Question: Convention for protein-level changes
0
gravatar for ognjen011
18 months ago by
ognjen011200
ognjen011200 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 • 322 views
ADD COMMENTlink written 18 months ago by ognjen011200

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 18 months ago • written 18 months ago by genomax84k

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

ADD REPLYlink written 18 months ago by RamRS27k
2
gravatar for RamRS
18 months ago by
RamRS27k
Houston, TX
RamRS27k 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 18 months ago • written 18 months ago by RamRS27k
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