The RNU4ATAC gene belongs to the category of non-coding genes, very rarely implicated in genetic diseases. However, mutations in this gene are responsible for three rare diseases that combine microcephaly and intellectual disability, growth retardation, and skeletal anomalies. This gene is transcribed into a small RNA involved in minor splicing, a poorly known and understood mechanism that allows the maturation of messenger RNA precursors of a subset of 750 genes among the 20,000 in the human genome. Our study describes a new clinical entity associated with this gene, which is at the crossroads of this group of pathologies and another group, the ciliopathies, thus highlighting an unsuspected link between RNU4ATAC and the primary cilium. This discovery not only benefits patients in diagnostic errancy, but also opens a whole field of investigations that will eventually allow a better understanding of the pathologies associated with RNU4ATAC and minor splicing.