TP53 Loss

Source

CIViC variant id 4452: TP53 Loss

Recipes that this example satisfies

None

Properties

id: civic.vid:4452: CIViC Variant ID, where vid stands for Variant ID, derived from the Variant ID provided by CIViC.
type: CategoricalVariant: This value is required by the specification for all Categorical Variant objects.
name: TP53 Loss: The name of the variant as provided by CIViC.
description: A plain text description of the variant.: This notes that TP53 Copy Number Loss is a categorical copy-number variant resulting from the deletion of one copy of the TP53 gene.
aliases: TP53 Copy Number Loss: Provided to clearly specify that this is a copy number event.
extensions: cytogenetic location: The cytogenetic location (17p13) was obtained from HGNC for TP53.
mappings: CIViC (exactMatch and relatedMatch): Mappings to CIViC’s page for TP53 Loss (exactMatch) and the related CIViC molecular profile for TP53 Deletion (relatedMatch) are included.

Constraints

Defining Location Constraint: The defining location is a VRS Sequence Location on chromosome 17 (refseq:NC_000017.11, GRCh38) spanning the genomic region of the TP53 gene (positions 7,668,420 to 7,687,490). The matchCharacteristic is set to is_within, and a liftover relation is included.
Feature Context Constraint: The featureContext is a MappableConcept for TP53 (hgnc:11998), with a primaryCoding linking to its HGNC entry and a cytogenetic location extension of 17p13.1.
Copy Change Constraint: The copyChange field is set to loss to specify the category of copy change.

Members

This example does not include members, as VRS does not support large-scale copy-number events of this type.

Full example: JSON

{
  "id": "civic.vid:4452",
  "type": "CategoricalVariant",
  "name": "TP53 Loss",
  "description": "TP53 Copy Number Loss is a categorical copy-number variant resulting from the deletion of one copy of the TP53 gene.",
  "aliases": [
    "TP53 Copy Number Loss"
  ],
  "extensions": [
    {
      "name": "cytogenetic location",
      "value": "17p13"
    }
  ],
  "constraints": [
    {
      "type": "DefiningLocationConstraint",
      "location": {
        "id": "ga4gh:SL.u9R1nbh-BFBoRI8Ravn3yBBSvp-u10LW",
        "description": "Genomic region between positions 7,668,420 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38).",
        "extensions": [
          {
            "name": "GRCh38 1-based, inclusive interval",
            "value": "chr17:(7668421\u20137687490)",
            "description": "Genomic region between positions 7,668,421 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38); 1-based, inclusive interval notation."
          },
          {
            "name": "GRCh38 0-based, half-open interval",
            "value": "chr17:(7668420\u20137687490)",
            "description": "Genomic region between positions 7,668,420 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38); 0-based, half-open interval notation."
          }
        ],
        "type": "SequenceLocation",
        "digest": "u9R1nbh-BFBoRI8Ravn3yBBSvp-u10LW",
        "sequenceReference": {
          "id": "refseq:NC_000017.11",
          "name": "NC_000017.11",
          "description": "Reference sequence for GRCh38 chromosome 17.",
          "aliases": [
            "GRCh38:17",
            "GRCh38:chr17",
            "ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7"
          ],
          "type": "SequenceReference",
          "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul"
        },
        "start": [
          null,
          7668420
        ],
        "end": [
          7687490,
          null
        ]
      },
      "relations": [
        {
          "primaryCoding": {
            "code": "liftover_to",
            "system": "ga4gh-gks-term:allele-relation"
          }
        }
      ],
      "matchCharacteristic": {
        "primaryCoding": {
          "code": "is_within",
          "system": "ga4gh-gks-term:location-match"
        }
      }
    },
    {
      "type": "FeatureContextConstraint",
      "featureContext": {
        "id": "hgnc:11998",
        "name": "TP53",
        "conceptType": "Gene",
        "primaryCoding": {
          "id": "hgnc:11998",
          "name": "TP53",
          "system": "https://genenames.org",
          "code": "HGNC:11998",
          "iris": [
            "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:11998"
          ]
        },
        "extensions": [
          {
            "name": "cytogenetic location",
            "value": "17p13.1"
          }
        ]
      }
    },
    {
      "type": "CopyChangeConstraint",
      "copyChange": "loss"
    }
  ],
  "members": [],
  "mappings": [
    {
      "coding": {
        "name": "TP53 Loss",
        "system": "https://civicdb.org",
        "code": "civic.vid:4452",
        "iris": [
          "https://civicdb.org/variants/4452/summary"
        ]
      },
      "relation": "exactMatch"
    },
    {
      "coding": {
        "name": "TP53 Deletion",
        "system": "https://civicdb.org/",
        "code": "civic.mpid:4456",
        "iris": [
          "https://civicdb.org/molecular-profiles/4456/summary"
        ]
      },
      "relation": "relatedMatch"
    }
  ]
}

Full example: YAML

id: civic.vid:4452
type: CategoricalVariant
name: TP53 Loss
description: TP53 Copy Number Loss is a categorical copy-number variant resulting from the deletion of one copy of the TP53 gene.
aliases:
  - TP53 Copy Number Loss
extensions:
  - name: cytogenetic location
    value: 17p13
constraints:
  - type: DefiningLocationConstraint
    location:
      id: ga4gh:SL.u9R1nbh-BFBoRI8Ravn3yBBSvp-u10LW
      description: Genomic region between positions 7,668,420 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38).
      extensions:
        - name: GRCh38 1-based, inclusive interval
          value: chr17:(7668421–7687490)
          description: Genomic region between positions 7,668,421 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38); 1-based, inclusive interval notation.
        - name: GRCh38 0-based, half-open interval
          value: chr17:(7668420–7687490)
          description: Genomic region between positions 7,668,420 to 7,687,490 on chromosome 17 (refseq:NC_000017.11, GRCh38); 0-based, half-open interval notation.
      type: SequenceLocation
      digest: u9R1nbh-BFBoRI8Ravn3yBBSvp-u10LW
      sequenceReference:
        id: refseq:NC_000017.11
        name: NC_000017.11
        description: Reference sequence for GRCh38 chromosome 17.
        aliases:
          - GRCh38:17
          - GRCh38:chr17
          - ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7
        type: SequenceReference
        refgetAccession: SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul
      start:
        - null
        - 7668420
      end:
        - 7687490
        - null
    relations:
      - primaryCoding:
          code: liftover_to
          system: ga4gh-gks-term:allele-relation
    matchCharacteristic:
      primaryCoding:
        code: is_within
        system: ga4gh-gks-term:location-match
  - type: FeatureContextConstraint
    featureContext:
      id: hgnc:11998
      name: TP53
      conceptType: Gene
      primaryCoding:
        id: hgnc:11998
        name: TP53
        system: https://genenames.org
        code: HGNC:11998
        iris:
          - https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:11998
      extensions:
        - name: cytogenetic location
          value: 17p13.1
  - type: CopyChangeConstraint
    copyChange: loss
members: []
mappings:
  - coding:
      name: TP53 Loss
      system: https://civicdb.org
      code: civic.vid:4452
      iris:
        - https://civicdb.org/variants/4452/summary
    relation: exactMatch
  - coding:
      name: TP53 Deletion
      system: https://civicdb.org/
      code: civic.mpid:4456
      iris:
        - https://civicdb.org/molecular-profiles/4456/summary
    relation: relatedMatch