Molecular characterization of cystinosis patients: predominance of the CTNS c.829dup mutation in Center of Tunisia

Cystinosis is a lysosomal storage disease caused by the accumulation of intralysosomal cystine in different tissues and organs including: brain, cornea, kidneys, liver and, pancreas. This pathology is due the mutations in the CTNS gene that encode the cystinosin protein. In this retrospective study, we aimed to explore the genetic and phenotypic diversity of Tunisian patients with cystinosis in order to identify recurrent variants and their correlation with clinico-pathology features. Our retrospective study was conducted between 2022 and 2025 in collaboration with pediatric departments of Sahloul hospital of Sousse, Taher Sfar hospital of Mahdia and Hedi Chaker Hospital of Sfax, Tunisia. The entire coding region of CTNS-cDNA was screened to identify mutations and polymorphisms in 10 families: 5 unrelated and 5 related families with cystinosis. Screening for the common 57-kb deletion was performed by standard multiplex PCR, followed by direct sequencing of coding exons and their flanking exon–intron boundaries in the CTNS gene. Molecular analysis of the CTNS gene was performed in affected individuals and their relatives, leading to the identification of six pathogenic variants. Two of them were previously reported in the Tunisian population: c.829dup (p.T277fs; rs752919200), c.971-1G > C (rs2142982540), c.1001 C > A (p.T334N; rs3375433), c.925G > A (p.G309C; rs758813679), and c.251delA (p.N84fs; rs1057516296). A novel frameshift mutation, c.529delA (p.N177Tfs) was also detected. The c.829dup variant was present in six homozygous patients (5 related and one unrelated) and one heterozygous patient. In total, 39 SNPs were identified, including ten novel variants that have not been reported in ClinVar. The most frequent was rs161400 (c.779 C > T; p.T260N), which co-occurred with all variants except with c.829dup; was also observed in heterozygous carriers of c.829dup exhibiting a severe cystinosis phenotype. Our findings underscore the potential phenotypic modulatory role of the rs161400 SNP, particularly in individuals carrying rare CTNS variants compared to patients carrying the recurrent c.829dup mutation. This study emphasizes the significance of the broader genetic landscape, including variant–variant interactions, in shaping the phenotypic heterogeneity observed among patients. Moreover, this study highlights the distinct mutational profile of Tunisian patients with cystinosis disease.