We described this patient has a novel heterozygous NR5A1 variant (c.929A > C, p. His310Pro) and a rare heterozygous MAP3K1 variant (c.2282T > C, p. Ile761Thr) and suspected that the rare MAP3K1 variant may accelerate the development of hypospadias. Here, NR5A1 is linked to hypospadias.