Muscle-eye-brain (MEB) disease is a congenital muscular dystrophy characterized by structural brain and eye defects. Here, we describe a 12-year-old boy with partial agenesis of corpus callosum, ventriculomegaly, flattened brainstem, diffuse pachygyria, blindness, profound cognitive deficiencies and generalized muscle weakness, yet without a clear dystrophic pattern on muscle biopsy. There was no glycosylation of α-dystroglycan and the genetic screening revealed a novel truncating mutation, c.1545delC (p.Tyr516Thrfs*21), and a previously identified missense mutation, c.1469G>A (p.Cys490Tyr), in the protein O-mannose beta-1,2-Nacetylglucosaminyltransferase 1 (POMGNT1) gene. These findings broaden the clinical spectrum of MEB to include pronounced hypotonia with severe brain and eye malformations, yet with mild histopathological changes in the muscle specimen, despite the absence of glycosylated α-dystroglycan.