uniprot variant classification DB retireve

Question

[cocchi.e89]

I'm working on some variants (exome, human) annotation. I'd like to retrieve the UNIPROT info about the variant (e.g. "disease" when known as disease causing variant etc). How can I do that? I tried with --uniprot VEP command but it only output the var uniprot transcript.

Thanks a lot in advance for any help!

Answer 1

[Elisabeth Gasteiger]

Are you aware of the UniProt index of human polymorphisms and disease mutations, https://www.uniprot.org/docs/humsavar ? This file lists all missense variants annotated in human UniProtKB/Swiss-Prot entries. It provides a variant classification (which is intended for research purposes only, not for clinical and diagnostic use!) into 'Disease', 'Polymorphism', 'Unclassified'. These labels are based on the variant annotation in the corresponding UniProtKB/Swiss-Prot entries, curated from literature reports.

[cocchi.e89]

that's great! Thank you very much @elisabethgasteiger

Answer 2

[Emily]

I'm afraid there's nothing the VEP can do to obtain that information. Does this offer anything that the ClinVar clinical significance doesn't already provide?