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

[Thomas Danhorn]

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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