Recurrent RNU4-2 n.64_65insT variant in ReNU syndrome identified in exome-negative cases

ReNU syndrome is a neurodevelopmental disorder (NDD) caused by pathogenic variants in RNU4-2, a non-coding gene encoding the U4 small nuclear RNA (snRNA). As a critical component of the major spliceosome, U4 snRNA is essential for pre-mRNA splicing; however, RNU4-2 is not captured by conventional exome sequencing (ES), often leaving affected individuals undiagnosed.

To evaluate the prevalence and clinical impact of RNU4-2 variants, we performed genome sequencing in 95 patients with NDDs in whom prior ES had failed to identify a causative variant.

We identified a recurrent RNU4-2 variant (NR_003137.3:n.64_65insT) in five patients (5.3%), four of whom are described here. All variants occurred de novo. Affected individuals exhibited severe intellectual disability, developmental delay, microcephaly, short stature, and consistent brain MRI findings, including ventricular enlargement and corpus callosum thinning. Distinctive facial features involving the lips and philtrum were consistently observed, including a characteristic combination of a tented upper lip with an exaggerated Cupid's bow, an everted lower lip, and a horizontally oriented philtrum. In addition, transient limb edema and rib dysplasia may expand the phenotypic spectrum. The n.64_65insT variant, located within the functional T-loop of the U4 snRNA, appears to be associated with more severe cognitive impairment than other RNU4-2 variants.

Our findings underscore RNU4-2 as a major cause of NDDs in ES-negative cases and further delineate the phenotypic spectrum of ReNU syndrome. Recognition of the characteristic "lip and philtrum gestalt" serves as a vital clinical clue, prompting targeted genetic evaluation for this frequently overlooked disorder.