De Novo Truncating Variants in the Last Exon of SEMA6B Cause Progressive Myoclonic Epilepsy

Kohei Hamanaka, Eri Imagawa, Eriko Koshimizu, Satoko Miyatake, Jun Tohyama, Takanori Yamagata, Akihiko Miyauchi, Nina Ekhilevitch, Fumio Nakamura, Takeshi Kawashima, Yoshio Goshima, Ahmad Rithauddin Mohamed, Gaik Siew Ch'ng, Atsushi Fujita, Yoshiteru Azuma, Ken Yasuda, Shintaro Imamura, Mitsuko Nakashima, Hirotomo Saitsu, Satomi MitsuhashiTakeshi Mizuguchi, Atsushi Takata, Noriko Miyake, Naomichi Matsumoto

Research output: Contribution to journalArticlepeer-review

28 Scopus citations


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.

Original languageEnglish
Pages (from-to)549-558
Number of pages10
JournalAmerican Journal of Human Genetics
Issue number4
StatePublished - 2 Apr 2020
Externally publishedYes


  • CRISPR-Cas9
  • SEMA6B
  • developmental and epileptic encephalopathy (DEE)
  • genome editing
  • nonsense-mediated mRNA decay (NMD)
  • progressive myoclonic epilepsy
  • semaphorin
  • zebrafish


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