Class: Variant

Genetic sequence variant (ClinVar model). Includes SNVs, indels, repeat expansions (C9orf72), and structural variants. Links to genes, proteins, and disease associations.

URI: biolink:SequenceVariant

 classDiagram
    class Variant
    click Variant href "../Variant/"
      MolecularEntity <|-- Variant
        click MolecularEntity href "../MolecularEntity/"

      Variant : als_class

      Variant : clinical_significance

      Variant : clinvar_id

      Variant : comment

      Variant : definition

      Variant : hgvs_c

      Variant : hgvs_p

      Variant : id

      Variant : ingest_date

      Variant : is_obsolete

      Variant : label

      Variant : last_updated

      Variant : maf

      Variant : rsid

      Variant : source

      Variant : source_version

      Variant : synonym

      Variant : variant_type





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



      Variant : xref

Inheritance

NamedEntity
- OntologyClass
  - MolecularEntity
    - Variant

Class Properties

Property	Value
Class URI	biolink:SequenceVariant

Slots

Name	Cardinality and Range	Description	Inheritance
clinvar_id	1 ClinvarIdentifier		direct
rsid	0..1 String	dbSNP reference SNP ID	direct
hgvs_c	0..1 String	HGVS coding sequence notation (e	direct
hgvs_p	0..1 String	HGVS protein notation (e	direct
variant_type	0..1 VariantTypeEnum		direct
clinical_significance	0..1 String	ClinVar clinical interpretation	direct
als_class	0..1 String	ALS-specific classification (causal, risk, modifier, protective)	direct
maf	0..1 Float	Minor allele frequency in gnomAD non-neuro cohort	direct
source_version	0..1 String	Source database/ontology version	OntologyClass
ingest_date	0..1 String	When entity was imported into ALS-KG	OntologyClass
id	1 String	Persistent unique identifier (IRI)	NamedEntity
label	1 String	Preferred human-readable label	NamedEntity
definition	0..1 String	Formal textual definition	NamedEntity
synonym	0..1 String	Alternative names	NamedEntity
xref	0..1 String	Cross-references to external ontologies	NamedEntity
comment	0..1 String	Informal notes or comments	NamedEntity
is_obsolete	0..1 String	Deprecation flag	NamedEntity
source	0..1 String	Original source/database	NamedEntity
last_updated	0..1 String	Last modification timestamp	NamedEntity

Usages

used by	used in	type	used
VariantDiseaseAssociation	has_variant	range	Variant
VariantProteinEffectAssociation	has_variant	range	Variant

Identifier and Mapping Information

Schema Source

from schema: https://cair2015.github.io/als-kg

Mappings

Mapping Type	Mapped Value
self	biolink:SequenceVariant
native	alskb:Variant

LinkML Source

Direct

name: Variant
description: Genetic sequence variant (ClinVar model). Includes SNVs, indels, repeat
  expansions (C9orf72), and structural variants. Links to genes, proteins, and disease
  associations.
from_schema: https://cair2015.github.io/als-kg
is_a: MolecularEntity
attributes:
  clinvar_id:
    name: clinvar_id
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    identifier: true
    domain_of:
    - Variant
    range: ClinvarIdentifier
    required: true
  rsid:
    name: rsid
    description: dbSNP reference SNP ID
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Variant
  hgvs_c:
    name: hgvs_c
    description: HGVS coding sequence notation (e.g. c.10A>G)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Variant
  hgvs_p:
    name: hgvs_p
    description: HGVS protein notation (e.g. p.Ala4Val)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Variant
  variant_type:
    name: variant_type
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Variant
    range: VariantTypeEnum
  clinical_significance:
    name: clinical_significance
    description: ClinVar clinical interpretation
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Variant
    - VariantDiseaseAssociation
  als_class:
    name: als_class
    description: ALS-specific classification (causal, risk, modifier, protective)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Variant
  maf:
    name: maf
    description: Minor allele frequency in gnomAD non-neuro cohort
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    domain_of:
    - Variant
    range: float
    minimum_value: 0.0
    maximum_value: 1.0
class_uri: biolink:SequenceVariant

