VEP output and stop gain mutation

Question

[seta]

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

Answer 1

[Ben_Ensembl]

Hi Seta,

Since SIFT and Polyphen are predictions of the pathogenicity of amino acid substitution, SIFT and Polyphen scores are calculated for missense variants: http://www.ensembl.org/info/genome/variation/prediction/protein_function.html

The 'IMPACT' is a separate prediction, which is a subjective classification of the consequence type. You can see the corresponding IMPACT for each consequence in the following table in the table on the following documentation page: http://www.ensembl.org/info/genome/variation/prediction/predicted_data.html

In this case, stop-gained variants have a 'HIGH' impact prediction, which means that the variant is assumed to have 'high (disruptive) impact in the protein, probably causing protein truncation, loss of function or triggering nonsense mediated decay'.

Your question about the related proteins being 'certainly truncated and non-functional' is quite tricky. The results obtained from the VEP are predictions. I would always advise experimental validation to assess the expression levels and functionality of the protein of interest.

In addition to WouterDeCoster's suggestion, you can also retrieve the BLOSUM62 amino acid conservation score using the VEP.

Best wishes

Ben Ensembl Helpdesk

[seta]

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:

rs  Condel  BLOSUM62
rs1 deleterious(0.89)   -2
rs2 neutral(0.297)  1
rs3 deleterious(0.76)   1
rs4 deleterious(0.93)   -3
rs5 neutral(0.465)  -1
rs7 neutral(0.014)  2
rs8 deleterious(0.567)  -2
rs9 neutral(0.458)  -1
rs10    neutral(0.345)  1

Thanks

[Ben_Ensembl]

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

Answer 2

[WouterDeCoster]

As the last question, sorry, could you please suggest any database/server to check the conserved amino acids (not domain) within the protein?

I think you are looking for GERP scores, which you can (for example) find in the UCSC genome browser.

[seta]

Thank you friend! I checked the variation database (track: All SNPs (150) from Table browser, but I didn't find GERP score.

[WouterDeCoster]

It's available in the browser under "Comparative Genomics", alternatively see also http://mendel.stanford.edu/SidowLab/downloads/gerp/