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. 2017 Feb 28;38(5):485–493. doi: 10.1002/humu.23191

Table 3.

Annotation elements: (A) basic triplet statement for “SCN5A‐p.Ser2014*” variant, (B) relations, and (C) evidence for the triplet “SCN5A‐p.Ser2014* decreases macroscopic conductance”

A. ANNOTATION
Element CV/Ontology Example
Subject HGVS nomenclature SCN5A‐p.Ser2014*
Relation cv_modification_effect.obo Decreases
Object BioObject/GO/ICEPO/ Protein Property/MGI phenotype Binding to SNT (BioObject) cardiac conduction (GO) macroscopic conductance (ICEPO) protein abundance (Protein Property)
B. RELATIONS
No impact No significant effect observed compared with the wild‐type

  • Does not cause phenotype

No observable morphological, physiological, and behavioral characteristics in the mutant compared with the wild‐type
Impacts Some significant effect observed compared with the wild‐type

  • Causes phenotype

Some observable morphological, physiological, and behavioral characteristics in the mutant compared with the wild‐type

  • Increases

Some significant increase observed in a quantifiable measure compared with the wild‐type

  • Decreases

Some significant decrease observed in a quantifiable measure compared with the wild‐type

  • Gains function

Mutant protein acquires a property absent from the wild‐type (new substrate, new cellular localization, etc.)

  • Depolarizes

Some significant shift of the curve in the depolarizing direction compared with the wild‐type

  • Hyperpolarizes

Some significant shift of the curve in the hyperpolarizing direction compared with the wild‐type

  • Hastens

Some significant higher value in the transition speed compared with the wild‐type

  • Slows

Some significant lower value in the transition speed compared with the wild‐type

  • Impacts temperature‐dependence of

Some significant impact dependent on the temperature compared with the wild‐type
C. EVIDENCE
Element CV/Ontology Example
Evidence code(s) Evidence and conclusion ontology Whole‐cell voltage clamp recording protocol/knockin evidence used in manual assertion/current density
Protein origin NCBI taxonomy Mus musculus (NCBITaxID10090)
Biological model species, cell type, anatomy, cell line NCBI taxonomy CALOHA anatomy ontology Cellosaurus Mus musculus (NCBITaxID10090) Heart muscle cell (CALOHA:TS‐0115)
Phenotype intensity Mild/moderate/severe Moderate
Evidence quality Gold/silver Gold
Reference Cross‐reference to PubMed PUBMED 24895455