Whole-exome sequencing and molecular dynamics confirm pathogenicity of a novel SLC6A6 mutation in Leber congenital amaurosis
Introduction
Inherited retinal diseases (IRDs) are a clinically and genetically heterogenous group where the robust advancement of next-generation sequencing technologies has facilitated genotype-assisted diagnosis. Leber congenital amaurosis (LCA) is a severe form of inherited retinal dystrophy that causes congenital blindness or near-blindness with a global prevalence of 3 per 100,000 live births.It is characterized by a loss of vision at birth or within the first few years of life with overlapping phenotypes to many syndromic and non-syndromic IRDs. With India's rich genetic heterogeneity, WES is a valuable tool for uncovering novel gene mutations linked to LCA. This genetic diversity expands our understanding of the disease's spectrum in the Indian population.
Methods
In our previous study, 92 Indian LCA families were screened through targeted resequencing, and 80% of probands exhibited mutations in known genes. Hence, the remaining 20% probands with additional family members (n = 40) were subjected to whole-exome sequencing. An in-house standard bioinformatics pipeline was used for variant calling and annotation. Homology modeling (Modeller-9.23) and molecular simulation were performed on an identified SLC6A6 gene variant that has not yet been associated with LCA to investigate its potential pathogenicity.
Results
Disease-causing pathogenic variants were identified in 15/20 families (75%) across 11 genes with 33% variants being novel. Among the identified 17 variants in 15 families, 35% were missense, 29% nonsense, 29% frameshift and 6% splice variants. Segregation analysis, control screening and in silico predictions confirmed the variant’s pathogenicity. All variants were classified as pathogenic according to ACMG guidelines. Homology modeling and molecular simulation in the membrane system for the p.Pro82Leu mutant in SLC6A6 protein showed significant modification in helical characteristics around the TM2 helix in the mutant, which could potentially hinder the regular function and cause disruption in taurine transport across the membrane leading to the disease.
Conclusion
Taurine being an essential amino acid for photoreceptor development and maintenance, our study suggests that mutation identified in SLC6A6 gene may cause LCA. This is the first report of SLC6A6 gene association with LCA and also the first case report in the Indian population.
