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Background  Previous studies have confirmed a family risk of nephrolithiasis (NL), but only 15% of all cases are associated with an identified monogenic factor. In clinical practice, our group encountered a patient with NL combined with cystic kidney disease that had 3 affected family members. No known mutations association with NL was detected in this family, and thus further investigation of the molecular cause of NL was deemed to be necessary.    Results  Quality analysis from the sequencing stage showed a more than 80-fold average depth and 95% coverage for each sample, and six mutations within six genes were chosen as candidate variants for further validation. Genotyping of rs182089527in the phosphodiesterase 1A ( PDE1A ) gene in the validation cohort indicated that the alternative allele was present in 15 patients with heterozygosity and in 1 patient with homozygosity, and exhibited significant enrichment in NL patients (Fisher’s exact test, adjusted  p  = 0.0042) and kidney cystic patients (Fisher’s exact test, adjusted  p  = 0.067) compared to controls. In addition, function analysis displayed a significant decrease in the protein and mRNA expression levels resulting from the rs182089527 mutant sequence compared with the wild-type sequence. Moreover, patients with this mutation displayed a high level of creatinine and urea in urinalysis.    Conclusions  Our study provides genetic evidence that the rs182089527 mutation in  PDE1A  is involved in the development of NL and kidney cysts, which should help to improve personalized medicine for diagnosis and treatment.    Electronic supplementary material  The online version of this article (dio: 10.1186/s12864-017-4247-8) contains supplementary material, which is available to authorized users.

PDE1A polymorphism contributes to the susceptibility of nephrolithiasis