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Zhang R, Lang Y, Shi X, Zhang Y, Liu X, Pan F, Qiao D, Teng X, Shao L. Three exonic variants in the COL4A5 gene alter RNA splicing in a minigene assay. Mol Genet Genomic Med 2024; 12:e2395. [PMID: 38400605 PMCID: PMC10891438 DOI: 10.1002/mgg3.2395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND X-linked Alport syndrome (XLAS) is an inherited renal disease caused by rare variants of COL4A5 on chromosome Xq22. Many studies have indicated that single nucleotide variants (SNVs) in exons can disrupt normal splicing process of the pre-mRNA by altering various splicing regulatory signals. The male patients with XLAS have a strong genotype-phenotype correlation. Confirming the effect of variants on splicing can help to predict kidney prognosis. This study aimed to investigate whether single nucleotide substitutions, located within three bases at the 5' end of the exons or internal position of the exons in COL4A5 gene, cause aberrant splicing process. METHODS We analyzed 401 SNVs previously presumed missense and nonsense variants in COL4A5 gene by bioinformatics programs and identified candidate variants that may affect the splicing of pre-mRNA via minigene assays. RESULTS Our study indicated three of eight candidate variants induced complete or partial exon skipping. Variants c.2678G>C and c.2918G>A probably disturb classic splice sites leading to corresponding exon skipping. Variant c.3700C>T may disrupt splicing enhancer motifs accompanying with generation of splicing silencer sequences resulting in the skipping of exon 41. CONCLUSION Our study revealed that two missense variants positioned the first nucleotides of the 5' end of COL4A5 exons and one internal exonic nonsense variant caused aberrant splicing. Importantly, this study emphasized the necessity of assessing the effects of SNVs at the mRNA level.
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Affiliation(s)
- Ran Zhang
- Department of Nephrologythe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Yanhua Lang
- Department of Materialsthe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Xiaomeng Shi
- Department of Nephrologythe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Yiyin Zhang
- Department of Nephrologythe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Xuyan Liu
- Department of Nephrologythe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Fengjiao Pan
- Department of Nephrologythe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Dan Qiao
- Department of Nephrologythe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Xin Teng
- Department of Ultrasoundthe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
| | - Leping Shao
- Department of Nephrologythe Affiliated Qingdao Municipal Hospital of Qingdao UniversityQingdaoChina
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Yang J, Ni L, Li A, Li M, Ruan S, Xiang D, Zhu Z, Ye L. A novel homozygous splice-site mutation of JK gene leads to Jk(a-b-) phenotype. Transfus Med 2024; 34:39-45. [PMID: 37950522 DOI: 10.1111/tme.13016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/28/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
OBJECTIVES This study aimed to investigate the molecular mechanism of the Jk(a-b-) phenotype in a Chinese transfusion patient. BACKGROUND Many different mutation types relating to Jk(a-b-) phenotype have been reported. However, the splice-site mutation is relatively rare and the related functional verification is lacking. MATERIALS AND METHODS In this study, the blood sample was collected from a transfusion patient with the Jk(a-b-) phenotype. Serotyping was performed using routine serological methods. The exons sequences and coding regions of the JK gene were amplified using polymerase chain reaction and directly sequenced. To perform a minigene splicing assay, the intronic mutation sequences were cloned into a pSPL3 splice reporting vector. The splicing reporter minigene assay was performed in HEK 293T cells. RESULTS The Jk(a-b-) phenotype of the blood sample was identified through serological testing. Sequencing results revealed that the sample had a novel homozygous splice-site mutation JK*02N (NM_015865.7: c.663+3A>C). Further analysis, including cDNA sequencing and minigene splicing assay, confirmed that the novel splice-site mutation resulted in exon skipping. Interestingly, different numbers of exons being skipped were obtained by the two methods. CONCLUSION This study revealed a novel homozygous splicing-site mutation associated with the Jk(a-b-) phenotype in Chinese population. Our results emphasise the importance of the in vitro functional method minigene splicing assay, while also acknowledging its potential limitations when compared to cDNA sequencing.
