Introduction: Alpha-dystroglycan O-glycosylation pathway is controlled by the POMT1 gene as the main cause and its biallelic pathogenic mutations in the recessive form are responsible for approximately one-fifth of the Walker-Warburg syndrome (WWS). The essential role of the Alpha-dystroglycan O-glycosylation pathway is in the development of muscle, brain, and eye. Congenital muscular dystrophy with severe brain and eye abnormalities constitute the most common symptoms of WWS. Case Presentation: A non-consanguineous couple from a population of 6000 was referred to Sadra genetics lab in Shahre Kord, due to a history of two pregnancies ending in abortion therapy based on abnormal sonography. In the first pregnancy, Meningocele was observed and in the second one, meningocele and cerebral hydrocephalus, multiple small cysts in the kidney, severe ventriculomegaly, dilated ventricle, and empty urinary bladder were seen. Whole Exome Sequencing (WES) test was requested by perinatologist for the second fetus. Afterwards, bioinformatics analysis was performed on the WES result based on the clinical data from ultrasound findings. Conclusion: A novel likely pathogenic homozygote variant in the POMT1 gene was established, confirmed, and cosegregated in the family. The correlation of sonographic findings with WWS syndrome was evaluated by both perinatologist and pediatric neurologist. Therefore, these findings could be used for the evaluation of the prenatal diagnosis in the family.