It looks like there is strong evidence suggesting that a particular mutation on a HLA gene leads to a change in the protein molecule resulting in T-cells enriched that cause autoimmunity. The authors also think this could provide clues for a cure. An excerpt:
Now, in the new study the researchers found that diabetes-causing mutations changed the charge at one end of the MHC peptide-binding
groove. In individuals not predisposed to type 1diabetes, MHC molecules
usually have a negatively charged residue at position 57. In contrast,
disease-causing MHC molecules have a neutral residue at position 57 and
consequently the surrounding region is more positively charged.
The result of this molecular change was that the mutated MHC molecules
selected a unique subset of T cells that bound to it strongly, with
“higher affinity.” These T cells may overreact and potentially
misidentify “self” peptides as dangerous rather than harmless.