{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T16:08:23Z","timestamp":1753891703989,"version":"3.41.2"},"reference-count":37,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,4,20]],"date-time":"2023-04-20T00:00:00Z","timestamp":1681948800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81800219","81873686","82060228"],"award-info":[{"award-number":["81800219","81873686","82060228"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005329","name":"Natural Science Foundation of Guizhou Province","doi-asserted-by":"publisher","award":["[2019]1196","[2021] normal 077"],"award-info":[{"award-number":["[2019]1196","[2021] normal 077"]}],"id":[{"id":"10.13039\/501100005329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004735","name":"Natural Science Foundation of Hunan Province","doi-asserted-by":"publisher","award":["2020JJ3057","2020JJ4830"],"award-info":[{"award-number":["2020JJ3057","2020JJ4830"]}],"id":[{"id":"10.13039\/501100004735","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Mol. Neurosci."],"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Tuberous sclerosis complex (TSC) is a genetic, variably expressed, multisystem disease characterized by benign tumors. It is caused by pathogenic variants of the TSC complex subunit 1 gene (<jats:italic>TSC1<\/jats:italic>) and the TSC complex subunit 2 gene (<jats:italic>TSC2<\/jats:italic>). Genetic testing allows for early diagnosis, genetic counseling, and improved outcomes, but it did not identify a pathogenic variant in up to 25% of all TSC patients. This study aimed to identify the disease-causing variant in a Han-Chinese family with TSC.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>A six-member, three-generation Han-Chinese family with TSC and three unrelated healthy women were recruited. A comprehensive medical examination, a 3-year follow-up, whole exome sequencing, Sanger sequencing, and segregation analysis were performed in the family. The splicing analysis results obtained from six <jats:italic>in silico<\/jats:italic> tools, minigene assay, and patients' lymphocyte messenger RNA were compared, and quantitative reverse transcription PCR was used to confirm the pathogenicity of the variant.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Two affected family members had variable clinical manifestations including a rare bilateral cerebellar ataxia symptom. The 3-year follow-up results suggest the effects of a combined treatment of anti-epilepsy drugs and sirolimus for TSC-related epilepsy and cognitive deficits. Whole exome sequencing, Sanger sequencing, segregation analysis, splicing analysis, and quantitative reverse transcription PCR identified the <jats:italic>TSC2<\/jats:italic> gene c.2742+5G&amp;gt;A variant as the genetic cause. This variant inactivated the donor splice site, a cryptic non-canonical splice site was used for different splicing changes in two affected subjects, and the resulting mutant messenger RNA may be degraded by nonsense-mediated decay. The defects of <jats:italic>in silico<\/jats:italic> tools and minigene assay in predicting cryptic splice sites were suggested.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>This study identified a <jats:italic>TSC2<\/jats:italic> c.2742+5G&amp;gt;A variant as the genetic cause of a Han-Chinese family with TSC and first confirmed its pathogenicity. These findings expand the phenotypic and genetic spectrum of TSC and may contribute to its diagnosis and treatment, as well as a better understanding of the splicing mechanism.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fnmol.2023.1091323","type":"journal-article","created":{"date-parts":[[2023,4,20]],"date-time":"2023-04-20T14:31:31Z","timestamp":1682001091000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["The TSC2 c.2742+5G&gt;A variant causes variable splicing changes and clinical manifestations in a family with tuberous sclerosis complex"],"prefix":"10.3389","volume":"16","author":[{"given":"Kuan","family":"Fan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Guo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhi","family":"Song","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lamei","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wen","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiao","family":"Hu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lina","family":"Gong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Deng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2023,4,20]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1007\/s13353-018-0444-7","article-title":"Splicing mutations in human genetic disorders: examples, detection, and confirmation","volume":"59","author":"Abramowicz","year":"2018","journal-title":"J. Appl. Genet."