New pathogenic variants and insights into pathogenic mechanisms in GRK1-related Oguchi disease

Purpose: Oguchi disease is a rare autosomal recessive subtype of congenital stationary night blindness (CSNB) caused by biallelic variants in S-arrestin (SAG) or G-Protein coupled receptor kinase 1 (GRK1). These proteins have essential roles in the deactivation of the phototransduction cascade. To date thirteen disease causing variants in GRK1 have been reported. The purpose of this study was to identify disease causing variants in GRK1 and to evaluate pathogenicity using the crystal structure and in-depth bioinformatic analyses.

Methods: Patient genomic DNA was sequenced by whole genome, whole exome or focused exome sequencing. Variants were confirmed and segregated by Sanger sequencing. Pathogenic variants, published and novel, were compared to non-disease associated missense variants identified using gnomAD. The potential impact of GRK1 missense variants were then assessed at the protein level using a series of computational tools.

Results: We identified eight previously unpublished cases with biallelic pathogenic GRK1 variants, including six novel variants, and reviewed all GRK1 pathogenic variants. This revealed a hotspot for missense changes between Glu362 and Pro391 in the kinase domain. All were rare and deemed pathogenic by bioinformatics prediction software. Further structure-based scoring showed that disease causing variants were located deeper in GRK1, forming more interactions with their surrounding residues, and within or closer to key binding sites within the active site. Non-pathogenic variants, however, were generally on the outer surface at locations distal to the active site.

Conclusion: We identified new GRK1 pathogenic variants in Oguchi disease patients and investigated how disease-causing variants may impede protein function, giving new insights into mechanism of pathogenicity. To aid future clinical interpretation, we identified the bioinformatics prediction tools best able to differentiate pathogenic from non-pathogenic variants, and created a Leiden Open Variation Database (LOVD v3.0) into which all variants described in this study have been entered (http://dna2.leeds.ac.uk/GRK1_LOVD/genes/GRK1).