[ensembl-dev] FW: VEP polyphen predictions

[Marc Jan Bonder]

Hi,

 

I have a question, I'm using VEP2.0 to translate SNP positions to amino
acids positions in transcripts and then predicting if it is damaging or not
using polyphen. I know that you also include polyphen annotations in the
latest version of VEP. This causes my question/problem when I try to
annotate the amino acids substitutions using my polyphen set up, I sometimes
get errors, it says that the returned amino acids are not in the transcript.
When I look in the VEP output, then it does return a polyphen annotation. I
use a convert table from the UCSC to translate the ensemble transcript ID's
to Swissprot id's.

 

An example of this error:

Input for VEP:

6             152453291          152453291          G/A       +

 

Output by VEP

6_152453291_G/A          6:152453291       A             ENSG00000131018
ENST00000367257                NON_SYNONYMOUS_CODING                3998
3998      1333      T/I          aCa/aTa               rs35591210
SIFT=tolerated(0.06);PolyPhen=benign(0.004);Condel=deleterious(0.885)

 

Input to polyphen:

Q8NF91-4           T             I

 

Output by Polyphen

ERROR: Neither AA1 (T) nor AA2 (I) in input matches Q8NF91-4 query sequence
residue (R) at position (1333)

 

There are more of these errors in my polyphen input. Is this because you
used another than the standard database for your polyphen annotations (not
the unireff100 database)? Or is it because my conversions from ensemble
transcript id to swissprot id's aren't correct? Or do you just convert the T
into a R and then rerun the prediction? Or is it something completely
different?

 

Regards,

 

Marc Jan Bonder

 

Bioinformatician at the University Medical Centre Groningen

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