GTPBP2

Author: pnrobinson

notebooks/GTPBP2/GTPBP2_JABELS_individuals.json

@@ -0,0 +1,291 @@
+{
+  "id": "PMID_26675814_DS_100_3",
+  "subject": {
+    "id": "DS-100-3",
+    "timeAtLastEncounter": {
+      "age": {
+        "iso8601duration": "P34Y"
+      }
+    },
+    "sex": "FEMALE"
+  },
+  "phenotypicFeatures": [
+    {
+      "type": {
+        "id": "HP:0000519",
+        "label": "Developmental cataract"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0000545",
+        "label": "Myopia"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0040081",
+        "label": "Abnormal circulating creatine kinase concentration"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0000750",
+        "label": "Delayed speech and language development"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0002342",
+        "label": "Moderate intellectual disability"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0025190",
+        "label": "Bilateral tonic-clonic seizure with generalized onset"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0007078",
+        "label": "Decreased amplitude of sensory action potentials"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0033580",
+        "label": "Compound motor action potential abnormality"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0007089",
+        "label": "Facial-lingual fasciculations"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001336",
+        "label": "Myoclonus"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0002378",
+        "label": "Hand tremor"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001310",
+        "label": "Dysmetria"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001265",
+        "label": "Hyporeflexia"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0002136",
+        "label": "Broad-based gait"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001332",
+        "label": "Dystonia"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0006855",
+        "label": "Cerebellar vermis atrophy"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0033049",
+        "label": "Globus pallidus hypointensity on susceptibility-weighted imaging"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0031505",
+        "label": "Abnormal circulating T4 concentration"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0002299",
+        "label": "Brittle hair"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0008070",
+        "label": "Sparse hair"
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000768",
+        "label": "Pectus carinatum"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0002650",
+        "label": "Scoliosis"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0003808",
+        "label": "Abnormal muscle tone"
+      },
+      "excluded": true
+    },
+    {
+      "type": {
+        "id": "HP:0001324",
+        "label": "Muscle weakness"
+      },
+      "excluded": true
+    }
+  ],
+  "interpretations": [
+    {
+      "id": "V3fB9y5L2cKgGhhsHdpgFbVz",
+      "progressStatus": "SOLVED",
+      "diagnosis": {
+        "disease": {
+          "id": "OMIM:617988",
+          "label": "Jaberi-Elahi syndrome"
+        },
+        "genomicInterpretations": [
+          {
+            "subjectOrBiosampleId": "DS-100-3",
+            "interpretationStatus": "CAUSATIVE",
+            "variantInterpretation": {
+              "acmgPathogenicityClassification": "PATHOGENIC",
+              "therapeuticActionability": "UNKNOWN_ACTIONABILITY",
+              "variationDescriptor": {
+                "id": "c1237_1GtoT_GTPBP2_NM_019096v5",
+                "geneContext": {
+                  "valueId": "HGNC:4670",
+                  "symbol": "GTPBP2"
+                },
+                "expressions": [
+                  {
+                    "syntax": "hgvs.c",
+                    "value": "NM_019096.5:c.1237-1G>T"
+                  },
+                  {
+                    "syntax": "hgvs.g",
+                    "value": "NC_000006.12:g.43623796C>A"
+                  },
+                  {
+                    "syntax": "hgvs.p",
+                    "value": "NP_061969.3:p.?"
+                  }
+                ],
+                "vcfRecord": {
+                  "genomeAssembly": "hg38",
+                  "chrom": "chr6",
+                  "pos": 43623796,
+                  "ref": "C",
+                  "alt": "A"
+                },
+                "moleculeContext": "genomic",
+                "allelicState": {
+                  "id": "GENO:0000136",
+                  "label": "homozygous"
+                }
+              }
+            }
+          }
+        ]
+      }
+    }
+  ],
+  "diseases": [
+    {
+      "term": {
+        "id": "OMIM:617988",
+        "label": "Jaberi-Elahi syndrome"
+      },
+      "onset": {
+        "ontologyClass": {
+          "id": "HP:0003593",
+          "label": "Infantile onset"
+        }
+      }
+    }
+  ],
+  "metaData": {
+    "created": "2025-12-08T21:00:02.176659Z",
+    "createdBy": "0000-0002-0736-9199",
+    "resources": [
+      {
+        "id": "hp",
+        "name": "human phenotype ontology",
+        "url": "http://purl.obolibrary.org/obo/hp.owl",
+        "version": "2025-11-24",
+        "namespacePrefix": "HP",
+        "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+      },
+      {
+        "id": "geno",
+        "name": "Genotype Ontology",
+        "url": "http://purl.obolibrary.org/obo/geno.owl",
+        "version": "2025-07-25",
+        "namespacePrefix": "GENO",
+        "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+      },
+      {
+        "id": "so",
+        "name": "Sequence types and features ontology",
+        "url": "http://purl.obolibrary.org/obo/so.owl",
+        "version": "2024-11-18",
+        "namespacePrefix": "SO",
+        "iriPrefix": "http://purl.obolibrary.org/obo/SO_"
+      },
+      {
+        "id": "omim",
+        "name": "An Online Catalog of Human Genes and Genetic Disorders",
+        "url": "https://www.omim.org",
+        "version": "06/01/25",
+        "namespacePrefix": "OMIM",
+        "iriPrefix": "https://www.omim.org/entry/"
+      },
+      {
+        "id": "hgnc",
+        "name": "HUGO Gene Nomenclature Committee",
+        "url": "https://www.genenames.org",
+        "version": "06/01/25",
+        "namespacePrefix": "HGNC",
+        "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"
+      }
+    ],
+    "phenopacketSchemaVersion": "2.0.2",
+    "externalReferences": [
+      {
+        "id": "PMID:26675814",
+        "description": "Identification of mutation in GTPBP2 in patients of a family with neurodegeneration accompanied by iron deposition in the brain."
+      }
+    ]
+  }
+}