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FGFR2(hgnc:3689)::v

Source

CIViC variant id 2202: FGFR2::v Fusion

Recipes that example satisfies

Gene Fusion

Properties

id: civic.vid:2202

CIViC Variant ID, where vid stands for Variant ID, derived from the Variant ID contained within the CIViC URL for this genomic alteration.

type: CategoricalVariant

This value is required by the specification for all Categorical Variant objects.

name: FGFR2(hgnc:3689)::v

Human-readable label given to the fusion by CIViC, with gene identifiers per the VICC Fusion representation recommendation.

description: An FGFR2 gene fusion, where the FGFR2 kinase domain is required to remain intact to satisfy the constraints of this categorical variant.

This field was populated with the description provided by CIViC.

aliases: FGFR2::v, FGFR2 fusion

An alias provided by CIViC the name without HGNC ids were included as example aliases.

extensions: null

No extensions included.

mappings: null

No mappings included.

Constraints

Adjacency Constraint

FGFR2 (hgnc:3689) is modeled as a mappable concept as the 5’ partner within the adjoinedElements array, with an Unspecified Element 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

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