[ensembl-dev] VEP not returning results

[Will McLaren]

Hi Pankaj,

There's an error in one of your HGVS inputs, but apart from this I see the
expected results for all three notations.

The correct one for the chromosomal location should be:

17:g.7676115_7676116delGG

You must use "g." for chromosomal coordinates, and provide the sequence on
the forward strand, so GG instead of CC. I've attached a screenshot of the
results I get when I use the instant VEP function on this input.

You will see many results because the TP53 gene has a large number of
alternate transcripts [1]. You may ask VEP to select one of these by
choosing the option "Select one selected consequence per variant" in the
"Restrict results" field of the Filtering section on the VEP web interface.

Regards

Will McLaren
Ensembl Variation

[1] :
http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000141510;r=17:7661779-7687550


​



On 10 January 2017 at 18:07, Pankaj Agarwal <p.agarwal at duke.edu> wrote:

> Hi,
>
>
>
> I have downloaded a set of frameshift mutations from COSMIC using
> Biomart.  My goal is to get the protein sequence of the transcript starting
> from the location of the frameshift mutation.
>
> I was hoping VEP could provide this information since it provides
> information about variants.
>
> The data that I downloaded from COSMIC includes the following fields (or
> importance here):
>
>
>
> Pubmed ID         15138567
>
> COSMIC Mutation ID      45724
>
> CDS Mutation Syntax     c.253_254delCC
>
> AA Mutation Syntax       p.P85fs*63
>
> Gene Name       TP53
>
> Accession Number          ENST00000269305
>
> COSMIC Sample ID          1399473
>
> Samp gene mutated       y
>
> Entrez Gene ID 7157
>
> Swissprot ID       P04637  ---> See if can get the protein sequence from
> here
>
> Ensembl Gene ID                             ENSG00000141510
>
> COSMIC Study ID                             blank (nothing)
>
> Genomic Coordinates (GRCh38)                17:7676115-7676116
>
> CDS Mutation Type         Deletion
>
> CDS Mutation Start         253
>
> CDS Mutation Stop          254
>
> AA Mutation Type           Deletion - Frameshift
>
> AA Mutation Start           85
>
> AA Mutation Stop            85
>
> Somatic status   Variant of unknown origin
>
>
>
> I tried to get results from VEP using the following 3 formats for this
> frameshift mutation:
>
>
>
> TP53:c.253_254delCC
>
> - this gave an error
>
>
>
> 17:c.253_254delCC
>
> - this returned nothing
>
>
>
> ENST00000269305:c.253_254delCC
>
> - this returned a table of results with a large number of results.
>
> (screenshot below)
>
>
>
> Please note that the results do include the COSMIC Mutation ID that is
> same as the one that I have for this variant.
>
>
>
> Why am I am getting different results for the same variant passed in
> different formats (all HGVS)?
>
> Is VEP well suited for what I am trying to do?
>
> Could you please suggest other ways I can get the a single NT or protein
> sequence for the unique frameshift mutation that I am using for the query.
>
>
>
> Thank you,
>
>
>
> - Pankaj
>
>
>
> -----------------------------
>
> Pankaj Agarwal, M.S
>
> Bioinformatician
>
> Data Analyst
>
> Applied Therapeutics
>
> Div. of Surgical Sciences
>
> Dept. of Surgery
>
> Duke University
>
> M: 919-244-6389 <(919)%20244-6389>
>
> O: 919-681-2251 <(919)%20681-2251>
>
> p.agarwal at duke.edu
>
>
>
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>
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