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uniprot variant classification DB retireve

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!

uniprot variant vep ensembl
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updated by Elisabeth Gasteiger Elisabeth Gasteiger • written by cocchi.e89 cocchi.e89

2 answers

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.

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written by Elisabeth Gasteiger Elisabeth Gasteiger

that's great! Thank you very much @elisabethgasteiger

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written by cocchi.e89 cocchi.e89

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?

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written by Emily Emily

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