cat-vrs/examples/json/adjacencyFusion-ex4.json at v1 · ga4gh/cat-vrs · GitHub

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{
  "id": "civic.vid:2202",
  "type": "CategoricalVariant",
  "name": "FGFR2(hgnc:3689)::v",
  "description": "An FGFR2 gene fusion, where the FGFR2 kinase domain is required to remain intact to satisfy the constraints of this categorical variant.",
  "aliases": [
    "FGFR2::v",
    "FGFR2 fusion"
  ],
  "constraints": [
    {
      "type": "AdjacencyConstraint",
      "orderKnown": true,
      "adjoinedElements": [
        {
          "id": "hgnc:3689",
          "conceptType": "Gene",
          "name": "FGFR2",
          "primaryCoding": {
            "id": "hgnc:3689",
            "name": "FGFR2",
            "system": "https://genenames.org",
            "code": "HGNC:3689",
            "iris": [
              "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:3689"
            ]
          }
        },
        {
          "type": "UnspecifiedElement"
        }
      ],
      "functionalDomains": [
        {
          "name": "FGFR2 protein product (refseq:NP_000132.3) protein tyrosine kinase domain",
          "type": "FunctionalDomain",
          "location": {
            "id": "ga4gh:SL.6VpekQsGUz74aAgQ0RklrrgJVwYNK8xx",
            "type": "SequenceLocation",
            "description": "Amino acid positions 456 - 768 within the FGFR2 protein (refseq:NP_000132.3), which is the protein product of the MANE Select coding transcript for FGFR2 (refseq:NM_000141.5). This sequence corresponds to the catalytic domain of the Protein Tyrosine Kinase.",
            "digest": "6VpekQsGUz74aAgQ0RklrrgJVwYNK8xx",
            "sequenceReference": {
              "id": "refseq:NP_000132.3",
              "type": "SequenceReference",
              "name": "NP_000132.3",
              "description": "The protein product of the MANE Select coding transcript for FGFR2 (refseq:NM_000141.5), corresponding to the RefSeq protein accession NP_000132.3.",
              "aliases": [
                "ensembl:ENSP00000351276.5",
                "ga4gh:SQ.hAWsXlUEul8pcUbRmOHRQ6osiUdGIiWs"
              ],
              "refgetAccession": "SQ.hAWsXlUEul8pcUbRmOHRQ6osiUdGIiWs",
              "residueAlphabet": "aa"
            },
            "start": 455,
            "end": 768
          },
          "status": "preserved"
        },
        {
          "name": "FGFR2(refseq:NM_000141.5) kinase domain",
          "type": "FunctionalDomain",
          "location": {
            "id": "ga4gh:SL.511EV3zYjlFNE3CEUMfu9YtuO7q6mOoG",
            "description": "Positions 1999 - 2937 of the FGFR2 MANE Select transcript (refseq:NM_000141.5), corresponding to FGFR2's kinase domain on the product protein (refseq:NP_000132.3).",
            "type": "SequenceLocation",
            "digest": "511EV3zYjlFNE3CEUMfu9YtuO7q6mOoG",
            "sequenceReference": {
              "id": "refseq:NM_000141.5",
              "name": "NM_000141.5",
              "description": "The MANE Select coding transcript for FGFR2.",
              "aliases": [
                "ga4gh:SQ.MHz9sixiWHMnZDi0pTaEqEM6nf08v2Vu"
              ],
              "type": "SequenceReference",
              "refgetAccession": "SQ.MHz9sixiWHMnZDi0pTaEqEM6nf08v2Vu",
              "residueAlphabet": "na"
            },
            "start": 1998,
            "end": 2937
          },
          "status": "preserved"
        }
      ]
    }
  ]
}