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PIK3CA p.R38H

Source

CIViC molecular profile id 1150: PIK3CA R38H

Recipes that this example satisfies

Function Variant

Properties

id: civic.mpid:1150

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: PIK3CA p.R38H

Following the naming convention used by CIViC.

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

Defining Allele Constraint

The allele field is populated with the VRS Allele for NM_006218.4:c.113G>A, as included within members.

Feature Context Constraint

The featureContext is a Mappable Concept for PIK3CA (hgnc:8975), with a primaryCoding linking to its HGNC entry.

Function Constraint

The functionConsequence is a Mappable Concept for gain of function (SO:0002053), with a primaryCoding linking to the Sequence Ontology term gain_of_function.

Members

The members field includes one VRS Allele object generated using the VICC Variation Normalizer for NM_006218.4:c.113G>A, on the MANE Select coding transcript for PIK3CA (refseq:NM_006218.4).

Full example: JSON

{
  "id": "civic.mpid:1150",
  "type": "CategoricalVariant",
  "name": "PIK3CA p.R38H",
  "description": "An example categorical variant that uses DefiningAlleleConstraint, FeatureContextConstraint, and FunctionConstraint.",
  "constraints": [
    {
      "type": "DefiningAlleleConstraint",
      "allele": {
        "id": "ga4gh:VA.gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi",
        "type": "Allele",
        "name": "NM_006218.4:c.113G>A",
        "description": "VRS Variation of NM_006218.4:c.113G>A, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
        "digest": "gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi",
        "expressions": [
          {
            "syntax": "hgvs.c",
            "value": "NM_006218.4:c.113G>A"
          }
        ],
        "location": {
          "id": "ga4gh:SL.rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi",
          "description": "Coding DNA (cDNA) position 113 of the PIK3CA MANE Select coding transcript (refseq:NM_006218.4), corresponding to genomic position 179198938 on chromosome 3 (refseq:NC_000003.12, GRCh38).",
          "extensions": [
            {
              "name": "GRCh38, 1-based, genomic position",
              "value": "chr3:179198938",
              "description": "Genomic position 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
            },
            {
              "name": "GRCh38, 1-based, inclusive interval notation",
              "value": "chr3:179198938-179198938",
              "description": "Genomic positions 179,198,938 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
            },
            {
              "name": "GRCh38, 0-based, half-open interval notation",
              "value": "chr3:179198937-179198938",
              "description": "Genomic positions 179,198,937 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
            }
          ],
          "type": "SequenceLocation",
          "digest": "rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi",
          "sequenceReference": {
            "id": "refseq:NM_006218.4",
            "name": "NM_006218.4",
            "description": "The MANE Select (GRCh38) coding transcript for PIK3CA.",
            "aliases": [
              "ensembl:ENST00000263967.4",
              "ga4gh:SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9"
            ],
            "type": "SequenceReference",
            "refgetAccession": "SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9",
            "residueAlphabet": "na"
          },
          "start": 435,
          "end": 436,
          "sequence": "G"
        },
        "state": {
          "type": "LiteralSequenceExpression",
          "sequence": "A"
        }
      }
    },
    {
      "type": "FeatureContextConstraint",
      "featureContext": {
        "id": "hgnc:8975",
        "conceptType": "Gene",
        "name": "PIK3CA",
        "primaryCoding": {
          "id": "hgnc:8975",
          "system": "https://www.genenames.org",
          "code": "HGNC:8975",
          "iris": [
            "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:8975"
          ]
        }
      }
    },
    {
      "type": "FunctionConstraint",
      "functionConsequence": {
        "id": "SO:0002053",
        "name": "gain of function",
        "primaryCoding": {
          "id": "SO:0002053",
          "name": "gain_of_function",
          "system": "http://www.sequenceontology.org",
          "code": "SO:0002053",
          "iris": [
            "http://www.sequenceontology.org/browser/current_release/term/SO:0002053"
          ]
        }
      },
      "description": "Function consequence described as gain of function using Sequence Ontology."
    }
  ],
  "members": [
    {
      "id": "ga4gh:VA.gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi",
      "type": "Allele",
      "name": "NM_006218.4:c.113G>A",
      "description": "VRS Variation of NM_006218.4:c.113G>A, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).",
      "digest": "gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi",
      "expressions": [
        {
          "syntax": "hgvs.c",
          "value": "NM_006218.4:c.113G>A"
        }
      ],
      "location": {
        "id": "ga4gh:SL.rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi",
        "description": "Coding DNA (cDNA) position 113 of the PIK3CA MANE Select coding transcript (refseq:NM_006218.4), corresponding to genomic position 179198938 on chromosome 3 (refseq:NC_000003.12, GRCh38).",
        "extensions": [
          {
            "name": "GRCh38, 1-based, genomic position",
            "value": "chr3:179198938",
            "description": "Genomic position 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
          },
          {
            "name": "GRCh38, 1-based, inclusive interval notation",
            "value": "chr3:179198938-179198938",
            "description": "Genomic positions 179,198,938 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
          },
          {
            "name": "GRCh38, 0-based, half-open interval notation",
            "value": "chr3:179198937-179198938",
            "description": "Genomic positions 179,198,937 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38)."
          }
        ],
        "type": "SequenceLocation",
        "digest": "rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi",
        "sequenceReference": {
          "id": "refseq:NM_006218.4",
          "name": "NM_006218.4",
          "description": "The MANE Select (GRCh38) coding transcript for PIK3CA.",
          "aliases": [
            "ensembl:ENST00000263967.4",
            "ga4gh:SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9"
          ],
          "type": "SequenceReference",
          "refgetAccession": "SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9",
          "residueAlphabet": "na"
        },
        "start": 435,
        "end": 436,
        "sequence": "G"
      },
      "state": {
        "type": "LiteralSequenceExpression",
        "sequence": "A"
      }
    }
  ]
}