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Affiliation(s)
- Jiaxuan Yang
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Lina Ni
- Department of Blood Transfusion, Weihai Central Hospital, Weihai, China
| | - Aijing Li
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Minghao Li
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Shulin Ruan
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Dong Xiang
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Ziyan Zhu
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
| | - Luyi Ye
- Immunohematology Lab, Shanghai Institute of Blood Transfusion, Shanghai Blood Center, Shanghai, China
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Liu X, Shi X, Xin Q, Liu Z, Pan F, Qiao D, Chen M, Zhang Y, Guo W, Li C, Zhang Y, Shao L, Zhang R. Identified eleven exon variants in PKD1 and PKD2 genes that altered RNA splicing by minigene assay. BMC Genomics 2023; 24:407. [PMID: 37468838 PMCID: PMC10354997 DOI: 10.1186/s12864-023-09444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 06/11/2023] [Indexed: 07/21/2023] Open
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is a common monogenic multisystem disease caused primarily by mutations in the PKD1 gene or PKD2 gene. There is increasing evidence that some of these variants, which are described as missense, synonymous or nonsense mutations in the literature or databases, may be deleterious by affecting the pre-mRNA splicing process. RESULTS This study aimed to determine the effect of these PKD1 and PKD2 variants on exon splicing combined with predictive bioinformatics tools and minigene assay. As a result, among the 19 candidate single nucleotide alterations, 11 variants distributed in PKD1 (c.7866C > A, c.7960A > G, c.7979A > T, c.7987C > T, c.11248C > G, c.11251C > T, c.11257C > G, c.11257C > T, c.11346C > T, and c.11393C > G) and PKD2 (c.1480G > T) were identified to result in exon skipping. CONCLUSIONS We confirmed that 11 variants in the gene of PKD1 and PKD2 affect normal splicing by interfering the recognition of classical splicing sites or by disrupting exon splicing enhancers and generating exon splicing silencers. This is the most comprehensive study to date on pre-mRNA splicing of exonic variants in ADPKD-associated disease-causing genes in consideration of the increasing number of identified variants in PKD1 and PKD2 gene in recent years. These results emphasize the significance of assessing the effect of exon single nucleotide variants in ADPKD at the mRNA level.
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Affiliation(s)
- Xuyan Liu
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Xiaomeng Shi
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Qing Xin
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Zhiying Liu
- Renal Division, Peking University First Hospital, Beijing, China
| | - Fengjiao Pan
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Dan Qiao
- Department of Nephrology, Dalian Medical University, Dalian, China
| | - Mengke Chen
- Department of Nephrology, Shandong First Medical University, Taian, China
| | - Yiyin Zhang
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Wencong Guo
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Changying Li
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China
| | - Yan Zhang
- Department of Nephrology, Weifang Medical University, Weifang, China
| | - Leping Shao
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China.
| | - Ruixiao Zhang
- Department of Emergency, the Affiliated Qingdao Municipal Hospital of Qingdao University, No.5 Donghai Middle Road, Qingdao, 266071, China.
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Shi X, Wang H, Zhang R, Liu Z, Guo W, Wang S, Liu X, Lang Y, Bottillo I, Dong B, Shao L. Minigene splicing assays reveal new insights into exonic variants of the SLC12A3 gene in Gitelman syndrome. Mol Genet Genomic Med 2023; 11:e2128. [PMID: 36597580 PMCID: PMC10094094 DOI: 10.1002/mgg3.2128] [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: 04/07/2022] [Revised: 09/15/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Gitelman syndrome (GS) is a type of salt-losing tubular disease, most of which is caused by SLC12A3 gene variants, and missense variants account for the majority. Recently, the phenomenon of exon skipping, in which variants disrupt normal pre-mRNA splicing, has been related to a variety of diseases. Therefore, we hypothesize that a certain proportion of SLC12A3 variants can result in disease via interfering with the normal splicing process. METHODS We analyzed 342 previously presumed SLC12A3 missense variants using bioinformatics programs and identified candidate variants that may alter the splicing of pre-mRNA through minigene assays. RESULTS Our study revealed that, among ten candidate variants, six variants (c.602G>A, c.602G>T, c.1667C>T, c.1925G>A, c.2548G>C, and c.2549G>C) led to complete or incomplete exon skipping by affecting exonic splicing regulatory elements and/or disturbing canonical splice sites. CONCLUSION It is worth mentioning that this is the largest study on pre-mRNA splicing of SLC12A3 exonic variants. In addition, our study emphasizes the importance of detecting splicing function at the mRNA level in GS and indicates that minigene analysis is a valuable tool for splicing functional assays of variants in vitro.