Induced

name: Variant
description: Genetic sequence variant (ClinVar model). Includes SNVs, indels, repeat
  expansions (C9orf72), and structural variants. Links to genes, proteins, and disease
  associations.
from_schema: https://cair2015.github.io/als-kg
is_a: MolecularEntity
attributes:
  clinvar_id:
    name: clinvar_id
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    identifier: true
    alias: clinvar_id
    owner: Variant
    domain_of:
    - Variant
    range: ClinvarIdentifier
    required: true
  rsid:
    name: rsid
    description: dbSNP reference SNP ID
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: rsid
    owner: Variant
    domain_of:
    - Variant
    range: string
  hgvs_c:
    name: hgvs_c
    description: HGVS coding sequence notation (e.g. c.10A>G)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: hgvs_c
    owner: Variant
    domain_of:
    - Variant
    range: string
  hgvs_p:
    name: hgvs_p
    description: HGVS protein notation (e.g. p.Ala4Val)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: hgvs_p
    owner: Variant
    domain_of:
    - Variant
    range: string
  variant_type:
    name: variant_type
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: variant_type
    owner: Variant
    domain_of:
    - Variant
    range: VariantTypeEnum
  clinical_significance:
    name: clinical_significance
    description: ClinVar clinical interpretation
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: clinical_significance
    owner: Variant
    domain_of:
    - Variant
    - VariantDiseaseAssociation
    range: string
  als_class:
    name: als_class
    description: ALS-specific classification (causal, risk, modifier, protective)
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: als_class
    owner: Variant
    domain_of:
    - Variant
    range: string
  maf:
    name: maf
    description: Minor allele frequency in gnomAD non-neuro cohort
    from_schema: https://cair2015.github.io/als-kg
    rank: 1000
    alias: maf
    owner: Variant
    domain_of:
    - Variant
    range: float
    minimum_value: 0.0
    maximum_value: 1.0
  source_version:
    name: source_version
    description: Source database/ontology version
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:hasVersion
    alias: source_version
    owner: Variant
    domain_of:
    - OntologyClass
    - Association
    range: string
  ingest_date:
    name: ingest_date
    description: When entity was imported into ALS-KG
    from_schema: https://cair2015.github.io/als-kg
    alias: ingest_date
    owner: Variant
    domain_of:
    - OntologyClass
    - Relationship
    - Association
    range: string
  id:
    name: id
    description: Persistent unique identifier (IRI)
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: schema:identifier
    alias: id
    owner: Variant
    domain_of:
    - NamedEntity
    range: string
    required: true
  label:
    name: label
    description: Preferred human-readable label
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdfs:label
    alias: label
    owner: Variant
    domain_of:
    - NamedEntity
    range: string
    required: true
  definition:
    name: definition
    description: Formal textual definition
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: IAO:0000115
    alias: definition
    owner: Variant
    domain_of:
    - NamedEntity
    range: string
  synonym:
    name: synonym
    description: Alternative names
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: oboInOwl:hasRelatedSynonym
    alias: synonym
    owner: Variant
    domain_of:
    - NamedEntity
    range: string
  xref:
    name: xref
    description: Cross-references to external ontologies
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: oboInOwl:hasDbXref
    alias: xref
    owner: Variant
    domain_of:
    - NamedEntity
    range: string
  comment:
    name: comment
    description: Informal notes or comments
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: rdfs:comment
    alias: comment
    owner: Variant
    domain_of:
    - NamedEntity
    range: string
  is_obsolete:
    name: is_obsolete
    description: Deprecation flag
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: owl:deprecated
    ifabsent: 'false'
    alias: is_obsolete
    owner: Variant
    domain_of:
    - NamedEntity
    range: string
  source:
    name: source
    description: Original source/database
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:source
    alias: source
    owner: Variant
    domain_of:
    - NamedEntity
    - Relationship
    - Association
    range: string
  last_updated:
    name: last_updated
    description: Last modification timestamp
    from_schema: https://cair2015.github.io/als-kg
    slot_uri: dcterms:modified
    alias: last_updated
    owner: Variant
    domain_of:
    - NamedEntity
    - Association
    range: string
class_uri: biolink:SequenceVariant