Enum: G2PVariantConsequence

The consequence of the reported variants at the protein (for protein-coding genes) or the RNA (for non-protein coding genes), per allele. These are Sequence Ontology terms developed for G2P and described in PMID:37982373; the descriptions below are the G2P-authored usage notes rather than the SO text definitions. As in the other SO-backed enums here, title is uniformly the SO term label and any differing G2P label is carried as an alias; for four of the six values the SO and G2P labels coincide, which is why only altered_gene_product_sequence and function_uncertain_variant carry an alias.

URI: valuesets:G2PVariantConsequence

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Permissible Values

Value	Title	Meaning	Description
ALTERED_GENE_PRODUCT_LEVEL	altered_gene_product_level	SO:0002314	A sequence variant that alters the level or amount of gene product produced. This high-level term can be applied where the direction of level change (increased vs decreased gene product level) is unknown or not confirmed, e.g., promoter or enhancer variants, some splice variants.
DECREASED_GENE_PRODUCT_LEVEL	decreased_gene_product_level	SO:0002316	A sequence variant that decreases the level or amount of gene product produced, e.g., a 5' UTR variant that reduced protein levels by disrupting translation, a 3' UTR variant that affects RNA stability, splice variants that decrease but do not stop expression, variants leading to nonsense-mediated-decay (NMD)-competent premature termination codon (PTCs), or gene-disrupting structural variants.
ABSENT_GENE_PRODUCT	absent_gene_product	SO:0002317	A sequence variant that results in no gene product. e.g., whole gene or other large scale disruptive structural variant, variants producing NMD-competent PTCs.
INCREASED_GENE_PRODUCT_LEVEL	increased_gene_product_level	SO:0002315	A variant that increases the level or amount of gene product produced, e.g., non-disruptive gene duplications, some promoter or enhancer variants.
ALTERED_GENE_PRODUCT_STRUCTURE	altered_gene_product_sequence	SO:0002318	A sequence variant that alters the sequence of a gene product. e.g., missense variants, NMD-incompetent PTCs, and other length-changing variants (in-frame indels, stop loss).
UNCERTAIN	function_uncertain_variant	SO:0002220	A sequence variant in which the function of a gene product is unknown with respect to a reference. Used by G2P where the consequence of the reported variants could not be determined.

Slots

Name	Description
g2p_variant_consequence	The consequence of a reported variant at the protein or RNA level, per allele

Identifier and Mapping Information

Annotations

property	value
stewards	https://www.ebi.ac.uk/gene2phenotype
publishers	https://www.ebi.ac.uk/gene2phenotype
source	https://www.ebi.ac.uk/gene2phenotype/about/terminology#variant-consequence-section
reference	PMID:37982373

Schema Source

from schema: https://w3id.org/valuesets

LinkML Source

name: G2PVariantConsequence
instantiates:
- valuesets_meta:ValueSetEnumDefinition
annotations:
  stewards:
    tag: stewards
    value: https://www.ebi.ac.uk/gene2phenotype
  publishers:
    tag: publishers
    value: https://www.ebi.ac.uk/gene2phenotype
  source:
    tag: source
    value: https://www.ebi.ac.uk/gene2phenotype/about/terminology#variant-consequence-section
  reference:
    tag: reference
    value: PMID:37982373
description: The consequence of the reported variants at the protein (for protein-coding
  genes) or the RNA (for non-protein coding genes), per allele. These are Sequence
  Ontology terms developed for G2P and described in PMID:37982373; the descriptions
  below are the G2P-authored usage notes rather than the SO text definitions. As in
  the other SO-backed enums here, title is uniformly the SO term label and any differing
  G2P label is carried as an alias; for four of the six values the SO and G2P labels
  coincide, which is why only altered_gene_product_sequence and function_uncertain_variant
  carry an alias.
title: G2P Variant Consequence
from_schema: https://w3id.org/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: STANDARD
rank: 1000
permissible_values:
  ALTERED_GENE_PRODUCT_LEVEL:
    text: ALTERED_GENE_PRODUCT_LEVEL
    description: A sequence variant that alters the level or amount of gene product
      produced. This high-level term can be applied where the direction of level change
      (increased vs decreased gene product level) is unknown or not confirmed, e.g.,
      promoter or enhancer variants, some splice variants.
    meaning: SO:0002314
    title: altered_gene_product_level
  DECREASED_GENE_PRODUCT_LEVEL:
    text: DECREASED_GENE_PRODUCT_LEVEL
    description: A sequence variant that decreases the level or amount of gene product
      produced, e.g., a 5' UTR variant that reduced protein levels by disrupting translation,
      a 3' UTR variant that affects RNA stability, splice variants that decrease but
      do not stop expression, variants leading to nonsense-mediated-decay (NMD)-competent
      premature termination codon (PTCs), or gene-disrupting structural variants.
    meaning: SO:0002316
    is_a: ALTERED_GENE_PRODUCT_LEVEL
    title: decreased_gene_product_level
  ABSENT_GENE_PRODUCT:
    text: ABSENT_GENE_PRODUCT
    description: A sequence variant that results in no gene product. e.g., whole gene
      or other large scale disruptive structural variant, variants producing NMD-competent
      PTCs.
    meaning: SO:0002317
    is_a: DECREASED_GENE_PRODUCT_LEVEL
    title: absent_gene_product
  INCREASED_GENE_PRODUCT_LEVEL:
    text: INCREASED_GENE_PRODUCT_LEVEL
    description: A variant that increases the level or amount of gene product produced,
      e.g., non-disruptive gene duplications, some promoter or enhancer variants.
    meaning: SO:0002315
    is_a: ALTERED_GENE_PRODUCT_LEVEL
    title: increased_gene_product_level
  ALTERED_GENE_PRODUCT_STRUCTURE:
    text: ALTERED_GENE_PRODUCT_STRUCTURE
    description: A sequence variant that alters the sequence of a gene product. e.g.,
      missense variants, NMD-incompetent PTCs, and other length-changing variants
      (in-frame indels, stop loss).
    meaning: SO:0002318
    title: altered_gene_product_sequence
    aliases:
    - altered gene product structure
  UNCERTAIN:
    text: UNCERTAIN
    description: A sequence variant in which the function of a gene product is unknown
      with respect to a reference. Used by G2P where the consequence of the reported
      variants could not be determined.
    meaning: SO:0002220
    title: function_uncertain_variant
    aliases:
    - uncertain