypoesthesia"
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{
"type": {
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"label": "Lactic acidosis"
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"excluded": true
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{
"type": {
"id": "HP:0011449",
"label": "Knee clonus"
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"label": "Ankle clonus"
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{
"type": {
"id": "HP:0003487",
"label": "Babinski sign"
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"excluded": true
},
{
"type": {
"id": "HP:0034295",
"label": "Reduced cerebral white matter volume"
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"excluded": true
},
{
"type": {
"id": "HP:0002079",
"label": "Hypoplasia of the corpus callosum"
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},
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"type": {
"id": "HP:0011096",
"label": "Peripheral demyelination"
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{
"type": {
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"label": "Enlarged cisterna magna"
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"label": "Encephalopathy"
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},
{
"type": {
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"label": "Talipes equinovarus"
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"interpretations": [
{
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"progressStatus": "SOLVED",
"diagnosis": {
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"id": "OMIM:620938",
"label": "Spastic paraplegia 93, autosomal recessive"
},
"genomicInterpretations": [
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"symbol": "NFU1"
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"expressions": [
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"syntax": "hgvs.c",
"value": "NM_001002755.4:c.146del"
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"geneContext": {
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"symbol": "NFU1"
},
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}
}
}
}
]
}
}
],
"diseases": [
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"term": {
"id": "OMIM:620938",
"label": "Spastic paraplegia 93, autosomal recessive"
},
"onset": {
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}
}
}
],
"metaData": {
"created": "2025-01-08T13:24:32.127840995Z",
"createdBy": "ORCID:0000-0002-0736-9199",
"resources": [
{
"id": "geno",
"name": "Genotype Ontology",
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"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": "2024-12-12",
"namespacePrefix": "HP",
"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
}
],
"phenopacketSchemaVersion": "2.0",
"externalReferences": [
{
"id": "PMID:25758857",
"reference": "https://pubmed.ncbi.nlm.nih.gov/25758857",
"description": "New spastic paraplegia phenotype associated to mutation of NFU1"
}
]
}
}
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