Hi all,
I annotated some variations (SNP) using VEP, there are two stop gain mutations, one at 2nd amino acid and another at the 110th amino acid position (the protein has about 300 amino acid). While the VEP says their impact is "HIGH", but it didn't return any value for SIFT or polyphen, could you please let me know why? Given the position of stop gain mutation, can we say the related protein is certainly truncated and non-functional at least at the bioinformatic analysis level?
As the last question, sorry, could you please suggest any database/server to check the conserved amino acids (not domain) within the protein?
Many thanks in advance
Hi Ben,
Thank you very much for your feedback. Regarding the BLOSUM62 amino acid conservation score, although I read about it, I am not sure for correct interpretation, could you please help me out about it? Also, please kindly let me know if there is any association between this score and Condel report from VEP? here is a short example, it will be great if you could please explain to me with this example:
Thanks
Hi Seta,
No problem- very happy to help. There is no association between Condel scores and BLOSUM62 scores. Condel is a measure of amino acid substitution on protein function. It integrates the output of a number of computational tools aimed at assessing the impact of non synonymous SNVs on protein function. To do this, it computes a weighted average of the scores (WAS) of these tools and provides a single score: https://bbglab.irbbarcelona.org/fannsdb/help/condel.html
BLOSUM matrices are used to score alignments between protein sequences: https://en.wikipedia.org/wiki/BLOSUM What do the scores in a BLOSUM matrix mean?
Best wishes
Ben Ensembl Helpdesk