Among all patients, 11.17% (39 out of 349) were found to carry KCTD13 CNV deletion (≤1), and none with CNV duplication (>2) in KCTD13. Chi-squared test analysis showed a statistically significant difference in the frequency of copy number deletion between the three groups (P = 4.90 × 10−5, Table 3), and there was an increasing trend in the rate of carrying copy number deletion of the gene as the severity of hypospadias increased (P_trend = 9.00 × 10−6, Figure 1). The gene discussed is KCTD13; the disease is hypospadias.