Amar J. Majmundar, Eugen Widmeier, John F. Heneghan, Ankana Daga, Chen-Han Wilfred Wu, Florian Buerger, Hannah Hugo, Ihsan Ullah, Ali Amar, Isabel Ottlewski, Daniela A. Braun, Tilman Jobst-Schwan, Jennifer A. Lawson, Muhammad Yasir Zahoor, Nancy M. Rodig, Velibor Tasic, Caleb P. Nelson, Shagufta Khaliq, Ria Schönauer, Jan Halbritter, John A. Sayer, Hanan M. Fathy, Michelle A. Baum, Shirlee Shril, Shrikant Mane, Seth L. Alper, and Friedhelm Hildebrandt
Nephrolithiasis (NL) affects 1 in 11 individuals worldwide, leading to significant patient morbidity. NL is associated with nephrocalcinosis (NC), a risk factor for chronic kidney disease. Causative genetic variants are detected in 11-28% of NL and/or NC, suggesting additional NL/NC-associated genetic loci await discovery. Therefore, we employed genomic approaches to discover novel genetic forms of NL/NC.Exome sequencing and directed sequencing of the OXGR1 locus were performed in a worldwide NL/NC cohort. Putatively deleterious rare OXGR1 variants were functionally characterized.Exome sequencing revealed a heterozygous OXGR1 missense variant (c.371TG, p.L124R) co-segregating with calcium oxalate NL and/or NC disease in an autosomal dominant inheritance pattern within a multi-generational family with five affected individuals. OXGR1 encodes 2-oxoglutarate (α-ketoglutarate) receptor 1 in the distal nephron. In response to its ligand α-ketoglutarate (AKG), OXGR1 stimulates the chloride-bicarbonate exchanger Pendrin, which also regulates transepithelial calcium transport in cortical connecting tubules. Strong amino acid conservation in orthologues and paralogues, severe in silico prediction scores, and extreme rarity in exome population databases suggested the variant was deleterious. Interrogation of the OXGR1 locus in 1107 additional NL/NC families identified five additional deleterious dominant variants in five families with calcium oxalate NL/NC. Rare, potentially deleterious OXGR1 variants were enriched in NL/NC subjects relative to ExAC controls (ΧRare, dominant loss-of-function OXGR1 variants are associated with recurrent calcium oxalate NL/NC disease.