[ensembl-dev] VEP - start_lost consequence on first codon of transcripts with incomplete CDS 5'

[Jose M. Gonzalez]

Thanks, Will, for taking care of this. It would be great if it was also 
implemented for caches built out of custom gene annotation with gtf2vep.pl.

Cyriac, thanks for your suggestion, although in our case we are greatly 
interested in finding the variant consequences in all the annotated 
transcripts of the gene.

Best,
Jose



On 09/06/16 15:26, Will McLaren wrote:
> Thanks Jose and Cyriac.
>
> This will be fixed in the next VEP release.
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 8 June 2016 at 18:23, Cyriac Kandoth <kandoth at cbio.mskcc.org 
> <mailto:kandoth at cbio.mskcc.org>> wrote:
>
>     Keeping variant consequence separate from the quality of the
>     transcript, neatly limits the complexity of VEP. A solution for
>     you, might be to pick and report the consequence of the variant on
>     the "canonical transcript". Or maybe the transcript that is
>     actually expressed in the tissue you're studying. This is they
>     motivation behind the --pick and --pick-order options in VEP:
>
>     http://useast.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_pick
>
>     ~Cyriac
>
>     On Jun 8, 2016 6:37 AM, "Jose M. Gonzalez" <jmg at sanger.ac.uk
>     <mailto:jmg at sanger.ac.uk>> wrote:
>
>         Hi,
>
>         We have noticed that VEP calls a "start_lost" consequence on
>         variants affecting the first codon of transcripts with an
>         incomplete CDS 5', i.e. those tagged with a 'cds_start_NF'
>         attribute. In most cases this first codon is not even a
>         canonical start codon. Here is an example:
>         http://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000116198;r=1:3829193-3829524;t=ENST00000461667;v=rs763522630;vdb=variation;vf=129057128
>
>         These are partial transcripts for which the true start codon
>         is not known, so we believe that a "start_lost" consequence
>         does not seem appropriate in this case. Perhaps a consequence
>         such as "missense_variant" or "synonymous_variant" would be
>         more adequate for variants falling on these codons.
>
>         Would it be possible for VEP to handle transcript attributes
>         indicating partial length in order to call these types of
>         consequences more accurately?
>
>         Thanks,
>         Jose
>
>         -- 
>         Jose M. Gonzalez
>         Senior Bioinformatician - GENCODE
>         HAVANA Team
>         Wellcome Trust Sanger Institute
>         Hinxton, UK
>
>
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