Gene panel sequencing identifies a likely monogenic cause in 7% of 235 Pakistani families with nephrolithiasis

• Published in: Human genetics 2019-03, Vol.138 (3), p.211-219
• Main Authors: Amar, Ali, Majmundar, Amar J., Ullah, Ihsan, Afzal, Ayesha, Braun, Daniela A., Shril, Shirlee, Daga, Ankana, Jobst-Schwan, Tilman, Ahmad, Mumtaz, Sayer, John A., Gee, Heon Yung, Halbritter, Jan, Knöpfel, Thomas, Hernando, Nati, Werner, Andreas, Wagner, Carsten, Khaliq, Shagufta, Hildebrandt, Friedhelm
• Format: Article
• Language: English
• Subjects: Adolescent; Adult; Aged; Alleles; Animals; Biomedical and Life Sciences; Biomedicine; Child; Child, Preschool; Cohort Studies; Consanguinity; DNA Mutational Analysis; Family; Family medical history; Female; Gene Expression Profiling - methods; Gene Function; Genes; Genetic analysis; Genetic Association Studies; Genetic Predisposition to Disease; Genotype; Geography, Medical; High-Throughput Nucleotide Sequencing; Hospitals; Human Genetics; Humans; Infant; Male; Medical schools; Metabolic Diseases; Middle Aged; Molecular Medicine; Morbidity; Mutation; Nephrolithiasis; Nephrolithiasis - epidemiology; Nephrolithiasis - genetics; Novels; Original Investigation; Pakistan - epidemiology; Phosphate transporter; Phosphates; Sodium; Sodium-Phosphate Cotransporter Proteins, Type IIa - genetics; Surveys; Xenopus laevis; Young Adult
• ISSN: 0340-6717; 1432-1203
• DOI: 10.1007/s00439-019-01978-x

Nephrolithiasis (NL) affects 1 in 11 individuals worldwide and causes significant patient morbidity. We previously demonstrated a genetic cause of NL can be identified in 11–29% of pre-dominantly American and European stone formers. Pakistan, which resides within the Afro-Asian stone belt, has a high prevalence of nephrolithiasis (12%) as well as high rate of consanguinity (> 50%). We recruited 235 Pakistani subjects hospitalized for nephrolithiasis from five tertiary hospitals in the Punjab province of Pakistan. Subjects were surveyed for age of onset, NL recurrence, and family history. We conducted high-throughput exon sequencing of 30 NL disease genes and variant analysis to identify monogenic causative mutations in each subject. We detected likely causative mutations in 4 of 30 disease genes, yielding a likely molecular diagnosis in 7% (17 of 235) of NL families. Only 1 of 17 causative mutations was identified in an autosomal recessive disease gene. 10 of the 12 detected mutations were novel mutations (83%). SLC34A1 was most frequently mutated (12 of 17 solved families). We observed a higher frequency of causative mutations in subjects with a positive NL family history (13/109, 12%) versus those with a negative family history (4/120, 3%). Five missense SLC34A1 variants identified through genetic analysis demonstrated defective phosphate transport. We examined the monogenic causes of NL in a novel geographic cohort and most frequently identified dominant mutations in the sodium–phosphate transporter SLC34A1 with functional validation.