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Affiliation(s)
- Xiaomeng Shi
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Hong Wang
- Department of Nephrology, Qingdao Eighth People's Hospital, Qingdao, China
| | - Ruixiao Zhang
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Zhiying Liu
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Wencong Guo
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Sai Wang
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China.,Department of Dermatology, Peking University First Hospital, Beijing, China
| | - Xuyan Liu
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yanhua Lang
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Irene Bottillo
- Division of Medical Genetics, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Bingzi Dong
- Department of Endocrinology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Leping Shao
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
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Xin Q, Liu Q, Liu Z, Shi X, Liu X, Zhang R, Hong Y, Zhao X, Shao L. Twelve exonic variants in the SLC12A1 and CLCNKB genes alter RNA splicing in a minigene assay. Front Genet 2022; 13:961384. [PMID: 36092934 PMCID: PMC9452827 DOI: 10.3389/fgene.2022.961384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Bartter syndrome (BS) is a rare renal tubular disease caused by gene variants in SLC12A1, KCNJ1, CLCNKA, CLCNKB, BSND or MAGED2 genes. There is growing evidence that many exonic mutations can affect the pre-mRNA normal splicing and induce exon skipping by altering various splicing regulatory signals. Therefore, the aim of this study was to gain new insights into the consequences of exonic mutations associated with BS on pre-mRNA splicing.Methods: We analyzed all the missense, nonsense and synonymous variants described in six pathogenic genes by bioinformatics programs and identified candidate mutations that may promote exon skipping through a minigene system.Results: Results of the study showed that 12 of 14 candidate variants distributed in SLC12A1 (c.728G>A, C.735C>G, c.904C>T, c.905G>A, c.1304C>T, c.1493C>T, c.2221A>T) and CLCNKB (c.226C>T, c.228A>C, c.229G>A, c.229G>C, c.1979C>A) were identified to induce splicing alterations. These variants may not only disrupt exonic splicing enhancers (ESEs) but also generate new exonic splicing silencers (ESSs), or disturb the classic splicing sites.Conclusion: To our knowledge, this is a comprehensive study regarding alterations in pre-mRNA of exonic variants in BS pathogenic genes. Our results reinforce the necessity of assessing the consequences of exonic variants at the mRNA level.
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Affiliation(s)
- Qing Xin
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Qihua Liu
- Department of Material Supply Management, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Zhiying Liu
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xiaomeng Shi
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xuyan Liu
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Ruixiao Zhang
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yefeng Hong
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiangzhong Zhao
- Medical Research Center, The Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Xiangzhong Zhao, ; Leping Shao,
| | - Leping Shao
- Department of Nephrology, the Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
- *Correspondence: Xiangzhong Zhao, ; Leping Shao,
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Fan L, Ji L, Xu Y, Shen G, Tang K, Li Z, Ye S, Shen X. A Novel Mutation c.3392G>T of COL2A1 Causes Spondyloepiphyseal Dysplasia Congenital by Affecting Pre-mRNA Splicing. Front Genet 2022; 13:827560. [PMID: 35692839 PMCID: PMC9174977 DOI: 10.3389/fgene.2022.827560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Spondyloepiphyseal dysplasia congenital (SEDC) is a rare chondrodysplasia caused by dominant pathogenic variants in COL2A1. Here, we detected a novel variant c.3392G > T (NM_001844.4) of COL2A1 in a Chinese family with SEDC by targeted next-generation sequencing. To confirm the pathogenicity of the variant, we generated an appropriate minigene construct based on HeLa and HEK293T cell lines. Splicing assay indicated that the mutated minigene led to aberrant splicing of COL2A1 pre-mRNA and produced an alternatively spliced transcript with a skipping of partial exon 48, which generated a predicted in-frame deletion of 15 amino acids (p. Gly1131_Pro1145del) in the COL2A1 protein. Due to the pathogenicity of the variation, we performed prenatal diagnosis on the proband’s wife, which indicated that the fetus carried the same mutation.
