Link

Class: SequenceVariant

An allele that varies in its sequence from what is considered the reference allele at that locus.

URI: biolink:SequenceVariant

GENO:0000002

WIKIDATA:Q15304597

SIO:010277

VMC:Allele

SO:0001059

SO:0001060


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Identifier prefixes

  • CAID
  • ClinVar
  • ClinVarVariant
  • WIKIDATA
  • DBSNP
  • dbSNP
  • MGI
  • ZFIN
  • FlyBase
  • FB
  • WB
  • WormBase

Parents

  • is_a: GenomicEntity - an entity that can either be directly located on a genome (gene, transcript, exon, regulatory region) or is encoded in a genome (protein)

Children

  • Snv - SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist

Referenced by class

Attributes

Own

Inherited from gene product:

  • id REQ
    • Description: A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI
    • range: String
    • in subsets: (translator_minimal)
  • name REQ
    • Description: A human-readable name for a thing
    • range: LabelType
    • in subsets: (translator_minimal)

Inherited from named thing:

  • category 1..*
    • Description: Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class.
  • In a neo4j database this MAY correspond to the neo4j label tag.
  • In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values bl:Protein, bl:GeneProduct, bl:MolecularEntity, … In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature f may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {bl:GenomicEntity, bl:MolecularEntity, bl:NamedThing}

Inherited from thing with taxon:

  • in taxon 0..*
    • Description: connects a thing to a class representing a taxon
    • range: OrganismTaxon
    • in subsets: (translator_minimal)

Domain for slot:

Other properties

     
Aliases:   allele
Local names:   allele (agr)
Mappings:   GENO:0000002
    WIKIDATA:Q15304597
    SIO:010277
    VMC:Allele
    SO:0001059
    SO:0001060
Alt Descriptions:   An enitity that describes a single affected, endogenous allele. These can be of any type that matches that definition (AGR)
    A contiguous change at a Location (VMC)
Comments:   This class is for modeling the specific state at a locus. A single dbSNP rs ID could correspond to more than one sequence variants (e.g CIViC:1252 and CIViC:1253, two distinct BRCA2 alleles for rs28897743)