if I have a SNP on the cDNA level, how can I find the corresponding mutation on the protein level?

Question

[roanzaid]

If a mutation doesn't have an rs number (example; c.356A>C on the cDNA level, X chromosome) how can I find the corresponding amino acid change? Note that this is my first time working with annotated VCF files, my knowledge is very minimal on the subject.

[Ankit]

Hi.

Just simply annotate the VCF file. Use ANNOVAR or Snpeff. You can even upload the VCF to wANNOVAR, which will give you the annotated files. The anotated file will have both cDNA change and protein change.

Answer 1

[finswimmer]

Go to VEP and put in the gene name (or better the transcript id, otherwise the result might be ambigious) and variant description. One of the results you will receive will be the amino acid change.

A similar function is provided by mutalyzer.

[roanzaid]

It worked, thank you so much!