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Nephrolithiasis is a common nephrologic disorder with complex etiology. To identify the genetic factor(s) for nephrolithiasis, we conducted a three-stage genome-wide association study (GWAS) using a total of 5,892 nephrolithiasis cases and 17,809 controls of Japanese origin. Here we found three novel loci for nephrolithiasis:  RGS14-SLC34A1-PFN3-F12  on 5q35.3 (rs11746443;  P  = 8.51×10 −12 , odds ratio (OR) = 1.19),  INMT-FAM188B-AQP1  on 7p14.3 (rs1000597;  P  = 2.16×10 −14 , OR = 1.22), and  DGKH  on 13q14.1 (rs4142110;  P  = 4.62×10 −9 , OR = 1.14). Subsequent analyses in 21,842 Japanese subjects revealed the association of SNP rs11746443 with the reduction of estimated glomerular filtration rate (eGFR) ( P  = 6.54×10 −8 ), suggesting a crucial role for this variation in renal function. Our findings elucidated the significance of genetic variations for the pathogenesis of nephrolithiasis.

A Genome-Wide Association Study of Nephrolithiasis in the Japanese Population Identifies Novel Susceptible Loci at 5q35.3, 7p14.3, and 13q14.1