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Cystinosis is caused by mutations in the<jats:italic>CTNS<\/jats:italic>gene that encodes the lysosomal cystine carrier protein cystinosin.<jats:italic>CTNS<\/jats:italic>mutations result in either complete absence or reduced cystine transporting function of the protein. The diagnosis of nephropathic cystinosis is generally based on measuring leukocyte cystine level, demonstration of corneal cystine crystals by the slit lamp examination and confirmed by genetic analysis of the<jats:italic>CTNS<\/jats:italic>gene.<\/jats:p><\/jats:sec><jats:sec><jats:title>Case presentation<\/jats:title><jats:p>A boy born to consanguineous Caucasian parents had the characteristic clinical features of the infantile nephropathic cystinosis including renal Fanconi syndrome (polydipsia\/polyuria, metabolic acidosis, hypokalemia, hypophosphatemia, low molecular weight proteinuria, glycosuria, cystine crystals in the cornea) and elevated WBC cystine levels. Initially we performed RFLP analysis of the common in the Northern European population 57-kb deletion of proband\u2019s DNA, then a direct Sanger sequencing which revealed no mutations in the coding part of the<jats:italic>CTNS<\/jats:italic>gene. To confirm the diagnosis we performed RT-PCR analysis of total RNA obtained from patient-derived fibroblasts in combination with cDNA sequencing. This revealed the skipping of exon 4 and exon 5 in the<jats:italic>CTNS<\/jats:italic>in our patient. Therefore, we detected a novel 9-kb homozygous deletion in the<jats:italic>CTNS<\/jats:italic>gene at genomic DNA level, spanning region from intron 3 to intron 5. In order to identify the inheritance pattern of the deletion we analyzed DNA of proband\u2019s mother and father. Both parents were found to be heterozygous carriers of the<jats:italic>CTNS<\/jats:italic>mutation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Analysis of<jats:italic>CTNS<\/jats:italic>gene transcript allowed to identify a large homozygous deletion in the patient with infantile nephropathic cystinosis. Mutational detection at RNA level may be an efficient tool to establish the genetic defect in some cystinosis patients.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12882-019-1589-2","type":"journal-article","created":{"date-parts":[[2019,10,31]],"date-time":"2019-10-31T10:04:05Z","timestamp":1572516245000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["CTNS\u00a0mRNA molecular analysis revealed a novel mutation in a child with infantile nephropathic cystinosis: a case report"],"prefix":"10.1186","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6459-2795","authenticated-orcid":false,"given":"Svetlana","family":"Papizh","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victoria","family":"Serzhanova","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5979-0727","authenticated-orcid":false,"given":"Alexandra","family":"Filatova","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mikhail","family":"Skoblov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vyacheslav","family":"Tabakov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lambert","family":"van den Heuvel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena","family":"Levtchenko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0702-4932","authenticated-orcid":false,"given":"Larisa","family":"Prikhodina","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,10,31]]},"reference":[{"key":"1589_CR1","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1056\/NEJMra020552","volume":"347","author":"WA Gahl","year":"2002","unstructured":"Gahl WA, Thoene JG, Schneider JA. 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A copy of the written consent is available for review by the Editor of this journal.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"400"}}