{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T22:46:20Z","timestamp":1784673980982,"version":"3.55.0"},"reference-count":67,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T00:00:00Z","timestamp":1768176000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["PI23\/00047"],"award-info":[{"award-number":["PI23\/00047"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["PI24\/00267"],"award-info":[{"award-number":["PI24\/00267"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","award":["634935"],"award-info":[{"award-number":["634935"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008431","name":"Consejer\u00eda de Educaci\u00f3n de la Junta de Castilla y Le\u00f3n","doi-asserted-by":"publisher","award":["Programa Estrat\u00e9gico, Escalera de Excelencia Instituto de Biomedicina y Gen\u00e9tica Molecular (IBGM) de Valladolid"],"award-info":[{"award-number":["Programa Estrat\u00e9gico, Escalera de Excelencia Instituto de Biomedicina y Gen\u00e9tica Molecular (IBGM) de Valladolid"]}],"id":[{"id":"10.13039\/501100008431","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Pathogenic germline variants in the ATM gene are associated with a 20\u201330% lifetime risk of breast cancer. Crucially, a relevant fraction of loss-of-function variants in breast cancer susceptibility genes disrupts pre-mRNA splicing. We aimed to perform splicing analysis of ATM splice-site variants identified in the large-scale sequencing project BRIDGES (Breast Cancer After Diagnostic Gene Sequencing). To this end, we bioinformatically selected 47 splice-site variants across 17 exons that were genetically engineered into three minigenes and assayed in MCF-7 cells. Aberrant splicing was observed in 38 variants. Of these, 30 variants, including 7 missense, yielded no or negligible expression of the minigene full-length (mgFL) transcript. A total of 69 different transcripts were characterized, 48 of which harboured a premature termination codon. Some variants, such as c.2922-1G&gt;A, generated complex patterns with up to 10 different transcripts. Alternative 3\u2032 or 5\u2032 splice-site usage was the predominant event. Integration of ATM minigene read-outs into the ACMG\/AMP (American College of Medical Genetics and Genomics\/Association for Molecular Pathology)-based specifications for the ATM gene enabled the classification of 30 ATM variants as pathogenic or likely pathogenic and 9 as likely benign. Overall, splicing assays provide key information for variant interpretation and the clinical management of patients.<\/jats:p>","DOI":"10.3390\/ijms27020765","type":"journal-article","created":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T14:57:25Z","timestamp":1768229845000},"page":"765","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Experimental Mis-Splicing Assessment and ACMG\/AMP-Guided Classification of 47 ATM Splice-Site Variants"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7838-0838","authenticated-orcid":false,"given":"In\u00e9s","family":"Llinares-Burguet","sequence":"first","affiliation":[{"name":"Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Gen\u00e9tica Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Cient\u00edficas\u2014Universidad de Valladolid (CSIC-UVa), 47003 Valladolid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5548-7114","authenticated-orcid":false,"given":"Lara","family":"Sanoguera-Miralles","sequence":"additional","affiliation":[{"name":"Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Gen\u00e9tica Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Cient\u00edficas\u2014Universidad de Valladolid (CSIC-UVa), 47003 Valladolid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4888-2885","authenticated-orcid":false,"given":"Elena","family":"Bueno-Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Gen\u00e9tica Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Cient\u00edficas\u2014Universidad de Valladolid (CSIC-UVa), 47003 Valladolid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1850-590X","authenticated-orcid":false,"given":"Ada","family":"Esteban-Sanchez","sequence":"additional","affiliation":[{"name":"Molecular Oncology Laboratory, Hospital Cl\u00ednico San Carlos, IdISSC (Instituto de Investigaci\u00f3n Sanitaria del Hospital Cl\u00ednico San Carlos), 28040 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Romano-Medina","sequence":"additional","affiliation":[{"name":"Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Gen\u00e9tica Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Cient\u00edficas\u2014Universidad de Valladolid (CSIC-UVa), 47003 Valladolid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-8199-3483","authenticated-orcid":false,"given":"Lobna","family":"Ramadane-Morchadi","sequence":"additional","affiliation":[{"name":"Molecular Oncology Laboratory, Hospital Cl\u00ednico San Carlos, IdISSC (Instituto de Investigaci\u00f3n Sanitaria del Hospital Cl\u00ednico San Carlos), 28040 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alicia","family":"Garc\u00eda-\u00c1lvarez","sequence":"additional","affiliation":[{"name":"Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Gen\u00e9tica Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Cient\u00edficas\u2014Universidad de Valladolid (CSIC-UVa), 47003 Valladolid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro","family":"P\u00e9rez-Segura","sequence":"additional","affiliation":[{"name":"Molecular Oncology Laboratory, Hospital Cl\u00ednico San Carlos, IdISSC (Instituto de Investigaci\u00f3n Sanitaria del Hospital Cl\u00ednico San Carlos), 28040 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doug F.","family":"Easton","sequence":"additional","affiliation":[{"name":"Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8023-2009","authenticated-orcid":false,"given":"Peter","family":"Devilee","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4068-9271","authenticated-orcid":false,"given":"Maaike P. G.","family":"Vreeswijk","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8113-1410","authenticated-orcid":false,"given":"Miguel","family":"de la Hoya","sequence":"additional","affiliation":[{"name":"Molecular Oncology Laboratory, Hospital Cl\u00ednico San Carlos, IdISSC (Instituto de Investigaci\u00f3n Sanitaria del Hospital Cl\u00ednico San Carlos), 28040 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9682-5589","authenticated-orcid":false,"given":"Eladio A.","family":"Velasco-Sampedro","sequence":"additional","affiliation":[{"name":"Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Gen\u00e9tica Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Cient\u00edficas\u2014Universidad de Valladolid (CSIC-UVa), 47003 Valladolid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,1,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/s41580-021-00394-2","article-title":"Cellular Functions of the Protein Kinase ATM and Their Relevance to Human Disease","volume":"22","author":"Lee","year":"2021","journal-title":"Nat. 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