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Garcia ABDM, Viola GD, Corrêa BDS, Fischer TDS, Pinho MCDF, Rodrigues GM, Ashton-Prolla P, Rosset C. An overview of actionable and potentially actionable TSC1 and TSC2 germline variants in an online Database. Genet Mol Biol 2024; 46:e20230132. [PMID: 38373162 PMCID: PMC10876083 DOI: 10.1590/1678-4685-gmb-2023-0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/26/2023] [Indexed: 02/21/2024] Open
Abstract
Tuberous Sclerosis Complex (TSC) is caused by loss of function germline variants in the TSC1 or TSC2 tumor suppressor genes. Genetic testing for the detection of pathogenic variants in either TSC1 or TSC2 was implemented as a diagnostic criterion for TSC. However, TSC molecular diagnosis can be challenging due to the absence of variant hotspots and the high number of variants described. This review aimed to perform an overview of TSC1/2 variants submitted in the ClinVar database. Variants of uncertain significance (VUS), missense and single nucleotide variants were the most frequent in clinical significance (37-40%), molecular consequence (37%-39%) and variation type (82%-83%) categories in ClinVar in TSC1 and TSC2 variants, respectively. Frameshift and nonsense VUS have potential for pathogenic reclassification if further functional and segregation studies were performed. Indeed, there were few functional assays deposited in the database and literature. In addition, we did not observe hotspots for variation and many variants presented conflicting submissions regarding clinical significance. This study underscored the importance of disseminating molecular diagnostic results in a public database to render the information largely accessible and promote accurate diagnosis. We encourage the performance of functional studies evaluating the pathogenicity of TSC1/2 variants.
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Affiliation(s)
- Arthur Bandeira de Mello Garcia
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Guilherme Danielski Viola
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Bruno da Silveira Corrêa
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Taís da Silveira Fischer
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Maria Clara de Freitas Pinho
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Centro Universitário CESUCA, Cachoeirinha, RS, Brazil
| | - Grazielle Motta Rodrigues
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
| | - Clévia Rosset
- Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Médicas, Porto Alegre, RS, Brazil
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Dufner Almeida LG, Nanhoe S, Zonta A, Hosseinzadeh M, Kom-Gortat R, Elfferich P, Schaaf G, Kenter A, Kümmel D, Migone N, Povey S, Ekong R, Nellist M. Comparison of the functional and structural characteristics of rare TSC2 variants with clinical and genetic findings. Hum Mutat 2019; 41:759-773. [PMID: 31799751 PMCID: PMC7154745 DOI: 10.1002/humu.23963] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 01/09/2023]
Abstract
The TSC1 and TSC2 gene products interact to form the tuberous sclerosis complex (TSC), an important negative regulator of the mechanistic target of rapamycin complex 1 (TORC1). Inactivating mutations in TSC1 or TSC2 cause TSC, and the identification of a pathogenic TSC1 or TSC2 variant helps establish a diagnosis of TSC. However, it is not always clear whether TSC1 and TSC2 variants are inactivating. To determine whether TSC1 and TSC2 variants of uncertain clinical significance affect TSC complex function and cause TSC, in vitro assays of TORC1 activity can be employed. Here we combine genetic, functional, and structural approaches to try and classify a series of 15 TSC2 VUS. We investigated the effects of the variants on the formation of the TSC complex, on TORC1 activity and on TSC2 pre‐mRNA splicing. In 13 cases (87%), the functional data supported the hypothesis that the identified TSC2 variant caused TSC. Our results illustrate the benefits and limitations of functional testing for TSC.
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Affiliation(s)
- Luiz G Dufner Almeida
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Santoesha Nanhoe
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Andrea Zonta
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Mitra Hosseinzadeh
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Regina Kom-Gortat
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Peter Elfferich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gerben Schaaf
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Annegien Kenter
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Daniel Kümmel
- Biochemistry and Structural Biology Section, Institute of Biochemistry, University of Munster, Munster, Germany
| | - Nicola Migone
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sue Povey
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Rosemary Ekong
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Mark Nellist
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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Ye Y, Zeng Y. Whole exome sequencing identifies a novel intron heterozygous mutation in TSC2 responsible for tuberous sclerosis complex. Sci Rep 2019; 9:4456. [PMID: 30872599 PMCID: PMC6418313 DOI: 10.1038/s41598-019-38898-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 12/21/2018] [Indexed: 11/09/2022] Open
Abstract
This study was aimed to identify the potentially pathogenic gene variants that contribute to the etiology of the tuberous sclerosis complex. A Chinese pedigree with tuberous sclerosis complex was collected and the exomes of two affected individuals were sequenced using the whole exome sequencing technology. The resulting variants from whole exome sequencing were filtered by basic and advanced biological information analysis and the candidate mutation was verified as heterozygous by sanger sequencing. After basic and advanced biological information analysis, a total of 9 single nucleotide variants were identified, which were all follow the dominant inheritance pattern. Among which, the intron heterozygous mutation c.600-145 C > T transition in TSC2 was identified and validated in the two affected individuals. In silico analysis with human splicing finder (HSF) predicted the effect of the c.600-145 C > T mutations on TSC2 mRNA splicing, and detected the creation of a new exonic cryptic donor site, which would result in a frame-shift, and finally premature termination codon. Our results reported the novel intron heterozygous mutation c.600-145 C > T in TSC2 may contribute to TSC, expanding our understanding of the causally relevant genes for this disorder.
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Affiliation(s)
- Yicong Ye
- Department of Cardiology, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
- Department of Cardiology, Chinese Academy of Medical College and Peking Union Medical College Hospital; Peking Union Medical College Hospital, Beijing, 100730, China
| | - Yong Zeng
- Department of Cardiology, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China.
- Department of Cardiology, Chinese Academy of Medical College and Peking Union Medical College Hospital; Peking Union Medical College Hospital, Beijing, 100730, China.
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