| | Gene | HGNC gene number | Autoimmune disease | References |
| Extended class I | OR2H2 | 8253 | SLE | [104] |
| Class I | RNF39 | 18064 | Behçet’s disease | [105] | TRIM39 | 10065 | Behçet’s disease | [105] | PSORS1 locus | 9573 | Systemic sclerosis, Psoriasis | [106–111] | MICA | 7090 | T1DM, AD, SLE | [112–114] | MICB | 7091 | SLE | [104] |
| Class III | BAT1–BAT5 | 13917–21 | Alzheimer’s, AIDS | [115, 116] | NFKBIL1 | 7800 | Sjögren’s syndrome, SLE, RA | [117, 118] | TNF Block | 11892 | Alzheimer’s, Psoriasis, Autoimmune hepatitis, Sarcoidosis | [115, 119–121] | AIF1 | 352 | T1DM | [122] | HSP70 genes | 5232–4 | MS | [123] | Complement genes | 1248, 1324, 1323 | SLE, myasthenia gravis, T1DM | [124–126] | SKIV2L | 10898 | SLE | [127] | ATF6B (CREBL1) | 2349 | SLE | [104] | NOTCH4 | 7884 | Systemic sclerosis | [128] | C6orf10 | 13922 | SLE | [104] | BTNL2 | 1142 | Ulcerative colitis, Sarcoidosis | [129, 130] |
| Class II | TAP2 | 44 | Psoriasis | [131] | PSMB8 | 9545 | Hypersensitivity pneumonitis | [132] | | | Psoriasis | [133] | TAP1 | 43 | Vitiligo | [134] | PSMB9 | 9546 | Psoriasis, Vitiligo | [133, 134] | HLA-DM | 4934, 4935 | Psoriasis, Antiphospholipid auto-antibodies, RA, SLE, T1DM | [131, 135–138] | HLA-DO | 4936, 4937 | common variable immunodeficiency | [139] |
| Class II Extended | HSD17B8 | 3554 | SLE | [104] | DAXX | 2681 | MS | [140] |
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Abbreviations: (HGNC) HUGO Gene Nomenclature Committee (http://www.genenames.org/); (SLE) systemic lupus erythematosus; (AIDS) acquired immune deficiency syndrome; (T1DM) type 1 diabetes mellitus; (AD) Addison’s disease; (RA) rheumatoid arthritis; (MS) multiple sclerosis, PSORS1 psoriasis locus genes (CDSN, PSORS1C1, PSORS1C2, CCHCR1, POU5F1, PSORS1C3), TNF Block genes (LTA, TNF, LTB, LST1), HSP70 genes (HSPA1L, HSPA1A, HSPA1B), Complement genes (C2, C4B, C4A).
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