Table 1 |.

Select gene variants linked to SLE and suggested function

Gene	Function	Ref.
IRF5 (promoter variants)	Increased expression, which leads to induction of proinflammatory cytokines and the definition of an inflammatory macrophage phenotype	126
IRF7 (single SNP)	Increased production of type I IFN by DCs	127
STAT4	Binds the transcription factor HMGA1; shared with rheumatoid arthritis	128
STAT1	Increased binding to a variant of the transcription factor ETS1	129
PRDM1	Linked to increased production of IL-6 and cathepsin S (needed for loading peptides into MHC-II)	16,17
IKZF1	Involved in the expression of C1QB and five type I IFN–response genes	130
Fc receptor genes	Clearance of apoptotic cells and immune complexes; antibody-mediated cell cytotoxicity	131
C1q, C4	Clearance of apoptotic cells; negative immune selection	132
C4	Decreased number of copy variants is linked to SLE	133
FCGR3B	Decreased number of copy variants is linked to SLE	134
NCF1	Decreased number of copies predispose to, whereas increased protects against, SLE	135
ITGAM	Impaired phagocytosis of complement-opsonized targets in monocytes, neutrophils and macrophages	136
NCF2	Essential to LC3-associated phagocytosis	137
ATG5, PRKCD, NCF1	Essential for autophagy	137
TLR7	Increased IFN-α production
TNFAIP3	Encodes the deubiquitinating enzyme A20, which is involved in the termination of NF-κB signaling; A20-deficient mice develop severe autoinflammatory disease	138,139
PTPN22	Expansion of effector and memory T cells and increased production of IFN-γ, TNF and GM-CSF	140
Major histocompatibility antigens
HLA-DR2 and HLA-DR3	Contributes to SLE in Europeans	134
HLA-DRB1*15:01 and HLA-DQB1*6:02	Contributes to SLE in Asians	141
HLA-DR3 and HLA-DR15	Contributes to SLE across all ancestries	6
BANK1 and BLK	Interaction between the SLE-associated variants	142
IgG1	A knockin mouse with a patient-identified IgG1 SNP developed lupus	143
APOL1	Linked to lupus nephritis	144
VGLL3	Sex-biased transcription factor	27