Frontiers in Molecular Neuroscience (Mar 2022)

Clinical and Functional Features of Epilepsy-Associated In-Frame Deletion Variants in SCN1A

  • Jing-Yang Wang,
  • Jing-Yang Wang,
  • Jing-Yang Wang,
  • Bin Tang,
  • Bin Tang,
  • Wen-Xiang Sheng,
  • Wen-Xiang Sheng,
  • Li-Dong Hua,
  • Yang Zeng,
  • Yang Zeng,
  • Cui-Xia Fan,
  • Cui-Xia Fan,
  • Wei-Yi Deng,
  • Wei-Yi Deng,
  • Mei-Mei Gao,
  • Mei-Mei Gao,
  • Wei-Wen Zhu,
  • Na He,
  • Tao Su,
  • Tao Su

DOI
https://doi.org/10.3389/fnmol.2022.828846
Journal volume & issue
Vol. 15

Abstract

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ObjectiveNaturally occurring in-frame deletion is a unique type of genetic variations, causing the loss of one or more amino acids of proteins. A number of in-frame deletion variants in an epilepsy-associated gene SCN1A, encoding voltage gated sodium channel alpha unit 1.1 (Nav1.1), have been reported in public database. In contrast to the missense and truncation variants, the in-frame deletions in SCN1A remains largely uncharacterized.MethodsWe summarized the basic information of forty-four SCN1A in-frame deletion variants and performed further analysis on six variants identified in our cases with epilepsy. Mutants of the six in-frame deletions and one truncating variant used as comparison were generated and co-transfected with beta-1 and -2 subunits in tsA201 cells, followed by patch clamp recordings.ResultsReviewing all the in-frame deletions showed that they spread over the entire Nav1.1 protein, without obvious “hot spots.” The dominant type (54%) was single residue loss. There was no obvious relationship between the length or locations of deletions and their clinical phenotypes. The six in-frame deletions were two single residue deletions (p.M400del and p.I1772del), one microdeletion (p.S128_F130del) and three macrodeletions (p.T303_R322del, p.T160_Y202del, and p.V1335_V1428del). They scatter and affect different functional domains, including transmembrane helices, pore region, and P-loop. Electrophysiological recordings revealed no measurable sodium current in all of the six mutants. In contrast, the truncating mutant p.M1619Ifs*7 that loses a long stretch of peptides retains partial function.SignificanceThe complete loss-of-function in these shortened, abnormal mutants indicates that Nav1.1 protein is a highly accurate structure, and many of the residues have no redundancy to ion conductance. In-frame deletions caused particularly deleterious effect on protein function possibly due to the disruption of ordered residues.

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