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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 : affected_regions





        Variant --> "*" GenomicRegion : affected_regions
        click GenomicRegion href "../../classes/GenomicRegion/"



      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 : genomic_contexts





        Variant --> "*" GenomicContextEnum : genomic_contexts
        click GenomicContextEnum href "../../enums/GenomicContextEnum/"



      Variant : identifiers

      Variant : name

      Variant : population_effects





        Variant --> "*" VariantPopulationEffect : population_effects
        click VariantPopulationEffect href "../../classes/VariantPopulationEffect/"



      Variant : regulatory_category





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



      Variant : regulatory_target_gene





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



      Variant : sequence_length

      Variant : synonyms

      Variant : type

      Variant : variant_type





        Variant --> "0..1" VariantTypeEnum : variant_type
        click VariantTypeEnum href "../../enums/VariantTypeEnum/"

Slots

Name Cardinality and Range Description Inheritance
name 1
String		 direct
description 0..1
String		 direct
gene 0..1
GeneDescriptor		 direct
regulatory_target_gene 0..1
GeneDescriptor		 Gene whose expression is affected, or proposed to be affected, by a regulator... 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
variant_type 0..1
VariantTypeEnum		 Optional controlled physical variant class direct
genomic_contexts *
GenomicContextEnum		 Sequence features overlapped by the variant direct
affected_regions *
GenomicRegion		 Named genomic regions affected by the physical alteration, including regulato... direct
regulatory_category 0..1
RegulatoryVariantCategoryEnum		 Functional classification of a variant's impact on gene expression, using the... direct
population_effects *
VariantPopulationEffect		 Population-scoped findings about this variant: how its classification, penetr... 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
- regulatory_target_gene
- evidence
- functional_effects
- synonyms
- identifiers
- external_assertions
- sequence_length
- clinical_significance
- type
- variant_type
- genomic_contexts
- affected_regions
- regulatory_category
- population_effects

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:
    - GenomicRegion
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - SeverityTier
    - DifferentialDiagnosis
    - Subtype
    - ReferenceRangeBand
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ComorbidityAssociation
    - Grouping
    - ModuleCollection
    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
    - GenomicRegion
    - GeneticContext
    - Dataset
    - ExperimentalModel
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - ModelVariable
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - SurrogateEndpointCollection
    - GeneClassificationCollection
    - ProteinStructure
    - ExternalAssertion
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - HistopathologyFinding
    - ImagingFinding
    - Environmental
    - Disease
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - InfectiousAgent
    - Transmission
    - Assay
    - Diagnosis
    - Inheritance
    - Variant
    - VariantPopulationEffect
    - FunctionalEffect
    - Mechanism
    - ModelingConsideration
    - Definition
    - CriteriaSet
    - ConditionDescriptor
    - GOEnrichment
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Grouping
    - GroupingCriteria
    - LogicalCriterion
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    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
    - ExperimentalPerturbation
    - GeneClassification
    - Pathophysiology
    - Variant
    - LogicalCriterion
    - DifferentiatingMechanism
    range: GeneDescriptor
    inlined: true
  regulatory_target_gene:
    name: regulatory_target_gene
    description: Gene whose expression is affected, or proposed to be affected, by
      a regulatory variant. Does not assert that the variant overlaps this gene. Describe
      the expression effect and its uncertainty in functional_effects and evidence.
      A variant that also overlaps the gene may specify both gene and regulatory_target_gene.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: regulatory_target_gene
    owner: Variant
    domain_of:
    - 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
    - Experiment
    - ExperimentalPerturbation
    - ExperimentalReadout
    - ExperimentalControl
    - ExecutableProtocol
    - ClinicalTrial
    - ComputationalModel
    - DifferentialDiagnosis
    - Subtype
    - CausalEdge
    - TreatmentMechanismTarget
    - EnvironmentalMechanismTarget
    - ModelDivergence
    - ModelMechanismLink
    - BiomarkerReadout
    - PhenotypeReadout
    - ReferenceRange
    - SurrogateEndpoint
    - ExternalAssertion
    - Finding
    - Prevalence
    - GeneCaseFraction
    - GeneDiseaseValidityAssertion
    - ProgressionInfo
    - ClinicalBurden
    - EpidemiologyInfo
    - Pathophysiology
    - Phenotype
    - Biochemical
    - HistopathologyFinding
    - ImagingFinding
    - Genetic
    - Environmental
    - Stage
    - AgentLifeCycle
    - AgentLifeCycleStage
    - AnimalModel
    - Treatment
    - TreatmentEffectModifier
    - DeliverySystem
    - InfectiousAgent
    - Transmission
    - Diagnosis
    - Inheritance
    - Variant
    - VariantPopulationEffect
    - ModelingConsideration
    - ClassificationAssignment
    - Definition
    - AlgorithmValidationStatus
    - CriteriaSet
    - AssociationSignal
    - AssociationStatistics
    - ComorbidityHypothesis
    - UpstreamConditionHypothesis
    - MechanisticHypothesis
    - Discussion
    - GroupingCriteria
    - GroupingMember
    - DifferentiatingMechanism
    - ModuleCollection
    - ModuleCollectionMember
    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
    - VariantPopulationEffect
    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
  variant_type:
    name: variant_type
    description: Optional controlled physical variant class. Complements the legacy
      free-text type without requiring it or replacing its narrative detail. Does
      not imply a coding or regulatory functional effect.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: variant_type
    owner: Variant
    domain_of:
    - GeneticContext
    - Variant
    range: VariantTypeEnum
  genomic_contexts:
    name: genomic_contexts
    description: Sequence features overlapped by the variant. Multiple values are
      allowed because an SV may span several features, or transcripts may differ.
      Specify relevant genes, transcripts, and overlap details in description; an
      intronic host gene need not be the regulatory target. Omit when unknown.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: genomic_contexts
    owner: Variant
    domain_of:
    - GeneticContext
    - Variant
    range: GenomicContextEnum
    multivalued: true
  affected_regions:
    name: affected_regions
    description: Named genomic regions affected by the physical alteration, including
      regulatory elements or chromosome intervals. Each item describes the named feature,
      which need not span the entire variant. Record only source-supported locations;
      disease-level regions need not have exact patient-specific breakpoints. Evidence
      belongs on the enclosing record. Location landmarks do not assert regulatory
      targeting or causal gene involvement. Existing free-text descriptions remain
      valid.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: affected_regions
    owner: Variant
    domain_of:
    - GeneticContext
    - Genetic
    - Variant
    range: GenomicRegion
    multivalued: true
    inlined: true
    inlined_as_list: true
  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:
    - Pathophysiology
    - Variant
    - FunctionalEffect
    range: RegulatoryVariantCategoryEnum
  population_effects:
    name: population_effects
    description: 'Population-scoped findings about this variant: how its classification,
      penetrance, severity, phenotype spectrum, or frequency differs in a named population.
      One record per population and source. Use when a variant''s effect is reported
      to depend on the population it is observed in, rather than collapsing it into
      the single population-blind clinical_significance.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: population_effects
    owner: Variant
    domain_of:
    - Variant
    range: VariantPopulationEffect
    multivalued: true
    inlined: true
    inlined_as_list: true