BRCA2 loss of function variants

Source

CIViC molecular profile id 186: BRCA2 Mutation Loss Of Function

Recipes that this example satisfies

Function Variant

Properties

id: civic.mpid:186: CIViC Molecular Profile ID, where mpid stands for Molecular Profile ID, derived from the Molecular Profile 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: BRCA2 loss of function variants: Representing the set of BRCA2 variants that result in loss of function.
description: A brief placeholder note.: This field was populated with an example value because CIViC does not provide a longform description.
aliases: null: No aliases included in this example.
extensions: null: No extensions included.
mappings: null: No mappings included.

Constraints

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

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.