Pediatr Nephrol (2010) 25:1263–1267 DOI 10.1007/s00467-010-1502-5 ORIGINAL ARTICLE Analysis of CTNS gene transcripts in nephropathic cystinosis Anna Taranta & Martijn J. Wilmer & Lambert P. van den Heuvel & Paola Bencivenga & Francesco Bellomo & Elena N. Levtchenko & Francesco Emma Received: 20 January 2010 / Revised: 23 February 2010 / Accepted: 1 March 2010 / Published online: 30 March 2010 # The Author(s) 2010. This article is published with open access at Springerlink.com Abstract Nephropathic cystinosis (NC) is an autosomal recessive disorder caused by mutations of the CTNS gene that encodes for a cystine transmembrane transporter. Several mutations have been described in the coding and promoter regions of the CTNS gene in affected individuals. We selected three patients with NC from two unrelated families, in whom sequence analysis of the CTNS gene detected only one or no mutations. Total RNA was isolated from peripheral blood mononuclear cells or fibroblasts and CTNS transcripts were analyzed. We observed a skipping of exon 5 (85 bp) in two siblings and an intron 9 retention of 75 bp associated with partial replication of exon 9 in the third patient. Genomic DNA analysis of intron regions surrounding exon 5 showed a point mutation in the hypothetical lariat branch site of intron 4 at position –24 (c.141–24 T> C) in the first two patients and a duplication of 266 bp including a part of exon and intron 9 in the third patient. Analysis of CTNS gene transcripts allowed identification of mutations in A. Taranta (*) : F. Bellomo : F. Emma Department of Nephrology and Urology, Division of Nephrology, Bambino Gesù Children’s Hospital and Research Institute, Piazza S. Onofrio, 4, 00165 Rome, Italy e-mail: taranta@opbg.net M. J. Wilmer : L. P. van den Heuvel Laboratory of Pediatrics and Neurology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands P. Bencivenga Laboratory of Scientific Research, Bambino Gesù Children’s Hospital and Research Institute, Rome, Italy L. P. van den Heuvel : E. N. Levtchenko Department of Pediatrics/Pediatric Nephrology, University Hospital Gasthuisberg, Leuven, Belgium patients in whom CTNS mutations could not be detected by traditional DNA sequencing. These results support the hypothesis that cystinosis is a monogenic disorder. Keywords Nephropathic cystinosis . CTNS gene . Splicing defect . DNA duplication Introduction Nephropathic cystinosis (NC) (OMIN 219800) is a rare autosomal recessive disorder (incidence in 1:100,000– 200,000 live births), which presents with renal proximal tubular dysfunction (Fanconi syndrome) during infancy and progresses to end-stage renal failure during the first decade of life if not treated with cysteamine [1]. Over time, patients with NC also present with dysfunction of several organs, including eyes, thyroid, liver, pancreas, male gonad, muscles, and brain [2]. NC is caused by mutations in the CTNS gene [3]. It encodes for cystinosin, an amino-acid- cystine carrier that is predicted to have seven transmem- brane domains and is primarily expressed in the lysosomal membrane [4]. Lack of cystinosin activity causes cystine accumulation and results in formation of intralysosomal cystine crystals. Approximately 10–20% of CTNS tran- scripts encode for a second cystinosin isoform, termed cystinosin-LKG, which results from an alternative splicing of exon 12 and is expressed in the plasma membrane and other cytosolic vesicles, in addition to lysosomes [5]. The CTNS gene maps to chromosome 17p13 and is composed of 12 exons, with the start codon located on exon 3 [3]. The most common CTNS mutation in northern Europe is a 57-kb deletion that originated in Germany around AD 500 [1]. To date, more than 90 mutations have been described in the coding region or flanking intronic