Conclusion We propose that bi-allelic LoF and missense variants in KIAA1109 cause an autosomal-recessive brain malformation disorder with cerebral parenchymal underdevelopment ranging from major cerebral parenchymal thinning with lissencephalic aspect to moderate parenchymal rarefaction, severe to mild ventriculomegaly, and cerebellar hypoplasia with brainstem dysgenesis, associated with club foot and arthrogryposis. Severe cases are incompatible with life. Although further studies have to be engaged, our findings suggest that KIAA1109 is potentially involved in cell cycle control, particularly of the central nervous system.