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'.
|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|
|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|
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
LOF is predicted to occur as variant is >55bp from penultimate exon
LOF is predicted but this transcript is rare
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).