{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T02:18:34Z","timestamp":1774318714240,"version":"3.50.1"},"reference-count":42,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2022,7,4]],"date-time":"2022-07-04T00:00:00Z","timestamp":1656892800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004329","name":"Slovenian research agency","doi-asserted-by":"publisher","award":["P3-0352"],"award-info":[{"award-number":["P3-0352"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Pathogenic\/likely pathogenic variants in susceptibility genes that interrupt RNA splicing are a well-documented mechanism of hereditary cancer syndromes development. However, if RNA studies are not performed, most of the variants beyond the canonical GT-AG splice site are characterized as variants of uncertain significance (VUS). To decrease the VUS burden, we have bioinformatically evaluated all novel VUS detected in 732 consecutive patients tested in the routine genetic counseling process. Twelve VUS that were predicted to cause splicing defects were selected for mRNA analysis. Here, we report a functional characterization of 12 variants located beyond the first two intronic nucleotides using RNAseq in APC, ATM, FH, LZTR1, MSH6, PALB2, RAD51C, and TP53 genes. Based on the analysis of mRNA, we have successfully reclassified 50% of investigated variants. 25% of variants were downgraded to likely benign, whereas 25% were upgraded to likely pathogenic leading to improved clinical management of the patient and the family members.<\/jats:p>","DOI":"10.3390\/ijms23137446","type":"journal-article","created":{"date-parts":[[2022,7,4]],"date-time":"2022-07-04T11:15:05Z","timestamp":1656933305000},"page":"7446","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Identification of Spliceogenic Variants beyond Canonical GT-AG Splice Sites in Hereditary Cancer Genes"],"prefix":"10.3390","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7902-8879","authenticated-orcid":false,"given":"Vita \u0160etraj\u010di\u010d","family":"Drago\u0161","sequence":"first","affiliation":[{"name":"Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia"},{"name":"Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ksenija","family":"Strojnik","sequence":"additional","affiliation":[{"name":"Cancer Genetics Clinic, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7154-2144","authenticated-orcid":false,"given":"Ga\u0161per","family":"Klan\u010dar","sequence":"additional","affiliation":[{"name":"Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Petra","family":"\u0160kerl","sequence":"additional","affiliation":[{"name":"Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vida","family":"Stegel","sequence":"additional","affiliation":[{"name":"Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana","family":"Blatnik","sequence":"additional","affiliation":[{"name":"Biotechnical Faculty, University of Ljubljana, SI-1000 Ljubljana, Slovenia"},{"name":"Cancer Genetics Clinic, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marta","family":"Banjac","sequence":"additional","affiliation":[{"name":"Cancer Genetics Clinic, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mateja","family":"Krajc","sequence":"additional","affiliation":[{"name":"Cancer Genetics Clinic, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8888-4810","authenticated-orcid":false,"given":"Srdjan","family":"Novakovi\u0107","sequence":"additional","affiliation":[{"name":"Department of Molecular Diagnostics, Institute of Oncology Ljubljana, SI-1000 Ljubljana, Slovenia"},{"name":"Faculty of Medicine, University of Ljubljana, SI-1000 Ljubljana, Slovenia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,7,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nrg775","article-title":"Listening to silence and understanding nonsense: Exonic mutations that affect splicing","volume":"3","author":"Cartegni","year":"2002","journal-title":"Nat. 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