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

[David Tamborero]

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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