Identification and functional validation of a novel disease-causing variant in the noncoding region of NYX

Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous group of disorders, with ~30% of cases remaining genetically unsolved. Complete congenital stationary night blindness (cCSNB) is a subtype of IRD, usually associated with reduced visual acuity, nystagmus and high myopia. Most cases are caused by variants in NYX, TRPM1, GRM6, GPR179 or LRIT3. This study aimed to identify the genetic defect in a subject with clinically diagnosed cCSNB lacking coding variants in known associated genes.

A male patient presented with an electroretinogram profile consistent with cCSNB in the absence of high myopia. Pathogenic variants were not detected using Sanger sequencing of the coding regions of all known CSNB-associated genes. Whole genome sequencing (WGS) and bioinformatic analysis using SpliceAI, Pangolin, REVEL, CADD v1.7, BayesDel and MetaRNN were performed to detect potential pathogenic variants. Functional impact of this variant has been analysed using LINSIGHT, ReMM and FunUV. A minigene assay was used to assess the splicing impact of the identified variant.

WGS identified a novel c.-57G>A variant in the 5' untranslated region, within exon 1 of NYX coding for nyctalopin. In silico predictions suggested this variant to alter splicing, which was confirmed by a minigene assay showing abnormal expression of NYX. The defect was predicted to reduce nyctalopin production, potentially explaining the milder cCSNB phenotype.

To our knowledge, this is the first report describing a noncoding variant in NYX causing CSNB but lacking high myopia. These results highlight the clinical importance of screening noncoding regions of known IRD genes in genetically unsolved cases. Whether the development of high myopia in cCSNB depends on the type and location of NYX variants remains to be elucidated.