Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
Eur J Hum Genet. 2024 Feb;32(2):238-242. doi: 10.1038/s41431-023-01495-6. Epub 2023 Nov 27.
A recent report described a nonsense variant simultaneously creating a donor splice site, resulting in a truncated but functional protein. To explore the generalizability of this unique mechanism, we annotated >115,000 nonsense variants using SpliceAI. Between 0.61% (donor gain delta score >0.8, for high precision) and 2.57% (>0.2, for high sensitivity) of nonsense variants were predicted to create new donor splice sites at or upstream of the stop codon. These variants were less likely than other nonsense variants in the same genes to be classified as pathogenic/likely pathogenic in ClinVar (p < 0.001). Up to 1 in 175 nonsense variants were predicted to result in small in-frame deletions and loss-of-function evasion through this "manufactured splice rescue" mechanism. We urge caution when interpreting nonsense variants where manufactured splice rescue is a strong possibility and correlation with phenotype is challenging, as will often be the case with secondary findings and newborn genomic screening programs.
最近的一份报告描述了一种无意义变异同时创建供体位点,导致截短但功能完整的蛋白质。为了探索这种独特机制的普遍性,我们使用 SpliceAI 注释了 >115,000 个无意义变异。在 0.61%(供体位点增益分数>0.8,高精度)和 2.57%(>0.2,高灵敏度)的无意义变异被预测在终止密码子或其上游创建新的供体位点。与同一基因中其他无意义变异相比,这些变异在 ClinVar 中被归类为致病性/可能致病性的可能性更小(p<0.001)。多达 1/175 个无意义变异被预测会导致小的框内缺失,并通过这种“制造的剪接拯救”机制逃避功能丧失。当制造的剪接拯救可能性很大且与表型相关具有挑战性时,我们应谨慎解释无意义变异,这种情况在二级发现和新生儿基因组筛查计划中经常出现。
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