Full example: YAML

id: civic.mpid:1150
type: CategoricalVariant
name: PIK3CA p.R38H
description: An example categorical variant that uses DefiningAlleleConstraint, FeatureContextConstraint, and FunctionConstraint.
constraints:
  - type: DefiningAlleleConstraint
    allele:
      id: ga4gh:VA.gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi
      type: Allele
      name: NM_006218.4:c.113G>A
      description: VRS Variation of NM_006218.4:c.113G>A, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
      digest: gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi
      expressions:
      - syntax: hgvs.c
        value: NM_006218.4:c.113G>A
      location:
        id: ga4gh:SL.rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi
        description: Coding DNA (cDNA) position 113 of the PIK3CA MANE Select coding transcript (refseq:NM_006218.4), corresponding to genomic position 179198938 on chromosome 3 (refseq:NC_000003.12, GRCh38).
        extensions:
          - name: GRCh38, 1-based, genomic position
            value: chr3:179198938
            description: Genomic position 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38).
          - name: GRCh38, 1-based, inclusive interval notation
            value: chr3:179198938-179198938
            description: Genomic positions 179,198,938 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38).
          - name: GRCh38, 0-based, half-open interval notation
            value: chr3:179198937-179198938
            description: Genomic positions 179,198,937 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38).
        type: SequenceLocation
        digest: rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi
        sequenceReference:
          id: refseq:NM_006218.4
          name: NM_006218.4
          description: The MANE Select (GRCh38) coding transcript for PIK3CA.
          aliases:
            - ensembl:ENST00000263967.4
            - ga4gh:SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9
          type: SequenceReference
          refgetAccession: SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9
          residueAlphabet: na
        start: 435
        end: 436
        sequence: "G"
      state:
        type: LiteralSequenceExpression
        sequence: A
  - type: FeatureContextConstraint
    featureContext:
      id: hgnc:8975
      conceptType: Gene
      name: PIK3CA
      primaryCoding:
        id: hgnc:8975
        system: https://www.genenames.org
        code: HGNC:8975
        iris:
          - https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:8975
  - type: FunctionConstraint
    functionConsequence:
      id: SO:0002053
      name: gain of function
      primaryCoding:
        id: SO:0002053
        name: gain_of_function
        system: http://www.sequenceontology.org
        code: SO:0002053
        iris:
          - http://www.sequenceontology.org/browser/current_release/term/SO:0002053
    description: Function consequence described as gain of function using Sequence Ontology.
members:
- id: ga4gh:VA.gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi
  type: Allele
  name: NM_006218.4:c.113G>A
  description: VRS Variation of NM_006218.4:c.113G>A, generated with the VICC Variation Normalizer (https://github.com/cancervariants/variation-normalization).
  digest: gFYUMkeAme8HeNqcBIDPYIB45_xRa9Qi
  expressions:
  - syntax: hgvs.c
    value: NM_006218.4:c.113G>A
  location:
    id: ga4gh:SL.rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi
    description: Coding DNA (cDNA) position 113 of the PIK3CA MANE Select coding transcript (refseq:NM_006218.4), corresponding to genomic position 179198938 on chromosome 3 (refseq:NC_000003.12, GRCh38).
    extensions:
      - name: GRCh38, 1-based, genomic position
        value: chr3:179198938
        description: Genomic position 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38).
      - name: GRCh38, 1-based, inclusive interval notation
        value: chr3:179198938-179198938
        description: Genomic positions 179,198,938 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38).
      - name: GRCh38, 0-based, half-open interval notation
        value: chr3:179198937-179198938
        description: Genomic positions 179,198,937 to 179,198,938 on chromosome 3 (refseq:NC_000003.12, GRCh38).
    type: SequenceLocation
    digest: rZhFJCEGRkU-G3EqaGuUpefj2bP94NLi
    sequenceReference:
      id: refseq:NM_006218.4
      name: NM_006218.4
      description: The MANE Select (GRCh38) coding transcript for PIK3CA.
      aliases:
        - ensembl:ENST00000263967.4
        - ga4gh:SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9
      type: SequenceReference
      refgetAccession: SQ.vV37R3hERpo6hA6RBsi9AaaMoY7ELvk9
      residueAlphabet: na
    start: 435
    end: 436
    sequence: "G"
  state:
    type: LiteralSequenceExpression
    sequence: A