The genomic analyses based on whole genome sequencing identified 13 mutations with a predicted high impact on the following overlapped genes: ACVR1, ADGRA2, BHMT2, BMPR1B, CCDC8, CDH1, EGF, F13A1, GSTP1, IRF6, MMP14, MYBPHL, and PHC2, of which ADGRA2, EGF, F13A1, GSTP1, and IRF6 showed homozygous mutations, and BMPR1B and CCDC8 had a low or no report in other clinical cases in bovine species regarding CLJ and hypospadias. Here, BHMT2 is linked to hypospadias.