Rare heterozygous deleterious GDF6 variants in patients with renal anomalies

Although over 50 genes are known to cause renal malformation if mutated, the underlying genetic basis, most easily identified in syndromic cases, remains unsolved in most patients. In search of novel causative genes, whole-exome sequencing in a patient with renal, i.e., crossed fused renal ectopia, and extrarenal, i.e., skeletal, eye, and ear, malformations yielded a rare heterozygous variant in theGDF6gene encoding growth differentiation factor 6, a member of the BMP family of ligands. Previously,GDF6variants were reported to cause pleiotropic defects including skeletal, e.g., vertebral, carpal, tarsal fusions, and ocular, e.g., microphthalmia and coloboma, phenotypes. To assess the role ofGDF6in the pathogenesis of renal malformation, we performed targeted sequencing in 193 further patients identifying rareGDF6variants in two cases with kidney hypodysplasia and extrarenal manifestations. During development,gdf6was expressed in the pronephric tubule ofXenopus laevis, andGdf6expression was observed in the ureteric tree of the murine kidney by RNA in situ hybridization. CRISPR/Cas9-derived knockout ofGdf6attenuated migration of murine IMCD3 cells, an effect rescued by expression of wild-type but not mutantGDF6, indicating affected variant function regarding a fundamental developmental process. Knockdown ofgdf6inXenopus laevisresulted in impaired pronephros development. Altogether, we identified rare heterozygousGDF6variants in 1.6% of all renal anomaly patients and 5.4% of renal anomaly patients additionally manifesting skeletal, ocular, or auricular abnormalities, adding renal hypodysplasia and fusion to the phenotype spectrum ofGDF6variant carriers and suggesting an involvement of GDF6 in nephrogenesis.