Command line VEP "Amino_acid" Output Column Inturperation: AA / AA * AA

Question

[jon.klonowski]

I am trying to understand the "Amino_acid" column annotation output by VEP.

I could only find that ensembl/VEP says "Amino_acids : Reference and variant amino acids" but the example is simple: "M/T".

The annotation I am interested in looks more like: R/R*X

V/VKDR*AX

S/R*X

[cpad0112]

I could only find that ensembl/VEP says "Amino_acids : Reference and variant amino acids" but the example is simple: "M/T".

Post the link for this documentation.

R/R*X

Can you elaborate this syntax?

For better understanding, you can force VEP to output HGVS representation of changes.

Answer 1

[Ben Moore]

Hi jon.klonowski,

The letters are the single letter IUPAC amino acid code: https://www.bioinformatics.org/sms/iupac.html

Where the * indicates a STOP codon and X indicates an unknown amino acid. The alternate amino acids returned in the VEP output will be calculated using the alleles you have supplied in the input data.

[jon.klonowski]

Thank you. IUPAC for all the AA other than Terminal codon and unknown AA. The Terminal codon annotation is same as HGVS. Was unfamiliar with the "unknown codon" annotation.

Thanks much!