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Kidney stone disease is a complex disorder with a strong genetic component. We conducted a genome-wide association study of 28.3 million sequence variants detected through whole-genome sequencing of 2,636 Icelanders that were imputed into 5,419 kidney stone cases, including 2,172 cases with a history of recurrent kidney stones, and 279,870 controls. We identify sequence variants associating with kidney stones at  ALPL  (rs1256328[T], odds ratio (OR)=1.21,  P =5.8 × 10 −10 ) and a suggestive association at  CASR  (rs7627468[A], OR=1.16,  P =2.0 × 10 −8 ). Focusing our analysis on coding sequence variants in 63 genes with preferential kidney expression we identify two rare missense variants SLC34A1 p.Tyr489Cys (OR=2.38,  P =2.8 × 10 −5 ) and TRPV5 p.Leu530Arg (OR=3.62,  P =4.1 × 10 −5 ) associating with recurrent kidney stones. We also observe associations of the identified kidney stone variants with biochemical traits in a large population set, indicating potential biological mechanism.

Common and rare variants associated with kidney stones and biochemical traits