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Background Nephropathic cystinosis is an autosomal recessive disease caused by a mutation in the CTNS gene which encodes cystinosin, a lysosomal cystine transporter. The spectrum of mutations in the CTNS gene is not well defined in the North African population. Here, we investigated twelve patients with nephropathic cystinosis belonging to eight Tunisian families in order to analyze the clinical and genetic characteristics of Tunisian children with infantile nephropathic cystinosis. Methods Clinical data were collected retrospectively. Molecular analysis of the CTNS gene was performed by Sanger sequencing. Results We describe a new splicing mutation c.971-1G > C in the homozygous state in 6/12 patients which seems to be a founder mutation. The reported deletion of 23nt c.771_793 Del (p.Gly258Serfs*30) was detected in a homozygous state in one patient and in a heterozygous compound state with the c.971-1G > C mutation in 3/12 patients. Two of 12 patients have a deletion of exons 4 and 5 of the CTNS gene. None of our patients had the most common 57-kb deletion. Conclusions The mutational spectrum in the Tunisian population is different from previously described populations. Thus, a molecular diagnostic strategy must be implemented in Tunisia, by targeting as a priority the common mutations described in this country. Such a strategy will allow a cost-effective diagnosis confirmation as well as early administration of treatment with oral cysteamine. Graphical abstract A higher resolution version of the Graphical abstract is available as Supplementary information, Author(s): Mariem El Younsi [sup.1] , Médiha Trabelsi [sup.2] , Sandra Ben Youssef [sup.3] , Inès Ouertani [sup.2] , Yousra Hammi [sup.3] , Ahlem Achour [sup.2] , Faouzi Maazoul [sup.2] [...]