{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:14:45Z","timestamp":1760058885720,"version":"build-2065373602"},"reference-count":28,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T00:00:00Z","timestamp":1746662400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Vertex Pharmaceuticals"},{"name":"German CF Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Accurate genetic diagnosis is essential for appropriate treatment in cystic fibrosis (CF). Large copy number variants like duplications in the CFTR gene are rare and often classified as variants of uncertain significance (VUSs) due to unknown characteristics of the inserted material, complicating diagnosis and treatment decisions. We identified a previously uncharacterized exon 22 duplication (CFTRdup22) in the CFTR gene in two anamnestically unrelated people with CF, both exhibiting a mild phenotype. Initial classification as a VUS was based on standard genetic testing. We employed a custom next-generation sequencing (NGS) panel to determine the exact breakpoints of the duplication and conducted mRNA sequencing to confirm its effect on splicing. DNA and RNA analyses allowed for precise breakpoint determination, confirming that the duplication was in tandem and the reading frame remained intact. This, as well as a residual CFTRdup22 function of ~30% as measured via intestinal current measurement, is consistent with a clinically milder CF phenotype. Collectively, the precise characterization of the variants\u2019 breakpoints, localization and orientation enabled us to reclassify the variant as likely pathogenic. This study highlights the importance of advanced genetic techniques, such as NGS and breakpoint analysis, in accurately identifying CF-causing variants. It underscores the importance of a comprehensive approach and persistence when suspecting a specific genetic condition. This can aid in reclassifying VUSs, providing a definitive diagnosis for the affected family and enabling appropriate therapeutic interventions, including the use of CFTR modulators.<\/jats:p>","DOI":"10.3390\/ijms26104487","type":"journal-article","created":{"date-parts":[[2025,5,8]],"date-time":"2025-05-08T06:47:15Z","timestamp":1746686835000},"page":"4487","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Identification and Characterization of a Rare Exon 22 Duplication in CFTR in Two Families"],"prefix":"10.3390","volume":"26","author":[{"given":"Simone","family":"Ahting","sequence":"first","affiliation":[{"name":"Institute of Human Genetics, University Hospital Leipzig, 04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Constance","family":"Henn","sequence":"additional","affiliation":[{"name":"Pediatricians Office Dr. Henn, Pediatric Pulmonology, 04177 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maike","family":"vom Hove","sequence":"additional","affiliation":[{"name":"Division of Pediatric Pulmonology and Allergology, Hospital for Children and Adolescents, University Medical Center Leipzig, 04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent","family":"Strehlow","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics, University Hospital Leipzig, 04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Patricia","family":"Duffek","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics, University Hospital Leipzig, 04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sophie","family":"Behrendt","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics, University Hospital Leipzig, 04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephan","family":"Drukewitz","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics, University Hospital Leipzig, 04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jasmin","family":"Berger","sequence":"additional","affiliation":[{"name":"Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charit\u00e9\u2013Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, 13353 Berlin, Germany"},{"name":"German Center for Lung Research, Associated Partner Site, 13353 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1666-8924","authenticated-orcid":false,"given":"Simon Y.","family":"Graeber","sequence":"additional","affiliation":[{"name":"Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charit\u00e9\u2013Universit\u00e4tsmedizin Berlin, Corporate Member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, 13353 Berlin, Germany"},{"name":"German Center for Lung Research, Associated Partner Site, 13353 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julia","family":"Hentschel","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics, University Hospital Leipzig, 04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,5,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1016\/j.ajhg.2014.12.017","article-title":"Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints","volume":"96","author":"Newman","year":"2015","journal-title":"Am. J. Hum. Genet."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1038\/s41436-018-0092-7","article-title":"DNA breakpoint assay reveals a majority of gross duplications occur in tandem reducing VUS classifications in breast cancer predisposition genes","volume":"21","author":"Richardson","year":"2019","journal-title":"Genet. Med."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e00645","DOI":"10.1002\/mgg3.645","article-title":"Identification of a novel large deletion and other copy number variations in the CFTR gene in patients with Cystic Fibrosis from a multiethnic population","volume":"7","author":"Abreu","year":"2019","journal-title":"Mol. Genet. Genomic Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1016\/j.jcf.2023.10.009","article-title":"Every CFTR variant counts\u2014Target-capture based next-generation-sequencing for molecular diagnosis in the German CF Registry","volume":"23","author":"Ahting","year":"2024","journal-title":"J. Cyst. Fibros."