Genetic and protein structure prediction analyses identify a rare pathogenic PKD1 variant causing autosomal dominant polycystic kidney disease.

Autosomal dominant polycystic kidney disease (ADPKD) is one of the most common monogenic kidney disorders. The diagnosis of ADPKD requires imaging findings showing multiple kidney cysts or genetic testing, in cases where a family history is unknown. We report a patient diagnosed with ADPKD based on the identification of a rare PKD1 variant. The patient was a 41-year-old female in whom cysts and calcification in the kidneys were incidentally detected. Whole-exome sequencing identified a rare PKD1 variant (NM_001009944.3: c.11557G > A/p.E3853K). Protein structure prediction of the PKD1-PKD2 complex showed that the variant may be pathogenic, leading to the diagnosis of autosomal dominant polycystic kidney disease. A detailed family history revealed that her relatives also had ADPKD, further supporting the diagnosis of ADPKD. Comprehensive genetic analysis and protein structure prediction led to the diagnosis of ADPKD and the identification of rare causative genes. These methods are useful for diagnosing hereditary kidney diseases of unknown etiologies.