},{"volume-title":"Diagnostic and Statistical Manual of Mental Disorders, 5th Edn","year":"2013","key":"B2"},{"key":"B3","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.yebeh.2017.02.007","article-title":"Influence of seizures on early development in tuberous sclerosis complex","volume":"70","author":"Capal","year":"2017","journal-title":"Epilepsy Behav"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-S2-S4","article-title":"An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs","volume":"14","author":"Chang","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"B5","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.pediatrneurol.2017.05.014","article-title":"Early detection of tuberous sclerosis complex: an opportunity for improved neurodevelopmental outcome","volume":"76","author":"Chung","year":"2017","journal-title":"Pediatr. Neurol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1016\/S0140-6736(08)61279-9","article-title":"Tuberous sclerosis","volume":"372","author":"Curatolo","year":"2008","journal-title":"Lancet"},{"key":"B7","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1016\/S1474-4422(15)00069-1","article-title":"Neurological and neuropsychiatric aspects of tuberous sclerosis complex","volume":"14","author":"Curatolo","year":"2015","journal-title":"Lancet Neurol."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1208","DOI":"10.1111\/epi.16892","article-title":"Early epileptiform EEG activity in infants with tuberous sclerosis complex predicts epilepsy and neurodevelopmental outcomes","volume":"62","author":"De Ridder","year":"2021","journal-title":"Epilepsia"},{"key":"B9","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1186\/s13023-018-0901-8","article-title":"TSC-associated neuropsychiatric disorders (TAND): findings from the TOSCA natural history study","volume":"13","author":"de Vries","year":"2018","journal-title":"Orphanet J. Rare Dis."},{"key":"B10","doi-asserted-by":"publisher","first-page":"e67","DOI":"10.1093\/nar\/gkp215","article-title":"Human Splicing Finder: an online bioinformatics tool to predict splicing signals","volume":"37","author":"Desmet","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"B11","doi-asserted-by":"publisher","first-page":"4169","DOI":"10.1093\/hmg\/ddy289","article-title":"A novel mouse model of hemangiopericytoma due to loss of Tsc2","volume":"27","author":"Du","year":"2018","journal-title":"Hum. Mol. Genet"},{"key":"B12","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1186\/s13023-018-0870-y","article-title":"Incidence of tuberous sclerosis and age at first diagnosis: new data and emerging trends from a national, prospective surveillance study","volume":"13","author":"Ebrahimi-Fakhari","year":"2018","journal-title":"Orphanet J. Rare Dis."},{"key":"B13","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1002\/humu.10295","article-title":"Nonclassical splicing mutations in the coding and noncoding regions of the ATM gene: maximum entropy estimates of splice junction strengths","volume":"23","author":"Eng","year":"2004","journal-title":"Hum. Mutat."},{"key":"B14","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/j.neurad.2009.12.006","article-title":"Cerebellar abnormality in children and young adults with tuberous sclerosis complex: MR and diffusion weighted imaging findings","volume":"37","author":"Ertan","year":"2010","journal-title":"J. Neuroradiol."},{"key":"B15","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1007\/s00415-018-9125-z","article-title":"The identification of a transthyretin variant p.D38G in a Chinese family with early-onset leptomeningeal amyloidosis","volume":"266","author":"Fan","year":"2019","journal-title":"J. Neurol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"3439","DOI":"10.1093\/nar\/24.17.3439","article-title":"Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information","volume":"24","author":"Hebsgaard","year":"1996","journal-title":"Nucleic Acids Res."},{"key":"B17","doi-asserted-by":"publisher","first-page":"16035","DOI":"10.1038\/nrdp.2016.35","article-title":"Tuberous sclerosis complex","volume":"2","author":"Henske","year":"2016","journal-title":"Nat. Rev. Dis. Primers"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1228","DOI":"10.1002\/humu.22101","article-title":"Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico\/in vitro studies on BRCA1 and BRCA2 variants","volume":"33","author":"Houdayer","year":"2012","journal-title":"Hum. Mutat."},{"key":"B19","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1212\/01.WNL.0000113745.58425.EF","article-title":"Monozygotic twins with tuberous sclerosis discordant for the severity of developmental deficits","volume":"62","author":"Humphrey","year":"2004","journal-title":"Neurology"},{"key":"B20","doi-asserted-by":"publisher","first-page":"1829","DOI":"10.1101\/gad.1110003","article-title":"Rheb GTPase is a direct target of TSC2 GAP activity and regulates mTOR signaling","volume":"17","author":"Inoki","year":"2003","journal-title":"Genes Dev."},{"key":"B21","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1186\/1471-2350-12-29","article-title":"Evidence for population variation in TSC1 and TSC2 gene expression","volume":"12","author":"Jentarra","year":"2011","journal-title":"BMC Med. Genet."