How can I know if snp is inside a protein domain?

Question

[iraun]

I've some snps covering my gene X. I want to know if any of those snps is included in a domain of the protein encoded by my gene X. Anyone can suggest me how can I know the coordinates of the domains of my gene to see if my snps are included in these regions? Or any other method to know this?

Thanks in advance,

Answer 1

[Pierre Lindenbaum]

VEP has got an option --domains

--domains Adds names of overlapping protein domains to output. Not used by default

[iraun]

Thanks Pierre, this is exactly what I was looking for.

[cdsouthan]

Pierre, you could write a nice paper on the nsSNP frequency and VEP scores across different InterPro domains/familes