[ensembl-dev] VEP Annotation and reading frame

[Emily Perry]

Please do not send identical questions in to Ensembl helpdesk and dev. 
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question.

On 30/03/2016 16:04, ptashkir at mskcc.org wrote:
> Hi,
>
>
> I'm looking for any insight into an issue we are having with the 
> annotation of missense variants in MAP3K14. It appears that after exon 
> 1, a different reading frame is selected for different exons.
>
> Please see the test case below, using the VEP web interface. We are 
> interested in RefSeq annotations, but even the ENSMBL annotations are 
> also confusing. Results are the same for our local install of version 82.
>
> For the RefSeq annotation, how is the reading frame selected? The 
> variant is annotated as  (p.W406C) , why is it not G407S? After exon 
> 1, it looks like reading frame is not consistent from exon to exon. 
> Splicing mutations are properly annotated however.
>
> All ensmbl annotations are listed as non-coding. You'll also notice on 
> the provided IGV screenshot that the MAP3K14-AS1 non-coding transcript 
> is well downstream of this exon6 mutation. Any insight is greatly 
> appreciated. Thanks!
>
>
> Test case: Ensembl GRCh37 release 84 - March 2016
> ####################
> INPUT:
> ####################
> 17 43362250 . C A . . .
>
>
> ######### VEP ANNOTATIONS RefSeq and ENSMBL: 
> ##################################
>
> NM_003954.3protein_coding 6/16-NM_003954.3:c.1218G>T 
> NP_003945.2:p.Trp406Cys
>
> ENST00000376926processed_transcript4/8-ENST00000376926.4:n.568G>T-
>
> ENST00000344686processed_transcript7/17-ENST00000344686.2:n.1325G>T-
>
> ENST00000587332processed_transcript6/16-ENST00000587332.1:n.1319G>T-
>
>
>
> Thanks,
>
> Ryan Ptashkin
> Computational Biologist
> Memorial Sloan Kettering Cancer Center
> ptashkir at mskcc.org <mailto:ptashkir at mskcc.org>
>
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-- 
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

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