Springer Nature is making Coronavirus research free. View research | View latest news | Sign up for updates

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

  • 580 Accesses

  • 2 Citations


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.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3
Fig. 4


  1. Beck L, Karaplis AC, Amizuka N, Hewson AS, Ozawa H, Tenenhouse HS (1998) Targeted inactivation of < em> Npt2</em> in mice leads to severe renal phosphate wasting, hypercalciuria, and skeletal abnormalities. Proc Natl Acad Sci 95:5372.

  2. Beckmann JS (1996) The Réunion paradox and the digenic model. Am J Hum Genet 59:1400–1402

  3. Braun DA, Lawson JA, Gee HY, Halbritter J, Shril S, Tan W, Stein D, Wassner AJ, Ferguson MA, Gucev Z et al (2016a) Prevalence of monogenic causes in pediatric patients with nephrolithiasis or nephrocalcinosis. Clin J Am Soc Nephrol 11:664–672

  4. Braun DA, Schueler M, Halbritter J, Gee HY, Porath JD, Lawson JA, Airik R, Shril S, Allen SJ, Stein D et al (2016b) Whole exome sequencing identifies causative mutations in the majority of consanguineous or familial cases with childhood-onset increased renal echogenicity. Kidney Int 89:468–475

  5. Daga A, Majmundar AJ, Braun DA, Gee HY, Lawson JA, Shril S, Jobst-Schwan T, Vivante A, Schapiro D, Tan W et al (2017) Whole exome sequencing frequently detects a monogenic cause in early onset nephrolithiasis and nephrocalcinosis. Kidney Int 93:204–213

  6. Fearn A, Allison B, Rice SJ, Edwards N, Halbritter J, Bourgeois S, Pastor-Arroyo EM, Hildebrandt F, Tasic V, Wagner CA et al (2018) Clinical, biochemical, and pathophysiological analysis of SLC34A1 mutations. Physiol Rep 6:e13715

  7. Germino G, Kirkali Z (2015) "Opening Remarks." Urinary stone disease research challenges and opportunities meeting minutes. National Institute of Diabetes and Digestive and Kidney Diseases. NIH Campus; Natcher Conference Center; Building 45, Auditorium; Bethesda

  8. Halbritter J, Diaz K, Chaki M, Porath JD, Tarrier B, Fu C, Innis JL, Allen SJ, Lyons RH, Stefanidis CJ et al (2012) High-throughput mutation analysis in patients with a nephronophthisis-associated ciliopathy applying multiplexed barcoded array-based PCR amplification and next-generation sequencing. J Med Genet 49:756

  9. Halbritter J, Porath JD, Diaz KA, Braun DA, Kohl S, Chaki M, Allen SJ, Soliman NA, Hildebrandt F, Otto EA (2013) Identification of 99 novel mutations in a worldwide cohort of 1,056 patients with a nephronophthisis-related ciliopathy. Hum Genet 132:865–884

  10. Halbritter J, Baum M, Hynes AM, Rice SJ, Thwaites DT, Gucev ZS, Fisher B, Spaneas L, Porath JD, Braun DA et al (2015) Fourteen monogenic genes account for 15% of nephrolithiasis/nephrocalcinosis. J Am Soc Nephrol 26:543–551

  11. Overall ADJ, Ahmad M, Thomas MG, Nichols RA (2003) An analysis of consanguinity and social structure within the UK asian population using microsatellite data. Ann Hum Genet 67:525–537

  12. Prié D, Ravery V, Boccon-Gibod L, Friedlander G (2001) Frequency of renal phosphate leak among patients with calcium nephrolithiasis. Kidney Int 60:272–276

  13. Prié D, Huart V, Bakouh N, Planelles G, Dellis O, Gérard B, Hulin P, Benqué-Blanchet F, Silve C, Grandchamp B et al (2002) Nephrolithiasis and osteoporosis associated with hypophosphatemia caused by mutations in the type 2a sodium–phosphate cotransporter. N Engl J Med 347:983–991

  14. Rajagopal A, Braslavsky D, Lu JT, Kleppe S, Clément F, Cassinelli H, Liu DS, Liern JM, Vallejo G, Bergadá I et al (2014) Exome sequencing identifies a novel homozygous mutation in the phosphate transporter SLC34A1 in hypophosphatemia and nephrocalcinosis. J Clin Endocrinol Metab 99:E2451–E2456

  15. Richard I, Broux O, Allamand V, Fougerousse F, Chiannilkulchai N, Bourg N, Brenguier L, Devaud C, Pasturaud P, Roudaut C et al (1995) Mutations in the proteolytic enzyme calpain 3 cause limb-girdle muscular dystrophy type 2A. Cell 81:27–40

