I have done a DGE recently and have been looking at the DGE list. One of the genes is HLA-A. However, when I dug deeper I realised there are hundreds of HLA-A genes with unique ENSEMBL number (of course it's HLA...). A few other HLA-A genes also show up on the table but are not significant at all.

Considering the way Salmon deals with multimapping reads, can I assume these expressing genes are different enough that they shouldn't be consider the same? Or should the expression of all HLA-A genes considered as one single gene for the purpose of identifying differentially expressed genes?

I do understand that this may be more of a biological question than bioinformatics, but I also want to see if it is a practice pouring the HLA genes (or other variable genes/loci of similar nature) with different sequences together when doing DGE, and whether the statistics would be valid if I do so?