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Affiliation(s)
- Lihong Fan
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Longfei Ji
- Department of Clinical Laboratory, The First People's Hospital of Huzhou, Huzhou, China
| | - Yuqing Xu
- Department of Reproductive Genetics, Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China
| | - Guosong Shen
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Kefeng Tang
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Zhi Li
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Sisi Ye
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
| | - Xueping Shen
- Center of Prenatal Diagnosis, Huzhou Maternity & Child Health Care Hospital, Huzhou, China
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Wang S, Shao Y, Wang Y, Lu J, Shao L. Identification of Four Novel COL4A5 Variants and Detection of Splicing Abnormalities in Three Chinese X-Linked Alport Syndrome Families. Front Genet 2022; 13:847777. [PMID: 35368650 PMCID: PMC8968133 DOI: 10.3389/fgene.2022.847777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/01/2022] [Indexed: 12/03/2022] Open
Abstract
Chronic renal disease associated with X-linked Alport syndrome (XLAS) is relatively rare. However, due to the lack of specificity in the pathologic and clinical manifestations of the disease, it is easy to be misdiagnosed. In this study, we included three Chinese families with XLAS and used targeted NGS to find gene variants. In family X1, the 36-year-old male proband had hematuria, massive proteinuria, sensorineural deafness and ESRD at 33. In silico prediction showed the novel c.1424-4C > G variant reduced the score of the normal 3’ splice site from 0.47 to 0.00 (according to BDGP). Transcriptional analysis from his peripheral blood cells indicated that it caused the insertion of an amino acid [p.(Lys474_Gly475insVal)]. In family X2, the proband was a 32-year-old male, who had hematuria, proteinuria, hypertension, hearing loss and progressed into ESRD at 30 years. He carried a novel missense variant c.2777G > T p.(Gly926Val). In family X3, the proband, a 16-year-old male, had hematuria, massive proteinuria, sensorineural deafness and ESRD; the results of renal pathological findings were consistent with AS. He carried a novel variant c.4529-2A > T, so did his mother with ESRD and probable XLAS. Bioinformatic analysis with BDGP showed that it abolished the acceptor site from 0.83 to 0.00. RT-PCR analysis from his kidney tissue indicated that it caused exon 50 skipping and exon 50 skipping along with inserting a cryptic exon derived from intron 49 p.[Gly1510Aspfs*11, Gly1510Alafs*35]. Another novel missense variant c.1552G > A p.(Gly518Arg) was identified in his mother and his aunt. No skewed X-chromosome inactivation was involved in these two female patients. In conclusion, four novel variants in COL4A5 were identified and transcriptional analysis is essential to investigate the pathogenicity of intronic variants. Thus we found a rare event in a female patient with XLAS caused by two COL4A5 variants in trans.
