MuPeXI finds peptide in a transcript which is labeled as "Nonsense mediated decay"

[gilhornung]

Dear Anne-Mette,

I came across an issue in MuPeXI.
I have a mutation in 3:48605804 (GRCH38, see below for full vcf line), which occurs in the gene UQCRC1.
MuPeXI finds peptides in the ENST00000415995 transcript, which is actually a "Nonsense mediated decay" transcript, based on its ensembl annotation. Obviously, it should not be considered as a source for peptides.

All the best,

Gil

vcf line:

3       48605804        .       C       T       122.87  PASS    .       GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1  0/1:179,62:0.257:.:.:.:.:.:.     0/0:121,0:0:.:.:.:.:.:.

one of the peptides in the mupexi file:

HLA-C06:02	.G.......	6.5456	0.025697	9511.3	3.6350	0.153380	MRQATFWSI	0.2283	0.408440	223.3	0.0797	0.500108	ENSG00000010256	ENST00000415995	G/R	0.257	1	2	3	48605804	43	M	UQCRC1	No	No	0.411875	9.998579e-01	1.346961e-10	0.4714048	12