Validating the splicing effect of rare variants in the SLC26A4 gene using minigene assay.

IF 2.1 4区 医学 Q3 GENETICS & HEREDITY
Yixin Zhao, Yan Long, Tao Shi, Xin Ma, Chengyu Lian, Hanjun Wang, Hongen Xu, Lisheng Yu, Xiaotao Zhao
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引用次数: 0

Abstract

Background: The SLC26A4 gene is the second most common cause of hereditary hearing loss in human. The aim of this study was to utilize the minigene assay in order to identify pathogenic variants of SLC26A4 associated with enlarged vestibular aqueduct (EVA) and hearing loss (HL) in two patients.

Methods: The patients were subjected to multiplex PCR amplification and next-generation sequencing of common deafness genes (including GJB2, SLC26A4, and MT-RNR1), then bioinformatics analysis was performed on the sequencing data to identify candidate pathogenic variants. Minigene experiments were conducted to determine the potential impact of the variants on splicing.

Results: Genetic testing revealed that the first patient carried compound heterozygous variants c.[1149 + 1G > A]; [919-2 A > G] in the SLC26A4 gene, while the second patient carried compound heterozygous variants c.[2089 + 3 A > T]; [919-2 A > G] in the same gene. Minigene experiments demonstrated that both c.1149 + 1G > A and c.2089 + 3 A > T affected mRNA splicing. According to the ACMG guidelines and the recommendations of the ClinGen Hearing Loss Expert Panel for ACMG variant interpretation, these variants were classified as "likely pathogenic".

Conclusions: This study identified the molecular etiology of hearing loss in two patients with EVA and elucidated the impact of rare variants on splicing, thus contributing to the mutational spectrum of pathogenic variants in the SLC26A4 gene.

利用微型基因检测验证 SLC26A4 基因罕见变体的剪接效应
背景:SLC26A4基因是导致人类遗传性听力损失的第二大常见原因。本研究的目的是利用微型基因检测法,在两名患者中鉴定与前庭导水管扩大(EVA)和听力损失(HL)相关的 SLC26A4 致病变体:对患者进行常见耳聋基因(包括GJB2、SLC26A4和MT-RNR1)的多重PCR扩增和新一代测序,然后对测序数据进行生物信息学分析,以确定候选致病变体。然后对测序数据进行生物信息学分析,找出候选致病变异体,并进行微型基因实验,以确定这些变异体对剪接的潜在影响:基因检测结果显示,第一位患者携带 SLC26A4 基因中的复合杂合变异 c.[1149 + 1G > A]; [919-2 A > G],而第二位患者携带同一基因中的复合杂合变异 c.[2089 + 3 A > T]; [919-2 A > G]。微型基因实验表明,c.1149 + 1G > A 和 c.2089 + 3 A > T 都会影响 mRNA 的剪接。根据ACMG指南和ClinGen听力损失专家组对ACMG变异解释的建议,这些变异被归类为 "可能致病":本研究确定了两名 EVA 患者听力损失的分子病因,阐明了罕见变异对剪接的影响,从而为 SLC26A4 基因致病变异的突变谱做出了贡献。
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来源期刊
BMC Medical Genomics
BMC Medical Genomics 医学-遗传学
CiteScore
3.90
自引率
0.00%
发文量
243
审稿时长
3.5 months
期刊介绍: BMC Medical Genomics is an open access journal publishing original peer-reviewed research articles in all aspects of functional genomics, genome structure, genome-scale population genetics, epigenomics, proteomics, systems analysis, and pharmacogenomics in relation to human health and disease.
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