Whole-genome discovery of pathogenic snRNA variants and efficient extended-exome screening

Pathogenic variants in small nuclear RNA (snRNA) genes have recently emerged as a major cause of Mendelian disorders, particularly neurodevelopmental disorders, yet they remain difficult to detect in routine diagnostics because conventional whole-exome sequencing (WES) does not capture snRNA loci. Here, we reanalyzed whole-genome sequencing (WGS) data from 1,578 unsolved probands and identified pathogenic variants in multiple snRNA genes, including RNU4-2, RNU2-2, RNU5B-1, and RNU4ATAC, accounting for 1.2% (19 patients) of previously unsolved cases. We then developed an snRNA-extended WES approach by incorporating capture probes targeting 50 snRNA genes into a standard exome design. Benchmarking demonstrated robust, uniform coverage across all targeted snRNA loci without increasing sequencing depth. Applying this approach to patient samples reliably detected disease-causing snRNA variants previously identified by WGS. Our results establish snRNA-extended WES as a cost-effective and scalable strategy to improve diagnostic yield and bridge the gap between recent gene discoveries and clinical genomic practice.