Nav1.1 is encoded by SCN1A, an 81-kb gene on the long arm of chromosome 2. Situated at position 2q24.3, SCN1A is part of a cluster of voltage-gated sodium channel genes that is home to SCN2A, SCN3A, SCN7A, as well as SCN9A, which encode Nav1.2, Nav1.3, Nax, and Nav1.7, respectively (Malo et al., Cytogenet Cell Genet 67:178, 1994). Organized into 26 exons, the Nav1.1 open-reading frame blueprints the instructions for a protein incorporating between 1976 and 2009 amino acids. The variance in length stems from alternative splice junctions at the end of exon 11 that produce a full-length isoform or two shortened versions thereof (Lossin et al., Neuron 34:877, 2002), on this web site referred to as Nav1.1[-33] and Nav1.1[-84] based on the number of base pairs deleted. This splicing variability is the cause for the inconsistencies in mutation reports across different research groups, as some are referring to full-length Nav1.1, while others reference Nav1.1[-33], which is approximately 15 times more abundant in the brain (personal observation). References to Nav1.1[-84], other than the original report, do not exist at this time.

A second site of SCN1A RNA processing variability was identified by Copley, who discovered two mutually exclusive exons, 5N and 5A, that give rise to a postnatal and an adulthood isoform of Nav1.1 (Copley, Trends Genet 20:171, 2004). While unique at the nucleic acid level (71 % identity), the amino-residue coding of these two alternative exons is nearly identical, differing only in three positions (90 % identity, Table 1). A similar situation may exist in exon 8 in analogy to murine Nav1.6 (Plummer et al., J Biol Chem 272:24008, 1997); the required genomic sequence analyses have not been conducted at this time. In the SCN1A infobase, full-length Nav1.1 that incorporates adult exon 5A coding is the reference, unless indicated otherwise.


Variable splicing of Nav1.1. (A) Predicted membrane topology of Nav1.1 with the 4x6 organization typical for voltage-gated sodium channels, namely four homologous domains (D1–D4) comprising six transmembrane regions each (S1–S6, from left to right). Amino- and carboxytermini end on the intracellular side. Arrows denote where differential splicing creates sequence variability in the final protein. Solid arrow: point where splice variants lack either 11 or 28 amino acids compared to full-length Nav1.1. Open arrows: amino acid differences owing to alternate encoding via exon 5N or 5A [41] as outlined in Table 1. (B) Alignment of the full-length Nav1.1 protein sequence with that of Nav1.1[-33] and Nav1.1[-84] at the exon 11/12 splice junction. Alternative endings of exon 11 create two shorter variants which omit residues 671–681 or 654–681. The isoform nomenclature refers to the nucleic acid level: compared to full-length Nav1.1 cDNA, the shorter isoforms miss 33 or 84 base pairs. Biochemical and electrophysiological analysis suggest a functional importance of the spliced fragments (personal observation).

Differences in amino acid coding between mutually exclusive exons 5N and 5A


ORF position

201 Tyr (Y) =>Phe (F) D1/S3
207 Asp (D)=>Asn (N)D1/S3-S4ex
211 Val (V)=>Phe (F)D1/S3-S4ex

Topology abbreviations as described here.