Congenital disorders of glycosylation (CDG) are associated with ciliary dysfunction due to altered glycosylation of ciliary glycoproteins. We describe a severe ciliopathy-like phenotype in a female infant associated with a novel homozygous missense variant NM_004870.4(MPDU1):c.503G>A/p.Gly168Glu. Our findings, based on the co-segregation of the variant with the phenotype and in-silico analysis, implicate this MPDU1 missense variant in this disorder. Matched phenotype includes symmetric growth restriction, facial dysmorphism, ichthyosis, hepatomegaly with severe duct plate malformation, renal cortical tubular and glomerular cysts, moderate cerebral tetraventricular dilatation, and severe pontocerebellar hypoplasia. According to this observation, CDG should be included in the workup of infantile ciliopathy-like disorder.