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?
•
written
by
alex.rubinsteyn
1 answer
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.
•
written
by
Devon Ryan
Log in to answer this question.
-
Inquiry related to vcf file and formatting
written by rheab1230 •
-
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
written by Sinji
-
Confusing HGVS notation for RNA changes
written by Ram
-
Tutorial: Leveraging Flow Order And Flow Signals From Ion Torrent Data
written by Biostar User •
