The exon of a variant

Question

[Dayna]

Hi every one

I have a very interesting variant, it aa.change is reported as :

SLC2A5:NM_001135585:exon3:c.C142T:p.Q48X,SLC2A5:NM_003039:exon3:c.C142T:p.Q48X,SLC2A5:NM_001328619:exon4:c.C142T:p.Q48X

So the cDNA change is c.C142T , p.Q48X. What does it mean to have 3 transcripts and 2 exons?

Thanks

Answer 1

[swbarnes2]

It means there are multiple transcripts reported for that gene, and in some transcripts, there are two exons upstream of the exon where your mutation sits, and in some transcripts, there are three.

Answer 2

[JC]

The gene has 3 transcripts (NM_001135585, NM_003039 and NM_001328619), in the first and second transcripts, your variant is in exon3, meaning that probably the transcripts have the same first three exons but are different at some point after that. The third transcript is different, and the variant even when seems to be in the same location, exon is the 4th. I guess some alternative splicing in the 5' UTR. You can view it here https://www.ncbi.nlm.nih.gov/gene/6518

[Dayna]

Thanks swbarnes2 and JC :)