jfjlaros
commented
5 years ago Mutalyzer indeed detects that the insertion is in an intron, which makes the location of the insertion uncertain. The insersion could be deep inside the intron, or in one of the splice sites with distinct effects on the protein. Therefore a protein description can not be given. The best way to deal with this is to use a genomic reference sequence.
I tried a trick to force a protein description by modifying the description to:
NM_000207.2:c.188delinsAACCTGCTCTGCGCGGCACGTCCTGGCAGTThis results in the following protein description:
NM_000207.2(INS_i001):p.(Val63Glufs*78)Interestingly enough, this variant description is corrected to the original one.
As for your second remark, this is indeed a flaw in the syntax checker. We will address this in the next major release of Mutalyzer.
jtdendunnen
the consequence of a specific intronic variant is the insertion on RNA levele of 29 nucleotides. Since I wanted to check the predicted consequences at protein level but Mutalyzer does not support r. variant descriptions I tried the c. description NM_000207.2 :c.187_188insAACCTGCTCTGCGCGGCACGTCCTGGCAG. Unfortunately Mutalyzer gives p.? with a warning (Variant hits one or more splice sites in selected transcript). Please give the predicted protein description.
When I try NM_000207.2 :c.187_188insaacctgctctgcgcggcacgtcctggcag I get an error (Although the syntax of this variant is correct, the effect can not be analysed). This error is not correct, syntax is not OK (nucleotides should be in Capitals). I was disappointed Mutalyzer does not suggest NM_000207.2 :c.187_188insAACCTGCTCTGCGCGGCACGTCCTGGCAG as correct.