Protein variant notation for an inserted stop codon?

Question

[alex.rubinsteyn]

How do I annotate the protein effect of an in-frame insertion of a "TAG" stop codon inside a cDNA sequence?

Typically, I would annotate an insertion with something like: p.K2_L3insQ (insert a glutamine between the lysine at position 2 and the leucine at position 3). If the inserted sequence resulted in a stop codon, should I annotate it as p.K2_L3insX (or p.K2_L3ins*)? Alternatively, I can imagine a notation like p.K2K*. Are either of these standard or is something else used altogether?

Answer 1

[Devon Ryan]

At the protein level, you're not inserting a stop, you're either converting an amino acid into a stop or performing a deletion. So p.L3* is what would typically be used.

Edit: BTW, the deletion version of this would be something like p.L3_K123del, assuming K123 was the last amino acid.