Question: uniprot variant classification DB retireve
0
gravatar for cocchi.e89
7 weeks ago by
cocchi.e8930
cocchi.e8930 wrote:

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!

ensembl uniprot vep variant • 123 views
ADD COMMENTlink modified 7 weeks ago by Elisabeth Gasteiger1.6k • written 7 weeks ago by cocchi.e8930
1
gravatar for Elisabeth Gasteiger
7 weeks ago by
Geneva
Elisabeth Gasteiger1.6k wrote:

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.

ADD COMMENTlink written 7 weeks ago by Elisabeth Gasteiger1.6k

that's great! Thank you very much @elisabethgasteiger

ADD REPLYlink written 6 weeks ago by cocchi.e8930
0
gravatar for Emily_Ensembl
7 weeks ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

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?

ADD COMMENTlink written 7 weeks ago by Emily_Ensembl18k
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