Enum: G2PCrossCuttingModifier

Additional qualifiers applied to the allelic requirement of a G2P gene-disease association. HPO inheritance qualifier terms (HP:0034335) are used where available. Potential secondary finding and restricted mutation set are G2P-specific and have no HPO equivalent.

URI: valuesets:G2PCrossCuttingModifier

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Permissible Values

Value	Title	Meaning	Description
DISPLAYS_ANTICIPATION	Genetic anticipation	HP:0003743	A phenomenon in which the severity of a disorder increases, or the age of onset decreases, as the disorder is passed from one generation to the next, typically due to expansion of a repeat sequence. For example, Myotonic Dystrophy is caused by triplet repeat expansion in the DMPK gene.
IMPRINTED_REGION	Imprinted	HP:0034338	Requires that the abnormal allele be paternal or maternal in origin, depending on the disease-gene relationship. Imprinting refers to a normal developmental process in which either the paternal or maternal allele is inactivated, depending on the specific locus, thus leading to expression from only one copy of the gene. Disease typically manifests when a deleterious variant is inherited from a parent whose copy of the gene would normally be expressed, but not when a deleterious variant is inherited from a parent whose copy of the gene would normally be inactivated.
TYPICALLY_DE_NOVO	Typically de novo	HP:0025352	Plausible disease causing mutations that occur post zygotically (formation of gametes). Note that this G2P wording is internally inconsistent: post-zygotic events are somatic, which is what TYPICALLY_MOSAIC describes, whereas gametogenesis is pre-zygotic. The mapped HPO term HP:0025352 carries the intended sense, defining conditions that are exclusively or predominantly observed to display de novo variants.
TYPICALLY_MOSAIC	Typified by somatic mosaicism	HP:0001442	Plausible disease causing mutations identified on one allele in a proportion of cells with the others being wild-type.
TYPIFIED_BY_INCOMPLETE_PENETRANCE	Typified by incomplete penetrance	HP:0003829	A condition in which not all individuals carrying the disease-causing genotype manifest the associated phenotype.
POTENTIAL_SECONDARY_FINDING	potential secondary finding		This includes ACMG Secondary Findings and/or late onset conditions.
RESTRICTED_MUTATION_SET	restricted mutation set		This is used when a disease is associated with a single recurrent variant or a set of variants only found in a particular protein domain.

Slots

Name	Description
g2p_cross_cutting_modifier	An additional qualifier on the allelic requirement of a gene-disease associat...

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#cross-cutting-modifier-section
standard	HPO inheritance qualifier

Schema Source

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

LinkML Source

name: G2PCrossCuttingModifier
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#cross-cutting-modifier-section
  standard:
    tag: standard
    value: HPO inheritance qualifier
description: Additional qualifiers applied to the allelic requirement of a G2P gene-disease
  association. HPO inheritance qualifier terms (HP:0034335) are used where available.
  Potential secondary finding and restricted mutation set are G2P-specific and have
  no HPO equivalent.
title: G2P Cross Cutting Modifier
from_schema: https://w3id.org/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: STANDARD
rank: 1000
permissible_values:
  DISPLAYS_ANTICIPATION:
    text: DISPLAYS_ANTICIPATION
    description: A phenomenon in which the severity of a disorder increases, or the
      age of onset decreases, as the disorder is passed from one generation to the
      next, typically due to expansion of a repeat sequence. For example, Myotonic
      Dystrophy is caused by triplet repeat expansion in the DMPK gene.
    meaning: HP:0003743
    title: Genetic anticipation
    aliases:
    - displays anticipation
  IMPRINTED_REGION:
    text: IMPRINTED_REGION
    description: Requires that the abnormal allele be paternal or maternal in origin,
      depending on the disease-gene relationship. Imprinting refers to a normal developmental
      process in which either the paternal or maternal allele is inactivated, depending
      on the specific locus, thus leading to expression from only one copy of the
      gene. Disease typically manifests when a deleterious variant is inherited from
      a parent whose copy of the gene would normally be expressed, but not when a
      deleterious variant is inherited from a parent whose copy of the gene would
      normally be inactivated.
    meaning: HP:0034338
    title: Imprinted
    aliases:
    - imprinted region
  TYPICALLY_DE_NOVO:
    text: TYPICALLY_DE_NOVO
    description: 'Plausible disease causing mutations that occur post zygotically
      (formation of gametes). Note that this G2P wording is internally inconsistent:
      post-zygotic events are somatic, which is what TYPICALLY_MOSAIC describes, whereas
      gametogenesis is pre-zygotic. The mapped HPO term HP:0025352 carries the intended
      sense, defining conditions that are exclusively or predominantly observed to
      display de novo variants.'
    meaning: HP:0025352
    title: Typically de novo
    aliases:
    - typically de novo
  TYPICALLY_MOSAIC:
    text: TYPICALLY_MOSAIC
    description: Plausible disease causing mutations identified on one allele in a
      proportion of cells with the others being wild-type.
    meaning: HP:0001442
    title: Typified by somatic mosaicism
    aliases:
    - typically mosaic
  TYPIFIED_BY_INCOMPLETE_PENETRANCE:
    text: TYPIFIED_BY_INCOMPLETE_PENETRANCE
    description: A condition in which not all individuals carrying the disease-causing
      genotype manifest the associated phenotype.
    meaning: HP:0003829
    title: Typified by incomplete penetrance
    aliases:
    - typified by incomplete penetrance
  POTENTIAL_SECONDARY_FINDING:
    text: POTENTIAL_SECONDARY_FINDING
    description: This includes ACMG Secondary Findings and/or late onset conditions.
    title: potential secondary finding
  RESTRICTED_MUTATION_SET:
    text: RESTRICTED_MUTATION_SET
    description: This is used when a disease is associated with a single recurrent
      variant or a set of variants only found in a particular protein domain.
    title: restricted mutation set