This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Identifying protein impact

This is a two part question;

(a) To identifying protein change by SV identifiers for genes

I have some structural variants identifiers for some genes, gathered from literature. I was wondering if there is anyway I could identify the protein change in this region. My current theory is to do a blastp to get the protein sequence. From here locate the SV by numbered change. Example of the sv identifiers are like so "ATR A1091V". I found some functional information from HGVS but many from internal data is unknown. Any help to resolve it in a simpler way would be helpful as I have a huge list.

(b) What does SV nomenclature mean ?

Example: "ATR A1091V" Also, I would like to understand what does the nomenclature actually mean. The change to A to V amino acid had in position 1091 ? Is that a copy number with 1 variant ? And if any of them are marked with ' * '; then its numbering to indicating termination ?

Thanks for any help.

next-gen
• 881 views • link
written by ira • ira

The nomenclature is best documented in the HGVS website. Hopefully, whatever resource you're using follows the nomenclature to a good extent, even if not 100%.

For example, ATR A1091V is understandable, but the proper nomenclature would be NP_001175:p.Ala1091Val

EDIT: I do not see this variant in dbSNP - the closest are p.Ser1095Leu and p.Tyr1087His

• 1 views • link
written by Ram Ram

0 answers

No answers yet.

Log in to answer this question.

More posts like this