In this study, 910 patients with CAKUT were included; of these, 400 children from 2011 to 2013 underwent Sanger sequencing, and 10 of 400 individuals (2.5%) were found to carry rare GEN1 variants (nine were heterozygous and one was compound heterozygous) without pathogenic variants identified in known genes causing CAKUT. Here, GEN1 is linked to congenital anomaly of kidney and urinary tract.