cat-vrs/examples/yaml/adjacencyFusion-ex4.yaml 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