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Affiliation(s)
- Sai Wang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
- Department of Dermatology, Peking University First Hospital, Beijing, China
| | - Yingfei Shao
- Wenzhou Medical University Renji College, Wenzhou, China
| | - Yixiu Wang
- Darpartment of Hepatic Surgery, Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingru Lu
- School of Medicine, Southeast University, Nanjing, China
| | - Leping Shao
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
- *Correspondence: Leping Shao,
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Zhang R, Chen Z, Song Q, Wang S, Liu Z, Zhao X, Shi X, Guo W, Lang Y, Bottillo I, Shao L. Identification of seven exonic variants in the SLC4A1, ATP6V1B1, and ATP6V0A4 genes that alter RNA splicing by minigene assay. Hum Mutat 2021; 42:1153-1164. [PMID: 34157794 DOI: 10.1002/humu.24246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/02/2021] [Accepted: 06/19/2021] [Indexed: 12/25/2022]
Abstract
Primary distal renal tubular acidosis (dRTA) is a rare tubular disease associated with variants in SLC4A1, ATP6V0A4, ATP6V1B1, FOXⅠ1, or WDR72 genes. Currently, there is growing evidence that all types of exonic variants can alter splicing regulatory elements, affecting the precursor messenger RNA (pre-mRNA) splicing process. This study was to determine the consequences of variants associated with dRTA on pre-mRNA splicing combined with predictive bioinformatics tools and minigene assay. As a result, among the 15 candidate variants, 7 variants distributed in SLC4A1 (c.1765C>T, p.Arg589Cys), ATP6V1B1 (c.368G>T, p.Gly123Val; c.370C>T, p.Arg124Trp; c.484G>T, p.Glu162* and c.1102G>A, p.Glu368Lys) and ATP6V0A4 genes (c.322C>T, p.Gln108* and c.1572G>A, p.Pro524Pro) were identified to result in complete or incomplete exon skipping by either disruption of exonic splicing enhancers (ESEs) and generation of exonic splicing silencers, or interference with the recognition of the classic splicing site, or both. To our knowledge, this is the first study on pre-mRNA splicing of exonic variants in the dRTA-related genes. These results highlight the importance of assessing the effects of exonic variants at the mRNA level and suggest that minigene analysis is an effective tool for evaluating the effects of splicing on variants in vitro.
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Affiliation(s)
- Ruixiao Zhang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Zeqing Chen
- Academy for Engineering and Technology, Fudan University, Shanghai, China
| | - Qijing Song
- Emergency Center, People's Hospital of Jimo District, Qingdao, China
| | - Sai Wang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China.,Department of Dermatology, Peking University First Hospital, Beijing, China
| | - Zhiying Liu
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Xiangzhong Zhao
- Central Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaomeng Shi
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Wencong Guo
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Yanhua Lang
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
| | - Irene Bottillo
- Division of Medical Genetics, Department of Molecular Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Leping Shao
- Department of Nephrology, The Affiliated Qingdao Municipal Hospital of Qingdao University, Qingdao, China
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Li Q, Wang Y, Pan Y, Wang J, Yu W, Wang X. Unraveling synonymous and deep intronic variants causing aberrant splicing in two genetically undiagnosed epilepsy families. BMC Med Genomics 2021; 14:152. [PMID: 34107977 PMCID: PMC8188693 DOI: 10.1186/s12920-021-01008-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
Background Variants identified through parent–child trio-WES yield up to 28–55% positive diagnostic rate across a variety of Mendelian disorders, there remain numerous patients who do not receive a genetic diagnosis. Studies showed that some aberrant splicing variants, which are either not readily detectable by WES or could be miss-interpreted by regular detecting pipelines, are highly relevant to human diseases. Methods We retrospectively investigated the negative molecular diagnostics through trio-WES for 15 genetically undiagnosed patients whose clinical manifestations were highly suspected to be genetic disorders with well-established genotype–phenotype relationships. We scrutinized the synonymous variants from WES data and Sanger sequenced the suspected intronic region for deep intronic variants. The functional consequences of variants were analyzed by in vitro minigene experiments. Results Here, we report two abnormal splicing events, one of which caused exon truncating due to the activation of cryptic splicing site by a synonymous variant; the other caused partial intron retention due to the generation of splicing sites by a deep intronic variant. Conclusions We suggest that, despite initial negative genetic test results in clinically highly suspected genetic diseases, the combination of predictive bioinformatics and functional analysis should be considered to unveil the genetic etiology of undiagnosed rare diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01008-8.
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Affiliation(s)
- Qiang Li
- Guiyang Maternal and Child Health Care Hospital, Guiyang, 550002, China.
| | | | - Yijun Pan
- Guiyang Maternal and Child Health Care Hospital, Guiyang, 550002, China
| | - Jia Wang
- Cipher Gene, Ltd., Beijing, 100080, China
| | - Weishi Yu
- Cipher Gene, Ltd., Beijing, 100080, China
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