Exome-wide Association Study Identifies GREB1L Mutations in Congenital Kidney Malformations

Renal agenesis and hypodysplasia (RHD) are major causes of pediatric chronic kidney disease and are highly genetically heterogeneous. We conducted whole-exome sequencing in 202 case subjects with RHD and identified diagnostic mutations in genes known to be asso- ciated with RHD in 7/202 case subjects. In an additional affected individual with RHD and a congenital heart defect, we found a homo- zygous loss-of-function (LOF) variant in SLIT3, recapitulating phenotypes reported with Slit3 inactivation in the mouse. To identify genes associated with RHD, we performed an exome-wide association study with 195 unresolved case subjects and 6,905 control sub- jects. The top signal resided in GREB1L, a gene implicated previously in Hoxb1 and Shha signaling in zebrafish. The significance of the association, which was p 1⁄4 2.0 3 105 for novel LOF, increased to p 1⁄4 4.1 3 106 for LOF and deleterious missense variants com- bined, and augmented further after accounting for segregation and de novo inheritance of rare variants (joint p 1⁄4 2.3 3 107). Finally, CRISPR/Cas9 disruption or knockdown of greb1l in zebrafish caused specific pronephric defects, which were rescued by wild-type human GREB1L mRNA, but not mRNA containing alleles identified in case subjects. Together, our study provides insight into the genetic land- scape of kidney malformations in humans, presents multiple candidates, and identifies SLIT3 and GREB1L as genes implicated in the pathogenesis of RHD.