Computational prediction of deleterious nonsynonymous SNPs in the CTNS gene: implications for cystinosis.

Background: Cystinosis is a rare autosomal recessive lysosomal storage disorder caused by mutations in the CTNS gene, which encodes cystinosin, a lysosomal cystine transporter. These mutations disrupt cystine efflux, leading to its accumulation in lysosomes and subsequent cellular damage. While more than 140 mutations have been identified, the functional and structural impacts of many nonsynonymous single nucleotide polymorphisms (nsSNPs) remain poorly understood. Nonsynonymous SNPs are of particular interest because they can directly alter protein structure and function, potentially leading to disease. Clinically, cystinosis most often presents with renal Fanconi syndrome, photophobia and vision loss due to corneal cystine crystals, and progressive neuromuscular complications such as distal myopathy and swallowing difficulties This study aimed to identify deleterious nsSNPs in the CTNS gene and evaluate their effects on cystinosin stability, structure, and function via computational tools and molecular dynamics simulations.

Results: From a dataset of 12,028 SNPs, 327 nsSNPs were identified, among which 19 were consistently classified as deleterious across multiple predictive tools, including SIFT, PolyPhen, and molecular dynamics simulations. Stability predictions revealed that most of these mutations destabilize cystinosin, with G308R and G308V located in the sixth transmembrane domain essential for transporter function having the most severe effects. Molecular dynamics simulations revealed that these mutations significantly increase local flexibility, alter hydrogen bonding patterns, and enhance solvent accessibility, resulting in structural perturbations. Notably, D305G and F142S disrupted the transmembrane domains essential for the function of cystinosin, whereas compared with the wild-type protein, G309V resulted in increased stability. Conservation analysis revealed that 16 of the 19 mutations affected highly conserved residues, indicating their crucial roles in the function of cystinosin. Additionally, protein interaction analyses suggested that mutations could impact associations with lysosomal and membrane transport proteins.

Conclusions: This study identified 19 deleterious nsSNPs in the CTNS gene that impair cystinosin stability and function. These findings highlight the structural and functional importance of key residues, such as G308, D305, and F142, which play critical roles in maintaining the active conformation and transport capacity of cystinosin. These insights provide a foundation for future experimental validation and the development of targeted therapeutic strategies to mitigate the effects of pathogenic mutations in cystinosis.