Schistosomus reflexus (SR) is one of the most common congenital anomalies found in cases of cattle dystocia; this disorder occurs mostly in cattle. Congenital anomalies such as SR are caused by various genetic and environmental factors, but no specific cause has been elucidated for SR. This study reports a case of SR in a Holstein dairy cattle fetus with congenital anomalies in Korea. Grossly, a distinct spine curvature was observed between the thoracic and lumbar vertebrae, accompanied by a consequential malformation from the sacrum to the occipital bone. Furthermore, the thoracic and abdominal organs were exposed. In computed tomography (CT) images, mild and severe kyphoscoliosis was observed in T1~11 and L1~6, respectively. Additionally, vertebral dysplasia was observed in S1~5 and Cd 1~5. To pinpoint the causal genes and mutations, we leveraged a custom 50K Hanwoo SNP-Chip and the Online Mendelian Inheritance in Animals (OMIA) database. As a result, we identified a nonsense mutation in apoptotic protease activating factor 1 (APAF1) within HH1 that was associated with a decrease in conception rate and an increase in abortion in Holstein dairy cattle. The genotype of the SR case was A/A, and most of the 1,142 normal Holstein dairy cattle tested as a control group had the genotype G/G. In addition, the A/A genotype did not exist in the control group. Based on the pathological, genetic, and radiological findings, the congenital abnormalities observed were diagnosed as SR.