De novo variants (DNVs) cause many genetic diseases. When DNVs are examined in the whole coding regions of genes in next-generation sequencing analyses, pathogenic DNVs often cluster in a specific region. One such region is the last exon and the last 50 bp of the penultimate exon, where truncating DNVs cause escape from nonsense-mediated mRNA decay [NMD(-) region]. Such variants can have dominant-negative or gain-of-function effects. Here, we first developed a resource of rates of truncating DNVs in NMD(-) regions under the null model of DNVs. Utilizing this resource, we performed enrichment analysis of truncating DNVs in NMD(-) regions in 346 developmental and epileptic encephalopathy (DEE) trios. We observed statistically significant enrichment of truncating DNVs in semaphorin 6B (SEMA6B) (p value: 2.8 × 10-8; exome-wide threshold: 2.5 × 10-6). The initial analysis of the 346 individuals and additional screening of 1,406 and 4,293 independent individuals affected by DEE and developmental disorders collectively identified four truncating DNVs in the SEMA6B NMD(-) region in five individuals who came from unrelated families (p value: 1.9 × 10-13) and consistently showed progressive myoclonic epilepsy. RNA analysis of lymphoblastoid cells established from an affected individual showed that the mutant allele escaped NMD, indicating stable production of the truncated protein. Importantly, heterozygous truncating variants in the NMD(+) region of SEMA6B are observed in general populations, and SEMA6B is most likely loss-of-function tolerant. Zebrafish expressing truncating variants in the NMD(-) region of SEMA6B orthologs displayed defective development of brain neurons and enhanced pentylenetetrazole-induced seizure behavior. In summary, we show that truncating DNVs in the final exon of SEMA6B cause progressive myoclonic epilepsy.

中文翻译：

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SEMA6B最后一个外显子的从头截短变体导致进行性肌阵挛性癫痫。

从头变异（DNV）导致许多遗传疾病。在下一代测序分析中，在基因的整个编码区域中检查DNV时，致病性DNV通常会聚集在特定区域中。这样的区域之一是倒数第二个外显子的最后一个外显子和最后50 bp，其中截短的DNV导致从无义介导的mRNA衰变[NMD（-）区域]逃逸。这样的变体可以具有显性负性或功能获得性效应。在这里，我们首先在DNV无效模型下开发了NMD（-）区域中DNV截断率的资源。利用这一资源，我们在346个发育和癫痫性脑病（DEE）三重症患者的NMD（-）区进行了截短的DNV富集分析。我们观察到了信号量6B（SEMA6B）中截短的DNV的统计学显着富集（p值：2.8×10-8；外显子组范围的阈值：2.5×10-6）。初步分析了346个个体，并对受DEE和发育障碍影响的1,406和4,293个独立个体进行了进一步筛查，共同确定了来自不相关家庭的5个人中SEMA6B NMD（-）地区的4个截短的DNV（p值：1.9×10 -13）并持续显示进行性肌阵挛性癫痫。从患病个体建立的淋巴母细胞的RNA分析表明突变等位基因逃脱了NMD，表明截短蛋白的稳定产生。重要的是，在普通人群中观察到了SEMA6B NMD（+）区的杂合截断变体，而SEMA6B最有可能是功能丧失耐受性。在SEMA6B直系同源物的NMD（-）区表达截短变体的斑马鱼显示脑神经元发育不良，并增强了戊四唑诱发的癫痫发作行为。总之，我们显示在SEMA6B的最后一个外显子中截短DNV会导致进行性肌阵挛性癫痫。