[ensembl-dev] why the frameshift variants are represented with 'X' as the aminoacid change?

David Tamborero david.tamborero at gmail.com
Wed Dec 5 16:25:19 GMT 2018


thank you, my (our) ignorance here.

thanks again!
d

El mié., 5 dic. 2018 a las 17:22, Thomas Danhorn (<danhornt at njhealth.org>)
escribió:

> Hi David,
>
> I don't know what clinicians do, but the IUPAC codes for amino acids (see
> e.g. http://www.bioinformatics.org/sms2/iupac.html and
>
> https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes)
>
> have "X" for "any amino acid", analogous to the "N" used for "any
> nucleotide".  This has been standard (at least in basic science) for a
> long time.
>
> Best regards,
>
> Thomas
>
>
> On Wed, 5 Dec 2018, David Tamborero wrote:
>
> > Hi Andrew,
> >
> > thanks for the answer!
> >
> > Indeed I m aware that you use * or Ter for stop codons; I m just a bit
> > surprised that you use 'X' (some old school people confuses it with the
> > stop codon, e.g. clinicians) instead of a 'fs' label or similar, which in
> > my humble opinion is more self-explanatory (but this can be due to my
> > ignorance of whether 'X' is accepted for that, although --regardless of
> > possible standards I do not know-- that I m finding several people that
> > gets confused by that is a fact!)
> >
> > br
> > d
> >
> > El mié., 5 dic. 2018 a las 12:54, Andrew Parton (<aparton at ebi.ac.uk>)
> > escribió:
> >
> >> Hi David,
> >>
> >> We use X to describe a partial codon - to refer to a stop codon we use
> >> either * or Ter.
> >>
> >> Kind Regards,
> >> Andrew
> >>
> >>> On 5 Dec 2018, at 11:04, David Tamborero <david.tamborero at gmail.com>
> >> wrote:
> >>>
> >>> Hi there,
> >>>
> >>> I m realizing that when inputing a frameshift genomic variant, VEP
> >> annotates the corresponding protein change using 'X' as the alt
> aminoacid
> >> (is not 'X' normally refering to the stop codon?)
> >>>
> >>> e.g. 8_90967511_CT/C  results in NBN p.466 R/X, but I will expect to
> >> have something like R466Gfs*18
> >>>
> >>> thanks!
> >>> d
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