AlleleMolecularConsequenceStatement

A statement about the expected effect of a variant allele at the level of genomic or transcript sequence (e.g. how it might affect splicing, truncate a gene product, etc.).

SEPIO:0000229
Descended from Statement

Scope and Usage

Molecular consequence statements typically describe the type of variation the allele represents (e.g. a deletion or insertion or translocation), the type of genomic or transcript feature the allele affects (e.g. that it occurs in a 3' UTR, or an exon), or its impact on the structure or processing of a gene (e.g. that it generates a copy number variation, results in a lost stop codon, disrupts a slice site, or causes a frameshift elongation). Molecular Consequence statements do not include predictions about the impact a variation might have on the function of an encoded gene product.

Example of usage. Molecular consequence statements are produced by software such as Annovar (http://annovar.openbioinformatics.org), SnpEff (http://snpeff.sourceforge.net) or Variant Effect Predictor (http://www.ensembl.org/vep), and often take the form of annotation of a variant with a term from the sequence ontology such as 'missense variant', 'frameshift variant', 'splice-site variant', 'frameshift elongation', 'substitution', 'inversion'.

Attributes

Name Type Cardinality Description IRI Defined in
contextualAllele ContextualAllele 1..1 The contextual (reference-specific) allele that is being classified SEPIO:0000275 AlleleMolecularConsequenceStatement
statementOutcome @id 1..1 Classification of allele based on the manner in which it alters the sequence SEPIO:0000197 AlleleMolecularConsequenceStatement
label string 0..1 A name given to the resource. RDFS:label Entity
description string 0..1 Description may include but is not limited to: an abstract, a table of contents, a graphical representation, or a free-text account of the resource. DC:description Entity
userLabelDictionary UserLabel 0..* An optional label defined by the user. Used for custom entities or to clarify the preferred user label on existing entities with non-preferred labels. SEPIO:0000422 Statement
outcomeQualifier string 0..1 Use “NOT” as the value of this property to assert that the statement is negated. SEPIO:0000346 Statement
evidenceLine EvidenceLine 0..* supporting evidence SEPIO:0000006 Statement
contribution Contribution 0..* The contributions (agent, time and role) made to this entity SEPIO:0000159 Statement
source string 0..* A string indicating the source of a Statement DC:source Statement

Instances

ID label description userLabelDictionary outcomeQualifier evidenceLine contextualAllele statementOutcome

CGEX:MolCon001

Protein ends at p.826 and this frameshift would create stop at p.852 (769+83) thus NMD would not occur. Instead an elongated protein

CGEX:CtxAll001

SO:0001589

(frameshift variant)

CGEX:MolCon003

LOF is predicted to occur as variant is >55bp from penultimate exon

CGEX:CtxAll002

SO:0001589

(frameshift variant)

CGEX:MolCon005

LOF is predicted but this transcript is rare

CGEX:CtxAll003

SO:0001589

(frameshift variant)

CGEX:MolCon272

This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and in vitro studies confirmed that it leads to aberrant splicing and reduced DSC2 protein levels (Heuser 2006 PMID:17186466).

CGEX:CtxAll127

SO:0001629

(splice-site variant)

CGEX:MolCon006

CGEX:CtxAll004

SO:0000191

(interior intron)

CGEX:MolCon066

CGEX:CtxAll044

SO:0001825

(conservative Inframe Deletion)

CGEX:MolCon070

CGEX:CtxAll046

SO:0001825

(conservative Inframe Deletion)

CGEX:MolCon074

CGEX:CtxAll048

SO:0001823

(conservative Inframe Insertion)

CGEX:MolCon075

CGEX:CtxAll124

SO:0001819

(synonymous variant)

CGEX:MolCon117

CGEX:CtxAll070

SO:0001583

(missense variant)

CGEX:MolCon169

CGEX:CtxAll099

SO:0001583

(missense variant)

CGEX:MolCon198

CGEX:CtxAll097

SO:0001583

(missense variant)

CGEX:MolCon201

CGEX:CtxAll098

SO:0001583

(missense variant)

CGEX:MolCon203

CGEX:CtxAll099

SO:0001583

(missense variant)

CGEX:MolCon223

CGEX:CtxAll106

SO:0001825

(conservative Inframe Deletion)

CGEX:MolCon227

CGEX:CtxAll107

SO:0001589

(frameshift variant)

CGEX:MolCon231

CGEX:CtxAll108

SO:0001823

(conservative Inframe Insertion)

CGEX:MolCon261

CGEX:CtxAll123

SO:0001819

(synonymous variant)

CGEX:MolCon265

CGEX:CtxAll124

SO:0001819

(synonymous variant)

CGEX:MolCon269

CGEX:CtxAll125

SO:0001819

(synonymous variant)