Class: FunctionalEffect

Describes the functional consequence of a genetic variant, including regulatory impact classification (LOE/mLOE/GOE) for non-coding variants and the type of regulatory element affected.

URI: dismech:class/FunctionalEffect

 classDiagram
    class FunctionalEffect
    click FunctionalEffect href "../../classes/FunctionalEffect/"
      FunctionalEffect : affected_cell_types





        FunctionalEffect --> "*" CellTypeDescriptor : affected_cell_types
        click CellTypeDescriptor href "../../classes/CellTypeDescriptor/"



      FunctionalEffect : affected_developmental_stage

      FunctionalEffect : description

      FunctionalEffect : function

      FunctionalEffect : regulatory_category





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



      FunctionalEffect : regulatory_element_type





        FunctionalEffect --> "0..1" RegulatoryElementTypeEnum : regulatory_element_type
        click RegulatoryElementTypeEnum href "../../enums/RegulatoryElementTypeEnum/"



      FunctionalEffect : regulatory_mechanism

      FunctionalEffect : type

Slots

Name	Cardinality and Range	Description	Inheritance
function	0..1 String		direct
description	0..1 String		direct
type	0..1 String		direct
regulatory_category	0..1 RegulatoryVariantCategoryEnum	Functional classification of a variant's impact on gene expression, using the...	direct
regulatory_element_type	0..1 RegulatoryElementTypeEnum	Type of gene regulatory element disrupted by a non-coding variant (e	direct
affected_cell_types	* CellTypeDescriptor	Cell types in which gene expression is specifically gained or lost	direct
affected_developmental_stage	0..1 String	Developmental stage or temporal window in which expression is modularly lost ...	direct
regulatory_mechanism	0..1 String	The specific molecular mechanism by which the regulatory variant exerts its e...	direct

Usages

used by	used in	type	used
Variant	functional_effects	range	FunctionalEffect

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: FunctionalEffect
description: Describes the functional consequence of a genetic variant, including
  regulatory impact classification (LOE/mLOE/GOE) for non-coding variants and the
  type of regulatory element affected.
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- function
- description
- type
- regulatory_category
- regulatory_element_type
- affected_cell_types
- affected_developmental_stage
- regulatory_mechanism

Induced

name: FunctionalEffect
description: Describes the functional consequence of a genetic variant, including
  regulatory impact classification (LOE/mLOE/GOE) for non-coding variants and the
  type of regulatory element affected.
from_schema: https://w3id.org/monarch-initiative/dismech
attributes:
  function:
    name: function
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: function
    owner: FunctionalEffect
    domain_of:
    - FunctionalEffect
    range: string
  description:
    name: description
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: description
    owner: FunctionalEffect
    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
  type:
    name: type
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: type
    owner: FunctionalEffect
    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: FunctionalEffect
    domain_of:
    - Variant
    - FunctionalEffect
    range: RegulatoryVariantCategoryEnum
  regulatory_element_type:
    name: regulatory_element_type
    description: Type of gene regulatory element disrupted by a non-coding variant
      (e.g., promoter, enhancer, silencer, insulator, TAD boundary).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: regulatory_element_type
    owner: FunctionalEffect
    domain_of:
    - FunctionalEffect
    range: RegulatoryElementTypeEnum
  affected_cell_types:
    name: affected_cell_types
    description: Cell types in which gene expression is specifically gained or lost.
      Particularly relevant for mLOE variants (modular loss in specific cell types)
      and GOE variants (ectopic gain in new cell types).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: affected_cell_types
    owner: FunctionalEffect
    domain_of:
    - FunctionalEffect
    range: CellTypeDescriptor
    multivalued: true
    inlined: true
    inlined_as_list: true
  affected_developmental_stage:
    name: affected_developmental_stage
    description: Developmental stage or temporal window in which expression is modularly
      lost or ectopically gained. Relevant for variants with temporal modularity (e.g.,
      Hemophilia B Leyden).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: affected_developmental_stage
    owner: FunctionalEffect
    domain_of:
    - FunctionalEffect
    range: string
  regulatory_mechanism:
    name: regulatory_mechanism
    description: The specific molecular mechanism by which the regulatory variant
      exerts its effect (e.g., TFBS disruption, enhancer adoption, promoter switching,
      repressor site loss, novel TFBS creation, heterochromatin spreading).
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: regulatory_mechanism
    owner: FunctionalEffect
    domain_of:
    - FunctionalEffect
    range: string