FGFR2(hgnc:3689)::v

Source: CIViC variant id 2202: FGFR2::v Fusion

Recipes that this example satisfies: None

Attributes

• id: civic.vid:2202, where vid stands for Variant ID, derived from the Variant ID contained within the CIViC URL for this genomic alteration.

• type: CategoricalVariant, as required by the specification.

• name: FGFR2(hgnc:3689)::v, with the FGFR2 gene identifier per the VICC Fusion representation recommendation using the HGNC identifier.

• 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 and FGFR2 fusion are included as aliases.

• extensions: No extensions are included in this example.

• mappings: No mappings are included in this example.

Constraints

Adjacency Constraint: FGFR2 (hgnc:3689) is modeled as a mappable concept as the 5’ partner within the adjoinedElements array, with an UnspecifiedElement serving as the unknown 3’ partner. The orderKnown field is set to true. Additionally, the functionalDomains field specifies two domains that must carry a preserved status: the FGFR2 protein tyrosine kinase domain (amino acids 456–768 of the protein product NP_000132.3) and the kinase domain on the MANE Select coding transcript (positions 1999–2937 of NM_000141.5). Any variant satisfying this categorical variant must leave both of these domains intact.

Members

This example does not include members.

Full example: JSON

{
  "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"
        }
      ]
    }
  ]
}

Full example: YAML