Ciliopathies are clinical disorders of the primary cilium with widely recognized phenotypic and genetic heterogeneity. Here we found that impaired ciliogenesis in fibroblasts derived from individuals with fetal akinesia deformation sequence (FADS).FADS refers to a broad spectrum of neuromuscular disorders arising from impaired fetal movement. We show that cells derived from two FADS individuals, one with an unknown genetic cause and one with bi-allelic pathogenic variants in RAPSN, have shorter and less primary cilia (PC), in association with alterations in posttranslational modifications in α -tubulin. Similarly, siRNA-mediated depletion of two known FADS proteins, the scaffold protein rapsyn and the nucleoporin NUP88, resulted in defective PC formation. Consistent with a role in ciliogenesis, rapsyn and NUP88 localized to centrosomes and PC. By proximity-ligation assays, we show that rapsyn and NUP88 are interacting and that both proteins are connecting to all three tubulin isoforms (α, ß, and γ ). The rapsyn-NUP88 interface, as well as their contact to microtubules, is perturbed in the examined FADS cells, similarly to their contact to microtubules. We suggest that the perturbed rapsyn-NUP88-tubulin interface leads to defects in PC formation and that defective ciliogenesis contributes to the pleiotropic defects seen in FADS.