Evaluation of the effect of c.2946+1G>T mutation on splicing in the SCN1A gene

Comput Biol Chem. 2015 Feb;54:44-8. doi: 10.1016/j.compbiolchem.2015.01.003. Epub 2015 Jan 5.


Mutations in the SCN1A gene have commonly been associated with a wide range of mild to severe epileptic syndromes. They generate a wide spectrum of phenotypes ranging from the relatively mild generalized epilepsy with febrile seizures plus (GEFS+) to other severe epileptic encephalopathies, including myoclonic epilepsy in infancy (SMEI), cryptogenic focal epilepsy (CFE), cryptogenic generalized epilepsy (CGE) and a distinctive subgroup termed as severe infantile multifocal epilepsy (SIMFE). The present study was undertaken to investigate the potential effects of a transition in the first nucleotide at the donor splice site of intron 15 of the SCN1A gene leading to CGES. Functional analyses using site-directed mutagenesis by PCR and subsequent ex-vivo splicing assays, revealed that the c.2946+1G>T mutation lead to a total skipping of exon 15. The exclusion of this exon did not alter the reading frame but induced the deletion of the amino acids (853 Leu -971 Val) which are a major part in the fourth, fifth and sixth transmembrane segments of the SCN1A protein. The theoretical implications of the splice site mutations predicted with the bioinformatic tool human splice finder were investigated and compared with the results obtained by the cellular assay.

Keywords: Cryptogenic generalized epilepsy; Directed mutagenesis; Exon skipping; Functional analysis; SCN1A gene.

MeSH terms

  • Amino Acid Sequence*
  • Base Sequence
  • Cloning, Molecular
  • Epilepsies, Myoclonic / genetics*
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Exons
  • Gene Expression
  • Humans
  • Introns*
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Mutation*
  • NAV1.1 Voltage-Gated Sodium Channel / chemistry
  • NAV1.1 Voltage-Gated Sodium Channel / genetics*
  • Phenotype
  • RNA Splice Sites
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Sequence Deletion*


  • NAV1.1 Voltage-Gated Sodium Channel
  • RNA Splice Sites
  • Recombinant Proteins
  • SCN1A protein, human