Question

convert CDS mutation to Amino acid mutations and obtain genomic coordinates

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4.5 years ago

kaurravneet4123 ▴ 20

I have a dataset of CDS_Mutations. I want to convert CDS_Mutations to AA_Mutations and obtain their genomic coordinates. Kindly if someone can guide me on how to do this. Many thanks.

SNP • 1.7k views

ADD COMMENT • link 4.5 years ago by kaurravneet4123 ▴ 20

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What format are they in? Can you show us a single line of the file, please?

ADD REPLY • link 4.5 years ago by Emily 23k

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In an excel file, I have columns of Gene name, CDS Mutation

Please see an example below:

TP53    c.672+62A>G 
CTNNB1  c.14015G>A  
HIST1H3B    c.*10C>T

And I want to find the AA mutations and genomic coordinates for each of the CDS mutations.

ADD REPLY • link updated 4.5 years ago by GenoMax 141k • written 4.5 years ago by kaurravneet4123 ▴ 20

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Many thanks, Emily. I will try VEP tool.

ADD REPLY • link 4.5 years ago by kaurravneet4123 ▴ 20

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Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

ADD REPLY • link 4.5 years ago by GenoMax 141k

score 0 · Answer 1 · 2019-10-22

You can use the data you have as HGVS input for the Ensembl VEP. That will give you amino acid substitutions, genomic coordinates and a bunch of other information. Since you only have gene names, and not versioned transcript IDs, your variants are somewhat ambiguous, as the VEP has to work out what transcript you're referring to, and it may get it wrong. This blog post talks about protein HGVS but the stuff about transcript choice is relevant here too.