We identified disease-causing variants in the non-coding gene RNU4ATAC in patients with Joubert syndrome, a rare neurodevelopmental disorder. These individuals also presented features overlapping with skeletal disorders already associated to RNU4ATAC, such as short stature and other anomalies. Our findings confirm that RNU4ATAC variants can lead to a combined neurological and skeletal phenotype. Importantly, the variants were initially missed by standard analyses and identified through targeted reanalysis of exome data, underlining the diagnostic relevance of revisiting existing data to uncover non-coding alterations. (By Fulvio D’Abrusco, https://jmg.bmj.com/content/early/2025/09/11/jmg-2025-110987 )