Reverse translate and get the genomic position

Question

[MAPK]

I have genomic mutation and corresponding protein mutation for several genes, for example c.2503G>T (genomic) and p.D835Y (protein) for FLT3 gene. What is the easiest way to determine the genomic location for this variation?

Answer 1

[Tky]

There is the Ensembl API can convert the CDS coordinates to genomic coordinates. You can also do for cDNA with a similar API.

Before you start, you need to get the transcript ID first for your gene (in your case, FLT3). Suppose we use the isoform 1 of FLT3, the transcript ID will be ENST00000241453. Then just paste the bellowing to the browser

http://rest.ensembl.org/map/cds/ENST00000241453/2503..2503?content-type=application/json

---NOTE-THIS-PART---------------^^^^^^^^^^^^^^^-^^^^--^^^^

{"mappings":[{"assembly_name":"GRCh38","end":28018505,"seq_region_name":"13","gap":0,"strand":-1,"coord_system":"chromosome","rank":0,"start":28018505}]}

So your genomic location will be chr13:28018505.

I made a VCF line with this information

chr13    28018505    .    C    A    .    PASS    DP=8194;AF=0.074;NP=4;PV=0.0

Then I run the annovar, the output is FLT3:NM_004119:exon20:c.G2503T:p.D835Y. So should work, just need to pay attention the genomic coordinate is GRCh38 rather than hg19

[MAPK]

Thank you. Do you know any other tools (particularly in R) for batch submission?

[Tky]

I think you can user Json parser for R. I am mainly using Perl ;-)