Table 3

SLE case-only recurrent non-synonymous SNVs

CHR	BP	SNV	Ref allele	Alt allele	Count SLE	Gene	Consequence	Amino acid change	SIFT
11	1 266 280	rs773068050	A	C	5	MUC5B	Missense variant	p.Thr2727Pro	Deleterious(0.05)
1	186 363 103	rs1292231132	C	A	4	C1orf27	Missense variant	p.Gln246Lys	Tolerated(0.21)
1	151 342 270	rs772030489	G	T	2	SELENBP1	Missense variant	p.Pro36Thr	Deleterious low confidence(0.01)
2	27 455 971	rs776014297	T	A	2	CAD	Missense variant	p.Met922Lys	Deleterious(0.04)
2	179 698 928	rs892049188	G	A	2	CCDC141	Missense variant	p.Ser1522Phe	Tolerated(0.08)
9	16 431 447	chr9:16 431 447	G	A	2	BNC2	Missense variant	p.His307Tyr	–
9	21 166 175	rs779242420	T	C	2	IFNA21	Missense variant	p.Tyr146Cys	Deleterious(0.01)
10	75 583 821	chr10:75 583 821	G	T	2	CAMK2G	Missense variant	p.His370Asn	Deleterious low confidence(0.03)
12	6 458 353	rs775543049	G	A	2	SCNN1A	Stop gained	p.Arg551*	–
12	48 482 728	rs750735162	T	C	2	SENP1	Missense variant	p.Thr155Ala	Deleterious low confidence(0)
12	56 350 882	rs1425141530	G	T	2	PMEL	Missense variant	p.Pro402His	Deleterious(0.02)
12	129 190 793	rs1386045604	C	G	2	TMEM132C	Missense variant	p.Pro1094Ala	Tolerated(0.21)
14	23 057 866	chr14:23 057 866	A	T	2	DAD1	Missense variant	p.Ser66Arg	Deleterious(0.04)
15	91 030 272	rs181919733	G	A	2	IQGAP1	Missense variant	p.Val1371Met	Tolerated(0.07)
17	41 143 320	rs1456586259	G	A	2	RUNDC1	Missense variant	p.Val477Ile	Tolerated(0.12)
19	4 891 395	rs139019426	T	C	2	ARRDC5	Missense variant	p.Gln231Arg	Tolerated(0.86)
19	18 273 781	rs777121279	G	A	2	PIK3R2	Missense variant	p.Gly372Ser	Deleterious(0)
19	55 240 959	rs764066889	G	A	2	KIR3DL3	Missense variant, splice region variant	p.Gly219Asp	Deleterious(0.02)

SIFT (Sorting Intolerant From Tolerant) prediction whether the amino acid substitution affects protein function.
BP, base pair; CHR, chromosome; SLE, systemic lupus erythematosus; SNV, single-nucleotide variant.