Find other variants causing same protein change

Question

[jakub]

Hi,

is there a simple way to annotate a VCF with other known ClinVar variants causing the same AA change? Sometimes ClinVar contains a pathogenic entry for a specific SNV, but another SNV resulting in the same AA acid change is not annotated in the database.

My approach would be to:

1. Use the "SameCodon" VEP plugin to retrieve other variation at this location
2. Screen the variant identifiers for the same amino acid change
3. Annotate above with ClinVar context (e.g. via dbNSFP)

Point 2 could actually be dropped, because it might be useful to know if there are other AA changes at the codon in question that cause disease. Would be grateful to hear if there is a more straightforward way to do this.

Best wishes, Jakub