Table 1.

Selected Non-HLA genes implicated in SS.

Pathway	Gene	Gene Function	Reference
T cell function and signalling
	PTPN22	T-cell receptor and B-cell receptor signalling	[90]
	CTLA4	negative regulator of the T cell function and thereby maintains peripheral tolerance	[91]
	GTF2IRD1-GTF2I	GTF2IRD1- Function not established GTF2I -general transcription factor IIi (TFII-I), important for transcription and signal transduction in T cells and B cells	(92)
	STAT4	Transcription factor regulating T-cell function	[19,92–97]
	TCRBV	T cell Receptor	[98]
B cell function and signalling
	BLK	Non-receptor tyrosine kinase involved in B-cell receptor signaling and B-cell development	[19]
	FAM167A-BLK	FAM167A- not established	(93)
	EBF-1	Transcription factor for B cell development	[93]
	BAFF	B-cell activating factor, crucial for B cell maturation	[99]
Antigen presentation, processing and costimulation
	Ro-52	Autoantigen	[100,101]
	TAP2	Antigen Processing	[102]
	CD40	Costimulatory molecule on B cells, other antigen presenting cells	[93]
	CD14	Pattern recognition receptor	[93]
	TNFSF4/OX40L	Cytokine expressed on multiple immune cells Binds to TNFRSF4 resulting in T-cell proliferation and cytokine production.	[93]
Cytokine, related factors and receptors
	IL-10	Anti-inflammatory	[103–105]
	IL-4 receptor alpha (IL-4Rα)	Cytokine of Th2 pathway	[106]
	IRF5(Interferon regulatory factor 5)	Transcription factor regulating IFN production	[19,92,107,108]
	IRF5-TNPO3	Transcription factor regulating IFN production	[93]
	IL-12 A	Important cytokine of Th1 pathway	[19]
	TNF-α	Pro-inflammatory	[109]
Chemokine Receptor
	CXCR5	Receptor for CXC chemokine ligand 13 Crucial for B cell homing and lymphoid follicle organisation	[19]
NFkB signalling
	IkBα	Inhibitor of NFkB	[110]
	TNFAIP3	Inhibitor of NFkB	[95]
	TNIP1	Inhibitor of NFkB	[19]
Miscellaneous
	FCGR	Bind to Fc portion of IgG Copy number variation decreases clearance of immune complexes	[111]
	MBL	Activates third pathway of complement	[112]
	NCR3	NK-cell-activating receptor NK cell–specific receptor interaction with with B7-H6 on SGEC causes INFγ release	[33]
	ApoE	Regulates inflammation	[113]
	Fas	Apoptosis	[114]
	MECP2	DNA methylation-induced transcription silencing	[115]
	CHRM3	Muscarinic receptor 3	[116]
	GST	Glutathione S-transferase prevents oxidative damage	[117]

PTPN22- Protein tyrosine phosphatase, non-receptor type 22

CTLA4 -Cytotoxic T lymphocyte–associated antigen 4

GTF2IRD1-GTF2I- General transcription factor Iii/GTF2I repeat domain containing 1

STAT4 -Signal transducer and activator of transcription 4

TCRBV - T cell receptor b variable

BLK- B lymphocyte kinase

FAM167A-BLK Family with Sequence Similarity 167, Member A

EBF-1 Early B-cell factor 1

BAFF B-cell activating factor

TAP2 Transporters associated with antigen processing

TNFSF4/OX40L- Tumor necrosis factor (ligand) superfamily, member 4

IRF5 -Interferon regulatory factor 5

TNF-α Tumor necrosis factor-α

CXCR5 Chemokine (C-X-C motif) receptor 5

TNFAIP3 Tumor necrosis factor, alpha-induced protein 3

TNIP1-- TNFAIP3-interacting protein 1

FCGR Immunoglobulin gamma Fc region receptor II-b

MBL Mannose-binding lectin

NCR3-- Natural-cytotoxicity-triggering receptor 3

MECP2 Methyl CpG binding protein 2

CHRM3 Muscarinic receptor 3

GST-Glutathione-S-transferase