Whole-exome sequencing reveals genetic variants associated with chronic kidney disease characterized by tubulointerstitial damages in North Central Region, Sri Lanka

Table 1 Association study for the SNPs isolated in whole-exome analysis

	SNP	Location	Gene	Transcript	HGVS coding	HGVS protein	Exome sequencing		Direct sequencing		P QTL Analysis (dichotomous analysis)	OR (slope)
							MAF
							Cases (n = 8)	Controls (n = 8)	Cases (n = 301)	Controls (n = 276)
1	rs2298668	11:82564294	PRCP	NM_005040	c.336A > C	E112D	0.313	0.063	0.207	0.224	0.42 (0.10)	1.12 (4.26)
2	–	11:82564317	PRCP	NM_005040	c.313T > A	F105I	0.063	0.063	0.046	0.033	0.23 (0.25)	1.45 (−6.33)
3	–	3:49161024	LAMB2	NM_002292	c.3838G > A	E1280K	0.063	0	0.003	0	(0.18)	(−34.09)
4	–	3:49161375	LAMB2	NM_002292	c.3583G > T	G1195W	0.063	0	0.008	0	0.24 (0.69)	(14.65)
5	rs34759087	3:49162284	LAMB2	NM_002292	c.2959G > A	E987K	0.188	0.125	0.110	0.104	0.70 (0.89)	1.07 (0.46)
6	–	3:49165978	LAMB2	NM_002292	c.1931G > A	R644H	0.063	0	0.002	0	(0.73)	(12.26)
7	rs2304456	3:186445052	KNG1	NM_000893	c.591T > G	I197M	0.313	0.063	0.313	0.278	0.22 (0.04)	1.17 (−4.73)
8	rs62321738	4:102816467	BANK1	NM_001127507	c.510C > G	S170R	0.313	0.063	0.133	0.129	0.80 (0.93)	1.05 (−0.027)
9	rs34970857	1:111060752	KCNA10	NM_005549	c.658G > A	V220M	0.250	0	0.133	0.084	0.005 (0.06)	1.74 (−6.48)
10	rs9656982	8:87226700	SLC7A13	NM_138817	c.1355T > C	M452T	0.375	0.188	0.127	0.164	0.08 (0.23)	1.33 (3.53)
11	rs7179270	15:30018627	TJP1	NM_003257	c.2368A > G	I790V	0.563	0.250	0.250	0.292	0.12 (0.32)	1.22 (2.38)

Chr chromosome, MAF minor allele frequency, OR odds ratio, QTL quantitative trait analysis

ISSN: 1347-4715