However, non-MHC alleles such as a functional polymorphism (rs2476601, Arginine 620 Tryptophan, R620W) in protein tyrosine phosphatase non-receptor type 22 (PTPN22), which encodes the lymphoid PTP (LYP), was reported to be significantly associated with multiple autoimmune disorders including type 1 diabetes mellitus (T1DM; [8]), rheumatoid arthritis [9], SLE [10], Hashimoto thyroiditis [11], autoimmune thyroid disease [12] and Grave’s disease [13]. This evidence concerns the gene PTPN22 and Hashimoto thyroiditis.