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‎notebooks/CST3/CST3_ADLDWA_individuals.json‎

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notebooks/SCN2A/phenopackets/PMID_33731876_fam61.json renamed to notebooks/CST3/phenopackets/PMID_38489591_Family_A_individual_1.json

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@@ -1,13 +1,22 @@
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{
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"id": "PMID_33731876_fam61",
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"id": "PMID_38489591_Family_A_individual_1",
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"subject": {
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"id": "fam61"
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"id": "Family A individual 1",
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"timeAtLastEncounter": {
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"age": {
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"iso8601duration": "P49Y"
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}
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},
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"vitalStatus": {
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"status": "DECEASED"
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},
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"sex": "MALE"
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},
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"phenotypicFeatures": [
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{
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"type": {
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"id": "HP:0000718",
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"label": "Aggressive behavior"
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"id": "HP:0002076",
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"label": "Migraine"
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}
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},
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{
@@ -18,108 +27,109 @@
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},
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{
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"type": {
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"id": "HP:0007270",
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"label": "Atypical absence seizure"
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"id": "HP:0001257",
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"label": "Spasticity"
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}
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},
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{
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"type": {
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"id": "HP:0000717",
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"label": "Autism"
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}
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"id": "HP:0000708",
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"label": "Atypical behavior"
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},
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"excluded": true
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},
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{
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"type": {
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"id": "HP:0010850",
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"label": "EEG with spike-wave complexes"
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"id": "HP:0004372",
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"label": "Reduced consciousness"
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}
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},
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{
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"type": {
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"id": "HP:0007359",
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"label": "Focal-onset seizure"
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"id": "HP:0001268",
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"label": "Mental deterioration"
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}
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},
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{
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"type": {
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"id": "HP:0001288",
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"label": "Gait disturbance"
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"id": "HP:0001250",
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"label": "Seizure"
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}
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},
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{
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"type": {
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"id": "HP:0002069",
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"label": "Bilateral tonic-clonic seizure"
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"id": "HP:0001288",
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"label": "Gait disturbance"
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}
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},
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{
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"type": {
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"id": "HP:0002487",
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"label": "Hyperkinetic movements"
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"id": "HP:0007371",
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"label": "Corpus callosum atrophy"
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}
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},
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{
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"type": {
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"id": "HP:0010864",
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"label": "Intellectual disability, severe"
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"id": "HP:0011931",
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"label": "Abnormal cerebellar peduncle morphology"
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}
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},
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{
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"type": {
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"id": "HP:0010841",
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"label": "Multifocal epileptiform discharges"
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}
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"id": "HP:0002453",
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"label": "Abnormal globus pallidus morphology"
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},
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"excluded": true
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},
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{
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"type": {
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"id": "HP:0031491",
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"label": "Continuous spike and waves during slow sleep"
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"id": "HP:0002669",
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"label": "Osteosarcoma"
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}
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},
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{
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"type": {
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"id": "HP:0012443",
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"label": "Abnormal brain morphology"
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},
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"excluded": true
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}
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],
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"interpretations": [
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{
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"id": "fam61",
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"id": "IWovFF5A0w9xTtfRYnnK1bev",
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"progressStatus": "SOLVED",
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"diagnosis": {
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"disease": {
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"id": "OMIM:613721",
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"label": "Developmental and epileptic encephalopathy 11"
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"id": "OMIM:621214",
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"label": "Leukodystrophy, adult-onset, autosomal dominant, without amyloid angiopathy"
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},
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"genomicInterpretations": [
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{
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"subjectOrBiosampleId": "fam61",
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"subjectOrBiosampleId": "Family A individual 1",
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"interpretationStatus": "CAUSATIVE",
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"variantInterpretation": {
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"acmgPathogenicityClassification": "PATHOGENIC",
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"therapeuticActionability": "UNKNOWN_ACTIONABILITY",
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"variationDescriptor": {
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"id": "var_HkkNzGzCBAXGhYDJJHOkLfebD",
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"id": "c360del_CST3_NM_000099v4",
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"geneContext": {
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"valueId": "HGNC:10588",
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"symbol": "SCN2A"
