Convert mouse amino acid location to genomic location

Question

[L. A. Liggett]

I have amino acid positions for a number of mouse mutations, for example DNMT3a R878H. Is there a way to convert this to a genome coordinate such aschr12:12345?

The Ensembl Rest API seems to be capable of such a task, and when I make a call for a human change it works as shown here:

https://rest.ensembl.org/map/translation/ENSP00000288602/100..300?content-type=application/json

But when trying to change the gene to mouse the call no longer works.

[Pierre Lindenbaum]

duplicate Amino Acid Change To Genomic Location ; Convert Amino Acid Change To Chromosomal Snp Coordinate ; Finding A Mutation Coordinate From Mutation Nomenclature And Gene Name ; ...

[L. A. Liggett]

Thanks Pierre, I did have a look at this but it is unclear how to perform such an analysis for mouse. It looks like the Ensembl API might be able to do it as illustrated here, but how to switch from human to mouse is not clear to me.

[Ram]

Give VEP a shot

[L. A. Liggett]

This doesn't seem to work for me either. I am trying to get the coordinates for the mouse DNMT3a R878H mutation in the question like this:

https://rest.ensembl.org/vep/human/hgvs/ENSMUSG00000020661:p.Arg878His?content-type=application/json

But this will not return anything.

[Ram]

1. Your URL contains human, not mouse/mus_musculus
2. The URL contains gene id followed by protein change, which is an entity mismatch.

This works:

https://rest.ensembl.org/vep/mus_musculus/hgvs/ENSMUSP00000020991:p.Arg878His?content-type=application/json

[Arup Ghosh]

"ENSMUSP00000020991" is actually protein id of "ENSMUSG00000020661".

[Ram]

Indeed. That's how I built the working URL from the "broken" URL

[L. A. Liggett]

This works great! But how did you find the protein id instead of the gene id?

[Ram]

1. Google the gene id to get to the ENSG entry
2. Expand the transcript table and ensure the "Translation ID" column is displayed
3. Everything is now available in a single view: