BRCA2 loss of function variants

Source: CIViC molecular profile id 186: BRCA2 Mutation Loss Of Function

Recipes that this example satisfies: Function Variant

Attributes

• id: civic.mpid:186, where mpid stands for Molecular Profile ID, derived from the Molecular Profile ID contained within the CIViC URL for this genomic alteration.

• type: CategoricalVariant, as required by the specification.

• name: BRCA2 loss of function variants, representing the set of BRCA2 variants that result in loss of function.

• description: A brief placeholder note.

• aliases: No aliases are included in this example.

• extensions: No extensions are included in this example.

• mappings: No mappings are included in this example.

Constraints

Feature Context Constraint: The featureContext is a MappableConcept for BRCA2 (hgnc:1101), with a primaryCoding linking to its HGNC entry.

Function Constraint: The functionConsequence is a MappableConcept for loss of function (SO:0002054), with a primaryCoding linking to the Sequence Ontology term loss_of_function_variant.

Members

This example does not include members.

Full example: JSON

{
  "id": "civic.mpid:186",
  "type": "CategoricalVariant",
  "name": "BRCA2 loss of function variants",
  "description": "An example categorical variant that uses FeatureContextConstraint and FunctionConstraint.",
  "constraints": [
    {
      "type": "FeatureContextConstraint",
      "featureContext": {
        "id": "hgnc:1101",
        "conceptType": "Gene",
        "name": "BRCA2",
        "primaryCoding": {
          "id": "hgnc:1101",
          "name": "BRCA2",
          "system": "https://www.genenames.org",
          "code": "HGNC:1101",
          "iris": [
            "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:1101"
          ]
        }
      }
    },
    {
      "type": "FunctionConstraint",
      "functionConsequence": {
        "id": "SO:0002054",
        "name": "loss of function",
        "primaryCoding": {
          "id": "SO:0002054",
          "name": "loss_of_function_variant",
          "system": "http://www.sequenceontology.org",
          "code": "SO:0002054",
          "iris": [
            "http://www.sequenceontology.org/browser/current_release/term/SO:0002054"
          ]
        }
      },
      "description": "Function consequence described as loss of function using Sequence Ontology."
    }
  ]
}

Full example: YAML