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

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

doi:10.3389/fnmol.2022.828846

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

Front Mol Neurosci. 2022 Mar 14:15:828846. doi: 10.3389/fnmol.2022.828846. eCollection 2022.

Authors

Jing-Yang Wang^{1

2

3}, Bin Tang^{1

2}, Wen-Xiang Sheng^{1

2}, Li-Dong Hua⁴, Yang Zeng^{1

2}, Cui-Xia Fan^{1

2}, Wei-Yi Deng^{1

2}, Mei-Mei Gao^{1

2}, Wei-Wen Zhu³, Na He³, Tao Su^{1

2}

Affiliations

¹ Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
² Key Laboratory of Neurogenetics and Channelopathies, Ministry of Education of China, Guangzhou, China.
³ Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
⁴ Translational Medicine Center, Maternal and Child Health Research Institute, Guangdong Women and Children's Hospital, Guangzhou, China.

Abstract

Objective: Naturally 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 (Na_v1.1), have been reported in public database. In contrast to the missense and truncation variants, the in-frame deletions in SCN1A remains largely uncharacterized.

Methods: We 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.

Results: Reviewing all the in-frame deletions showed that they spread over the entire Na_v1.1 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.

Significance: The complete loss-of-function in these shortened, abnormal mutants indicates that Na_v1.1 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.

Keywords: SCN1A; epilepsy; in-frame deletion; sodium channel; variant.