[ensembl-dev] VEP not returning results

[Pankaj Agarwal]

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)
[cid:image001.jpg at 01D26B42.6EAF4700]

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
O: 919-681-2251
p.agarwal at duke.edu<mailto:p.agarwal at duke.edu>

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