Table 2

Rare and low-frequency variants associated with T1DM, T2DM and other autoimmune diseases

Disease	Gene/Locus	Method	Reference
T1DM	IFIH1	Candidate gene sequencing	23
	PTPN22	Targeted deep sequencing	22
	STK39 LRP1B	Deep imputation of genotyped data	13
	TYK2 RBM17	Fine mapping of T1DM risk loci	20
T2DM	CCND2 PAM PDX1	WGS and imputation	80
	Xq23 EHMT2	Reanalysis of data from GWAS	81
	GLP1R G6PC2	HumanExome BeadChip	82
	SGSM2 MADD TBC1D30 KANK1	Analysis of exome array data	83
	PPARG	Targeted gene sequencing	84
RA	IL2RA IL2RB	Candidate gene sequencing	85
	TYK2	Immunochip	86
SLE	BLK	Genotyping	87
	TREXI	Genotyping	88
IBD	IL23R	Candidate gene sequencing	89
	NOD2	Candidate gene sequencing	90 91
	PRDM1	WES	92
	CARD9 RNF186	Targeted gene sequencing	93

GWAS, genome-wide association study; IBD, inflammatory bowel disease; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus; T1DM, type 1 diabetes mellitus; T2DM, type 2 diabetes mellitus; WES, whole-exome sequencing; WGS, whole-genome sequencing.