Question: Convention for protein-level changes
0
gravatar for ognjen011
5 months ago by
ognjen011160
ognjen011160 wrote:

I have come to understand that G37 or Gly37 are changes to aminoacid Gly at position 37.

I ran into this paper: https://www.nature.com/articles/s41467-017-00257-5

What is PheSerTyr13?

nomenclature protein • 197 views
ADD COMMENTlink written 5 months ago by ognjen011160

From table 4 legend in paper you linked:

We identify independent associations for each category of variants: SNP, HLA (classical allele) and AA (HLA amino acid). For amino acid polymorphism, the label specifies the amino acid and the position. For example, ‘HLA-A Val95’ means amino acid Val at position 95 of the HLA-A protein

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax67k

Yes, but the specific multiple-amino-acids-in-a-position case is not addressed in that, no?

ADD REPLYlink written 5 months ago by RamRS21k
2
gravatar for RamRS
5 months ago by
RamRS21k
Houston, TX
RamRS21k wrote:

These invented notations rarely deserve to be called nomenclatures. You'd have better luck emailing the authors, as anything we might deduce would be accurate guesswork at best and a shot in the dark at worst.

My guess: it's a locus where the amino acid could be a Phe, a Ser or a Tyr. As in, it's a multiallelic nucleotide variant at the second base in a T [T/C/A] Y codon, with one of 3 possible nucleotides: T, C and A. TTY gives Phe, TCY gives Ser and TAY gives Tyr.

Y denotes pYrimidine (T or C)

ADD COMMENTlink modified 5 months ago • written 5 months ago by RamRS21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1157 users visited in the last hour