  16. Rizvi SAH, Naqvi SAA, Hussain Z, Hashmi A, Hussain M, Zafar MN, Mehdi H, Khalid R (2002) The management of stone disease. BJU Int 89:62–68

  17. Romeo G, Bittles AH (2014) Consanguinity in the contemporary world. Hum Hered 77:6–9

  18. Rule AD, Bergstralh EJ, Melton LJ, Li X, Weaver AL, Lieske JC (2009) Kidney stones and the risk for chronic kidney disease. Clin J Am Soc Nephrol 4:804–811

  19. Sadowski CE, Lovric S, Ashraf S, Pabst WL, Gee HY, Kohl S, Engelmann S, Vega-Warner V, Fang H, Halbritter J et al (2015) A single-gene cause in 29.5% of cases of steroid-resistant nephrotic syndrome. J Am Soc Nephrol 26:1279–1289

  20. Scales CD, Smith AC, Hanley JM, Saigal CS (2012) Prevalence of kidney stones in the United States. Eur Urol 62:160–165

  21. Schlingmann KP, Ruminska J, Kaufmann M, Dursun I, Patti M, Kranz B, Pronicka E, Ciara E, Akcay T, Bulus D et al (2016) Autosomal-recessive mutations in SLC34A1 encoding sodium-phosphate cotransporter 2A cause idiopathic infantile hypercalcemia. J Am Soc Nephrol 27:604–614

  22. Stechman MJ, Loh Nellie Y, Thakker Rajesh V (2007) Genetics of hypercalciuric nephrolithiasis. Ann N Y Acad Sci 1116:461–484

  23. Tasian GE, Ross ME, Song L, Sas DJ, Keren R, Denburg MR, Chu DI, Copelovitch L, Saigal CS, Furth SL (2016) Annual incidence of nephrolithiasis among children and adults in South Carolina from 1997 to 2012. Clin J Am Soc Nephrol 11:488–496

  24. Warejko JK, Tan W, Daga A, Schapiro D, Lawson JA, Shril S, Lovric S, Ashraf S, Rao J, Hermle T et al (2018) Whole exome sequencing of patients with steroid-resistant nephrotic syndrome. Clin J Am Soc Nephrol 13:53–62

Download references


F.H. is the William E. Harmon Professor of Pediatrics. This research is supported by a grant from the National Institutes of Health to F.H. (5R01DK068306-14). A.M. is supported by a NIH Training Grant in Pediatric Nephrology (T32DK007726), by the 2017 Post-doctoral Fellowship Grant from the Harvard Stem Cell Institute Kidney Group, and by the 2018 Polycystic Kidney Disease Foundation Jared J. Grantham Research Fellowship. H.Y.G is supported by the National Research Foundation of Korea (2018R1A5A2025079). T.J.S. is supported by the Deutsche Forschungsgemeinschaft (Jo 1324/1-1). S.K. is supported by Higher Education Commission, Pakistan through National Research Program for Universities grant (HEC1987). A.A. is supported by International Research Support Initiative Program grant for doctoral studies by Higher Education Commission, Pakistan. J.A.S. is supported by Kidney Research UK and the Northern Counties Kidney Research Fund. C.A.W. is supported by the National Center of Competence in Research NCCR Kidney. CH financed by the Swiss National Science Foundation.

Author information

A.A., A.J.M, I.U., D.B., S.S., A.D., T.J.S., J.A.S., H.Y.G., and J.H. developed and performed gene panel amplification and massive parallel sequencing, performed variant calling, devised and performed the mutational analysis strategy and application, and conducted assessments of genotype-phenotype correlations. A.A., Ay.A., M.A., and S.K recruited patients and gathered detailed clinical information for the study. T.K., N.H., A.W., and C.W. performed functional SLC34A1 studies in cell lines and oocytes. All authors critically reviewed the paper. F.H. conceived of and directed the project. A.A., A.J.M, and F.H. wrote the paper.

Correspondence to Friedhelm Hildebrandt.

Ethics declarations

Conflict of interest

F.H. is a co-founder of Goldfinch Biopharma Inc. The other authors declare that they have no competing financial interests. No part of this manuscript has been previously published.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Amar, A., Majmundar, A.J., Ullah, I. et al. Gene panel sequencing identifies a likely monogenic cause in 7% of 235 Pakistani families with nephrolithiasis. Hum Genet 138, 211–219 (2019).

Download citation