ENPP6 is a novel candidate gene for autosomal recessive CAKUT

Introduction Congenital anomalies of the kidney and urinary tract (CAKUT) are a leading cause of childhood chronic kidney disease. Current genetic testing yields a molecular diagnosis in 12–20% of CAKUT cases, leaving the cause of most cases unknown. Methods To identify novel candidate genes, we performed exome sequencing in 1,265 families with CAKUT. We assessed the functional effects of ENPP6 variants using a fluorescent-probe cell assay, Xenopus larvae overexpression and rescue experiments, Enpp6 -/- mice, and LC-MS analysis of urinary metabolites. Results In a boy with posterior urethral valves, we identified a homozygous missense variant, p.Met243Val, in the ectonucleotide pyrophosphatase/phosphodiesterase 6 ( ENPP6 ) gene. GeneMatcher identified three additional individuals with homozygous ENPP6 missense variants (p.Met363Thr, p.Val410Met, and p.Val235Ile) and possible kidney or urogenital phenotypes. Variant p.Met243Val showed consistent partial loss of function across assays, whereas results for p.Met363Thr were inconclusive, and p.Val410Met and p.Val235Ile showed no evidence of altered enzymatic function. Xenopus studies demonstrated dosage-sensitive effects of enpp6 on pronephric development and functional conservation between human ENPP6 and Xenopus enpp6 . The index patient homozygous for p.Met243Val excreted β-glycerophosphocholine in urine, a phenotype observed in Enpp6 -/- mice but absent in unaffected wild-type and heterozygous family members. Enpp6 -/- mice showed no CAKUT phenotype on macroscopic or histological examination. Conclusion Functional and in vivo biochemical findings support a partial loss of ENPP6 function due to p.Met243Val. These findings support ENPP6 as a candidate gene for CAKUT, and additional families with CAKUT and ENPP6 loss-of-function variants are needed to establish causality.