It indicated that patients with KCTD13 CNV deletion have a significantly increased risk for proximal hypospadias (OR = 10.07, 95% CI = 2.91–34.84, P = 2.70 × 10−4) and midshaft hypospadias (OR = 6.08, 95% CI = 1.69–21.84, P = 0.006) compared to the distal hypospadias. This evidence concerns the gene KCTD13 and hypospadias.