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"valueId": "HGNC:2475",
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"symbol": "CST3"
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},
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"expressions": [
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{
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"syntax": "hgvs.c",
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"value": "NM_001040142.2:c.5798A>T"
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"value": "NM_000099.4:c.360del"
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},
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{
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"syntax": "hgvs.g",
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"value": "NC_000002.12:g.165389604A>T"
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"value": "NC_000020.11:g.23633999del"
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},
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{
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"syntax": "hgvs.p",
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"value": "NP_000090.1:p.(Ala121HisfsTer16)"
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}
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],
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"vcfRecord": {
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"genomeAssembly": "hg38",
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"chrom": "chr2",
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"pos": "165389604",
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"ref": "A",
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"alt": "T"
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"chrom": "chr20",
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"pos": 23633996,
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"ref": "CT",
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"alt": "C"
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},
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"moleculeContext": "genomic",
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"allelicState": {
@@ -136,76 +146,66 @@
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"diseases": [
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{
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"term": {
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"id": "OMIM:613721",
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"label": "Developmental and epileptic encephalopathy 11"
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"id": "OMIM:621214",
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"label": "Leukodystrophy, adult-onset, autosomal dominant, without amyloid angiopathy"
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},
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"onset": {
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"ontologyClass": {
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"id": "HP:0011463",
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"label": "Childhood onset"
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"age": {
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"iso8601duration": "P14Y"
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}
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}
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}
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],
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"metaData": {
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"created": "2024-05-11T07:08:55.784386157Z",
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"createdBy": "ORCID:0000-0002-0736-9199",
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"created": "2026-01-06T11:16:17.340705Z",
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"createdBy": "0000-0002-0736-9199",
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"resources": [
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{
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"id": "hp",
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"name": "human phenotype ontology",
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"version": "2025-11-24",
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"namespacePrefix": "HP",
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"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
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},
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{
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"id": "geno",
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"name": "Genotype Ontology",
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"url": "http://purl.obolibrary.org/obo/geno.owl",
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"version": "2022-03-05",
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"version": "2025-07-25",
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"namespacePrefix": "GENO",
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"iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
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},
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{
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"id": "hgnc",
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"name": "HUGO Gene Nomenclature Committee",
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"url": "https://www.genenames.org",
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"version": "06/01/23",
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"namespacePrefix": "HGNC",
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"iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"
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"id": "so",
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"name": "Sequence types and features ontology",
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"url": "http://purl.obolibrary.org/obo/so.owl",
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"version": "2024-11-18",
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"namespacePrefix": "SO",
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"iriPrefix": "http://purl.obolibrary.org/obo/SO_"
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},
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{
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"id": "omim",
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"name": "An Online Catalog of Human Genes and Genetic Disorders",
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"url": "https://www.omim.org",
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"version": "January 4, 2023",
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"version": "06/01/25",
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"namespacePrefix": "OMIM",
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"iriPrefix": "https://www.omim.org/entry/"
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},
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{
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"id": "so",
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"name": "Sequence types and features ontology",
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"url": "http://purl.obolibrary.org/obo/so.obo",
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"version": "2021-11-22",
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"namespacePrefix": "SO",
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"iriPrefix": "http://purl.obolibrary.org/obo/SO_"
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},
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{
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"id": "hp",
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"name": "human phenotype ontology",
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"url": "http://purl.obolibrary.org/obo/hp.owl",
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"version": "2024-04-04",
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"namespacePrefix": "HP",
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"iriPrefix": "http://purl.obolibrary.org/obo/HP_"
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},
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{
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"id": "mondo",
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"name": "Mondo Disease Ontology",
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"url": "http://purl.obolibrary.org/obo/mondo.obo",
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"version": "2023-09-12",
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"namespacePrefix": "MONDO",
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"iriPrefix": "http://purl.obolibrary.org/obo/MONDO_"
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"id": "hgnc",
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"name": "HUGO Gene Nomenclature Committee",
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"url": "https://www.genenames.org",
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"version": "06/01/25",
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"namespacePrefix": "HGNC",
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"iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"
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}
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],
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"phenopacketSchemaVersion": "2.0",
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"phenopacketSchemaVersion": "2.0.2",
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"externalReferences": [
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{
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"id": "PMID:33731876",
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"reference": "https://pubmed.ncbi.nlm.nih.gov/33731876",
208-
"description": "Computational analysis of 10,860 phenotypic annotations in individuals with SCN2A-related disorders"
207+
"id": "PMID:38489591",
208+
"description": "Dominant CST3 variants cause adult onset leukodystrophy without amyloid angiopathy."
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}
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]
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}

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