Noncoding mutation in contributes to inherited retinal degenerations.

PURPOSE: Despite the extensive use of next-generation sequencing (NGS) technology to identify disease-causing genomic variations, a major gap in our understanding of Mendelian diseases is the unidentified molecular lesion in a significant portion of patients. For inherited retinal degenerations (IRDs), although currently close to 300 disease-associated genes have been identified, the mutations in approximately one-third of patients remain unknown. With mounting evidence that noncoding mutations might contribute significantly to disease burden, we aimed to systematically investigate the contributions of noncoding regions in the genome to IRDs.

METHODS: In this study, we focused on , which has been linked to various IRD phenotypes, including Leber congenital amaurosis (LCA), retinitis pigmentosa (RP), and macular dystrophy (MD). As several noncoding mutant alleles have been reported in and we observed that the mutation carrier frequency of is higher in patient cohorts with unsolved IRDs, we hypothesized that mutations in the noncoding regions of might be a significant contributor to pathogenicity. To test this hypothesis, we performed whole-genome sequencing (WGS) for 25 patients with unassigned IRD who carry a single mutation in .

RESULTS: Three noncoding variants in , including a 2,890 bp deletion and two deep-intronic variants (c.2710+233G>A and c.1468-263G>C), were identified as putative second hits of in three patients with LCA. The mutant alleles were validated with direct sequencing or in vitro assays.

CONCLUSIONS: The results highlight the significance of the contribution of noncoding pathogenic variants to unsolved IRD cases.