Deng Haiyue, Zhang Yanqin, Ding Jie, Wang Fang
Department of Pediatrics, Peking University First Hospital, Beijing, China.
Front Med (Lausanne). 2022 Mar 21;9:838983. doi: 10.3389/fmed.2022.838983. eCollection 2022.
The incorrect interpretation of missense and synonymous variants can lead to improper molecular diagnosis and subsequent faulty genetic counselling. The aim of this study was to evaluate the pathogenicity of presumed missense and synonymous variants detected by next-generation sequencing to provide evidence for diagnosis and genetic counselling.
Patients' clinical findings and genetic data were analysed retrospectively. An minigene assay was conducted to assess the effect of presumed missense and synonymous variants on RNA splicing.
Five unclassified variants, which were detected in five of 343 patients with hereditary kidney diseases, were analysed. All of them were predicted to affect splicing by Human Splicing Finder. The presumed missense variant c.4793T > G [p. (Leu1598Arg)] resulted in a loss of alternative full-length transcript during the splicing process. The transcript carried synonymous variant c.765G > A [p. (Thr255Thr)], led to an in-frame deletion of exon 13. Nevertheless, variants c.3566G > A [p. (Gly1189Glu)] in and c.3990G > A [p. (Pro1330Pro)], c.4766C > T [p. (Pro1589Leu)] in exhibited no deleterious effect on splicing. Among the five patients harbouring the abovementioned variants, three patients were genetically diagnosed with autosomal recessive Alport syndrome, one patient was highly suspected of having thin basement membrane nephropathy, and the other patient was clinically diagnosed with Alport syndrome.
presumed missense variant p. (Leu1598Arg) and synonymous variant p. (Thr255Thr) affect RNA splicing, which highlights the prime importance of transcript analysis of unclassified exonic sequence variants for better molecular diagnosis and genetic counselling. Meanwhile, the reliability of splicing predictions by predictive tools for exonic substitutions needs to be improved.
错义变异和同义变异的错误解读可能导致分子诊断不当及后续错误的遗传咨询。本研究旨在评估通过下一代测序检测到的假定错义变异和同义变异的致病性，为诊断和遗传咨询提供依据。
对患者的临床发现和遗传数据进行回顾性分析。进行了一项微型基因检测，以评估假定的错义变异和同义变异对RNA剪接的影响。
对在343例遗传性肾病患者中的5例检测到的5个未分类变异进行了分析。所有这些变异均被人类剪接预测工具预测会影响剪接。假定的错义变异c.4793T>G [p.（Leu1598Arg）]导致剪接过程中替代全长转录本的缺失。携带同义变异c.765G>A [p.（Thr255Thr）]的转录本导致外显子13的框内缺失。然而，[基因名称未明确]中的变异c.3566G>A [p.（Gly1189Glu）]和[基因名称未明确]中的c.3990G>A [p.（Pro1330Pro）]、c.4766C>T [p.（Pro1589Leu）]对剪接未显示有害影响。在携带上述变异的5例患者中，3例患者被基因诊断为常染色体隐性遗传性阿尔波特综合征，1例患者高度怀疑患有薄基底膜肾病，另1例患者临床诊断为阿尔波特综合征。
假定的错义变异p.（Leu1598Arg）和同义变异p.（Thr255Thr）影响RNA剪接，这突出了对未分类外显子序列变异进行转录本分析对于更好的分子诊断和遗传咨询的至关重要性。同时，外显子替换预测工具的剪接预测可靠性有待提高。
