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Class: Variant

A genetic variant associated with a disease, including coding and non-coding regulatory variants. For regulatory variants, use regulatory_category to classify the variant's impact on gene expression (LOE/mLOE/GOE per Cheng et al. 2024).

URI: dismech:class/Variant

 classDiagram
    class Variant
    click Variant href "../../classes/Variant/"
      Variant : clinical_significance





        Variant --> "0..1" ClinicalSignificanceEnum : clinical_significance
        click ClinicalSignificanceEnum href "../../enums/ClinicalSignificanceEnum/"



      Variant : description

      Variant : evidence





        Variant --> "* _recommended_" EvidenceItem : evidence
        click EvidenceItem href "../../classes/EvidenceItem/"



      Variant : external_assertions





        Variant --> "*" ExternalAssertion : external_assertions
        click ExternalAssertion href "../../classes/ExternalAssertion/"



      Variant : functional_effects





        Variant --> "*" FunctionalEffect : functional_effects
        click FunctionalEffect href "../../classes/FunctionalEffect/"



      Variant : gene





        Variant --> "0..1" GeneDescriptor : gene
        click GeneDescriptor href "../../classes/GeneDescriptor/"



      Variant : identifiers

      Variant : name

      Variant : regulatory_category





        Variant --> "0..1" RegulatoryVariantCategoryEnum : regulatory_category
        click RegulatoryVariantCategoryEnum href "../../enums/RegulatoryVariantCategoryEnum/"



      Variant : sequence_length

      Variant : synonyms

      Variant : type

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
description 0..1
String		 direct
gene 0..1
GeneDescriptor		 direct
evidence * recommended
EvidenceItem		 direct
functional_effects *
FunctionalEffect		 direct
synonyms *
String		 direct
identifiers *
Uriorcurie		 direct
external_assertions *
ExternalAssertion		 External curated assertions or registry records relevant to this entity direct
sequence_length 0..1
Integer		 direct
clinical_significance 0..1
ClinicalSignificanceEnum		 direct
type 0..1
String		 direct
regulatory_category 0..1
RegulatoryVariantCategoryEnum		 Functional classification of a variant's impact on gene expression, using the... direct

Usages

used by used in type used
Genetic variants range Variant
Disease variants range Variant

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/monarch-initiative/dismech

Mappings

Mapping Type Mapped Value
self dismech:Variant
native dismech:Variant

LinkML Source

Direct

name: Variant
description: A genetic variant associated with a disease, including coding and non-coding
  regulatory variants. For regulatory variants, use regulatory_category to classify
  the variant's impact on gene expression (LOE/mLOE/GOE per Cheng et al. 2024).
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- name
- description
- gene
- evidence
- functional_effects
- synonyms
- identifiers
- external_assertions
- sequence_length
- clinical_significance
- type
- regulatory_category

Induced

name: Variant
description: A genetic variant associated with a disease, including coding and non-coding
  regulatory variants. For regulatory variants, use regulatory_category to classify
  the variant's impact on gene expression (LOE/mLOE/GOE per Cheng et al. 2024).
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  name:
    name: name
    examples:
    - value: Adolescent Nephronophthisis
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: name
    owner: Variant
    domain_of:
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycleStage
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ComorbidityAssociation
    range: string
    required: true
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: Variant
    domain_of:
    - Descriptor
    - DietaryModification
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    range: string
  gene:
    name: gene
    examples:
    - value: '{preferred_term: MEFV}'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: gene
    owner: Variant
    domain_of:
    - GeneticContext
    - Pathophysiology
    - Variant
    range: GeneDescriptor
    inlined: true
  evidence:
    name: evidence
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: evidence
    owner: Variant
    domain_of:
    - PhenotypeContext
    - Dataset
    - ExperimentalModel
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - ModelMechanismLink
    - ExternalAssertion
    - Finding
    - Prevalence
    - ProgressionInfo
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    range: EvidenceItem
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  functional_effects:
    name: functional_effects
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: functional_effects
    owner: Variant
    domain_of:
    - Variant
    range: FunctionalEffect
    multivalued: true
    inlined: true
    inlined_as_list: true
  synonyms:
    name: synonyms
    examples:
    - value: '[''CYFRA 21-1'']'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: synonyms
    owner: Variant
    domain_of:
    - Pathophysiology
    - Biochemical
    - Environmental
    - Disease
    - Variant
    range: string
    multivalued: true
  identifiers:
    name: identifiers
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: identifiers
    owner: Variant
    domain_of:
    - Variant
    range: uriorcurie
    multivalued: true
  external_assertions:
    name: external_assertions
    description: External curated assertions or registry records relevant to this
      entity
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: external_assertions
    owner: Variant
    domain_of:
    - Disease
    - Variant
    range: ExternalAssertion
    multivalued: true
    inlined: true
    inlined_as_list: true
  sequence_length:
    name: sequence_length
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: sequence_length
    owner: Variant
    domain_of:
    - Variant
    range: integer
  clinical_significance:
    name: clinical_significance
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: clinical_significance
    owner: Variant
    domain_of:
    - Variant
    range: ClinicalSignificanceEnum
  type:
    name: type
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: type
    owner: Variant
    domain_of:
    - Variant
    - FunctionalEffect
    range: string
  regulatory_category:
    name: regulatory_category
    description: Functional classification of a variant's impact on gene expression,
      using the LOE/mLOE/GOE framework (Cheng et al. 2024, PMID:38436667) or traditional
      coding categories (LOF/GOF/DN).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: regulatory_category
    owner: Variant
    domain_of:
    - Variant
    - FunctionalEffect
    range: RegulatoryVariantCategoryEnum