},{"key":"B22","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1007\/s10571-006-9106-0","article-title":"Giant cells: contradiction to two-hit model of tuber formation?","volume":"27","author":"Jozwiak","year":"2007","journal-title":"Cell. Mol. Neurobiol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1177\/197140090601900503","article-title":"Cerebellar lesions in children with tuberous sclerosis complex","volume":"19","author":"Jurkiewicz","year":"2006","journal-title":"Neuroradiol. J."},{"key":"B24","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1002\/acn3.494","article-title":"Everolimus for treatment of tuberous sclerosis complex-associated neuropsychiatric disorders","volume":"4","author":"Krueger","year":"2017","journal-title":"Ann. Clin. Transl. Neurol."},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.3390\/ijms22136677","article-title":"Brain symptoms of tuberous sclerosis complex: pathogenesis and treatment","author":"Mizuguchi","year":"2021","journal-title":"Int. J. Mol. Sci"},{"key":"B26","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/j.pediatrneurol.2013.08.001","article-title":"Tuberous sclerosis complex diagnostic criteria update: recommendations of the 2012 International Tuberous Sclerosis Complex Consensus Conference","volume":"49","author":"Northrup","year":"2013","journal-title":"Pediatr. Neurol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1111\/j.1749-6632.1991.tb37754.x","article-title":"Epidemiology of tuberous sclerosis","volume":"615","author":"Osborne","year":"1991","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"B28","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1177\/088307389300800206","article-title":"The value of the Mini-Mental State Examination in childhood: a preliminary study","volume":"8","author":"Ouvrier","year":"1993","journal-title":"J. Child Neurol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1089\/cmb.1997.4.311","article-title":"Improved splice site detection in Genie","volume":"4","author":"Reese","year":"1997","journal-title":"J. Comput. Biol."},{"key":"B30","doi-asserted-by":"publisher","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":"B31","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1016\/j.pediatrneurol.2016.07.003","article-title":"Applying the lessons of tuberous sclerosis: the 2015 Hower Award Lecture","volume":"63","author":"Roach","year":"2016","journal-title":"Pediatr. Neurol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1177\/0883073807307098","article-title":"A preliminary study of the mini-mental state examination in a Spanish child population","volume":"22","author":"Rubial-Alvarez","year":"2007","journal-title":"J. Child Neurol"},{"key":"B33","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.pediatrneurol.2016.03.015","article-title":"Advances and future directions for tuberous sclerosis complex research: recommendations from the 2015 strategic planning conference","volume":"60","author":"Sahin","year":"2016","journal-title":"Pediatr. Neurol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1038\/sj.ejhg.5201402","article-title":"Mutational analysis of the TSC1 and TSC2 genes in a diagnostic setting: genotype\u2013phenotype correlations and comparison of diagnostic DNA techniques in tuberous sclerosis complex","volume":"13","author":"Sancak","year":"2005","journal-title":"Eur. J. Hum. Genet."},{"key":"B35","doi-asserted-by":"publisher","first-page":"e1005637","DOI":"10.1371\/journal.pgen.1005637","article-title":"Mosaic and intronic mutations in TSC1\/TSC2 explain the majority of TSC patients with no mutation identified by conventional testing","volume":"11","author":"Tyburczy","year":"2015","journal-title":"PLoS Genet."},{"key":"B36","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1016\/j.gene.2005.07.015","article-title":"Characterization and prediction of alternative splice sites","volume":"366","author":"Wang","year":"2006","journal-title":"Gene"},{"key":"B37","doi-asserted-by":"publisher","first-page":"758903","DOI":"10.3389\/fcvm.2021.758903","article-title":"Novel SCN5A and GPD1L variants identified in two unrelated Han-Chinese patients with clinically suspected Brugada syndrome","volume":"8","author":"Yuan","year":"2021","journal-title":"Front. Cardiovasc. Med."}],"container-title":["Frontiers in Molecular Neuroscience"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fnmol.2023.1091323\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,20]],"date-time":"2023-04-20T14:31:37Z","timestamp":1682001097000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fnmol.2023.1091323\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,20]]},"references-count":37,"alternative-id":["10.3389\/fnmol.2023.1091323"],"URL":"https:\/\/doi.org\/10.3389\/fnmol.2023.1091323","relation":{},"ISSN":["1662-5099"],"issn-type":[{"type":"electronic","value":"1662-5099"}],"subject":[],"published":{"date-parts":[[2023,4,20]]},"article-number":"1091323"}}