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Meckel-Gruber syndrome (MKS) is a lethal recessive disorder characterised by multiple severe birth defects. The disease is associated with mutations in genes that are required for the generation of cilia, which are cellular structures with multiple roles ranging from motility to sensation. Cui et al. recover a mouse mutant with developmental defects similar to those seen in humans with MKS, including polycystic kidneys and laterality defects. The authors map the mutation in these mice to a previously uncharacterised, highly conserved domain of a centrosome-localised protein called Mks1. They show that the mutation disrupts Mks1’s function in late-stage ciliogenesis. These results clarify mechanisms underlying birth defects in MKS and provide molecular insight into how ciliogenesis occurs.