[ensembl-dev] protein position column for indels
David Tamborero
david.tamborero at gmail.com
Thu Jul 25 16:11:20 BST 2019
Hi ensembl devs,
I m struggling to fully understand how the 'protein position' column is
calculated when I check the variant hgvsp representation
this happens only for indels; some examples (left=hgvsp entry;
right=protein position entry):
frameshift:
ENSP00000277541.6:p.Gln2444ThrfsTer34 2444
ENSP00000256474.2:p.Lys159ArgfsTer14 158-159
ENSP00000324856.6:p.Tyr253SerfsTer32 252-254
inframe deletions:
ENSP00000356379.4:p.Tyr1373del 1373-1374
ENSP00000361824.3:p.Glu2207del 2207
ENSP00000339004.3:p.His57del 53-54
ENSP00000268125.5:p.Phe96_Phe99del 96-99
ENSP00000413720.3:p.Ala171_Ala174del 171-175
ENSP00000368332.4:p.Ala114_Ala115del 110-112
inframe insertions:
ENSP00000369497.3:p.Glu238_Ser239insArg 239
ENSP00000339867.2:p.Asp687_Gly688insPhe 687-688
ENSP00000445920.1:p.Val188_Ala192dup 188-192
ENSP00000361824.3:p.Arg2308_Met2309dup 2308-2310
I m guessing that this may be related in part to right/left alignement
discrepancies in the reported coordinates between these two columns (e.g.
ENSP00000368332.4:p.Ala114_Ala115del --> 110-112 or
ENSP00000339004.3:p.His57del ---> 53-54) ?
and that there is certain issue that sometimes makes you report in the
protein column 'n' or 'n+1' positions -where n is the number of affected
residues according to the HGVSp (e.g.
ENSP00000277541.6:p.Gln2444ThrfsTer34-->2444 or
ENSP00000445920.1:p.Val188_Ala192dup -- > 188-192 report 'n' whereas
ENSP00000413720.3:p.Ala171_Ala174del -->171-175 or
ENSP00000368332.4:p.Ala114_Ala115del-->110-112 report 'n+1')?
apologies if this is documented somewhere, i ve been not able to find the
details of that entry
thanks in advance!
d
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