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Graeber, S.Y., Sommerburg, O., Yu, Y., Berges, J., Hirtz, S., Scheuermann, H., Berger, J., Duerr, J., and Mall, M.A. (2025). Intestinal current measurement detects age-dependent differences in CFTR function in rectal epithelium. Front. Pharmacol., 16.","DOI":"10.3389\/fphar.2025.1537095"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1097\/MPA.0b013e3182156e47","article-title":"A novel exon duplication of the cystic fibrosis transmembrane conductance regulator in a patient presenting with adult-onset recurrent pancreatitis","volume":"40","author":"Kopp","year":"2011","journal-title":"Pancreas"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1152\/physrev.00007.2018","article-title":"Structure, gating, and regulation of the cftr anion channel","volume":"99","author":"Vergani","year":"2019","journal-title":"Physiol. Rev."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"14147","DOI":"10.1074\/jbc.M116.772335","article-title":"Stabilization of a nucleotide-binding domain of the cystic fibrosis transmembrane conductance regulator yields insight into disease-causing mutations","volume":"292","author":"Vernon","year":"2017","journal-title":"J. Biol. Chem."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Rapino, D., Sabirzhanova, I., Lopes-Pacheco, M., Grover, R., Guggino, W.B., and Cebotaru, L. (2015). Rescue of NBD2 mutants N1303K and S1235R of CFTR by small-molecule correctors and transcomplementation. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0119796"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"357","DOI":"10.5152\/balkanmedj.2021.21199","article-title":"The Genetic Analysis of Cystic Fibrosis Patients With Seven Novel Mutations in the CFTR Gene in the Central Anatolian Region of Turkey","volume":"38","author":"Pekcan","year":"2021","journal-title":"Balkan Med. J."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Graeber, S.Y., Vitzthum, C., and Mall, M.A. (2021). Potential of Intestinal Current Measurement for Personalized Treatment of Patients with Cystic Fibrosis. J. Pers. Med., 11.","DOI":"10.3390\/jpm11050384"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"D980","DOI":"10.1093\/nar\/gkt1113","article-title":"ClinVar: Public archive of relationships among sequence variation and human phenotype","volume":"42","author":"Landrum","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet. Med."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1007\/s00439-020-02199-3","article-title":"The Human Gene Mutation Database (HGMD\u00ae): Optimizing its use in a clinical diagnostic or research setting","volume":"139","author":"Stenson","year":"2020","journal-title":"Hum. Genet."},{"key":"ref_17","unstructured":"Johns Hopkins University, and The Hospital for Sick Childre (2025, April 22). The Clinical and Functional TRanslation of CFTR (CFTR2). Available online: http:\/\/cftr2.org."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1002\/humu.23276","article-title":"CFTR-France, a national relational patient database for sharing genetic and phenotypic data associated with rare CFTR variants","volume":"38","author":"Claustres","year":"2017","journal-title":"Hum. Mutat."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1038\/s41586-020-2308-7","article-title":"The mutational constraint spectrum quantified from variation in 141,456 humans","volume":"581","author":"Karczewski","year":"2020","journal-title":"Nature"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1016\/j.ajhg.2016.08.016","article-title":"REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants","volume":"99","author":"Ioannidis","year":"2016","journal-title":"Am. J. Hum. Genet."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.cell.2018.12.015","article-title":"Predicting Splicing from Primary Sequence with Deep Learning","volume":"176","author":"Jaganathan","year":"2019","journal-title":"Cell"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"D1243","DOI":"10.1093\/nar\/gkae974","article-title":"The UCSC Genome Browser database: 2025 update","volume":"53","author":"Perez","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1053\/j.gastro.2004.07.006","article-title":"CFTR Cl- channel function in native human colon correlates with the genotype and phenotype in cystic fibrosis","volume":"127","author":"Hirtz","year":"2004","journal-title":"Gastroenterology"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1164\/rccm.202110-2249OC","article-title":"Effects of Elexacaftor\/Tezacaftor\/Ivacaftor Therapy on CFTR Function in Patients with Cystic Fibrosis and One or Two F508del Alleles","volume":"205","author":"Graeber","year":"2022","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1164\/rccm.201604-0893OC","article-title":"Comparison of Lung Clearance Index and Magnetic Resonance Imaging for Assessment of Lung Disease in Children with Cystic Fibrosis","volume":"195","author":"Stahl","year":"2017","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1164\/rccm.202201-0219OC","article-title":"Effects of Elexacaftor\/Tezacaftor\/Ivacaftor Therapy on Lung Clearance Index and Magnetic Resonance Imaging in Patients with Cystic Fibrosis and One or Two F508del Alleles","volume":"206","author":"Graeber","year":"2022","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2400004","DOI":"10.1183\/13993003.00004-2024","article-title":"Impact of elexacaftor\/tezacaftor\/ivacaftor therapy on lung clearance index and magnetic resonance imaging in children with cystic fibrosis and one or two F508del alleles","volume":"64","author":"Stahl","year":"2024","journal-title":"Eur. Respir. J."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1152\/japplphysiol.00338.2021","article-title":"Correction of sensor crosstalk error in Exhalyzer D multiple-breath washout device significantly impacts outcomes in children with cystic fibrosis","volume":"131","author":"Wyler","year":"2021","journal-title":"J. Appl. Physiol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/10\/4487\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:29:25Z","timestamp":1760030965000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/10\/4487"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,8]]},"references-count":28,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2025,5]]}},"alternative-id":["ijms26104487"],"URL":"https:\/\/doi.org\/10.3390\/ijms26104487","relation":{},"ISSN":["1422-0067"],"issn-type":[{"type":"electronic","value":"1422-0067"}],"subject":[],"published":{"date-parts":[[2025,5,8]]}}}