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Aliases for SCN1A Gene

Aliases for SCN1A Gene

  • Sodium Channel, Voltage Gated, Type I Alpha Subunit 2 3
  • Sodium Channel, Voltage-Gated, Type I, Alpha Subunit 2 3
  • Voltage-Gated Sodium Channel Subunit Alpha Nav1.1 3 4
  • Sodium Channel Protein Type I Subunit Alpha 3 4
  • GEFSP2 3 6
  • EIEE6 3 6
  • FEB3A 3 6
  • SCN1 3 4
  • NAC1 3 4
  • FHM3 3 6
  • SMEI 3 6
  • Sodium Channel, Voltage-Gated, Type I, Alpha Polypeptide 3
  • Sodium Channel Voltage Gated Type 1 Alpha Subunit 3
  • Sodium Channel Protein, Brain I Alpha Subunit 3
  • Sodium Channel Protein Brain I Subunit Alpha 4
  • Sodium Channel Protein Type 1 Subunit Alpha 3
  • Febrile Convulsions 3 2
  • Nav1.1 3
  • HBSCI 3
  • FEB3 3

External Ids for SCN1A Gene

Previous HGNC Symbols for SCN1A Gene

  • SCN1
  • FEB3

Previous GeneCards Identifiers for SCN1A Gene

  • GC02M164900
  • GC02M165387
  • GC02M166809
  • GC02M167048
  • GC02M166671
  • GC02M166553
  • GC02M158727

Summaries for SCN1A Gene

Entrez Gene Summary for SCN1A Gene

  • The vertebrate sodium channel is a voltage-gated ion channel essential for the generation and propagation of action potentials, mainly in nerve and muscle. Voltage-sensitive sodium channels are heteromeric complexes consisting of a large central pore-forming glycosylated alpha subunit, and two smaller auxiliary beta subunits. This gene encodes the large alpha subunit, and mutations in this gene have been associated with several epilepsy, convulsion and migraine disorders. Alternative splicing results in multiple transcript variants. The RefSeq Project has decided to create four representative RefSeq records. Three of the transcript variants are supported by experimental evidence and the fourth contains alternate 5' untranslated exons, the exact combination of which have not been experimentally confirmed for the full-length transcript.[provided by RefSeq, Jan 2011]

GeneCards Summary for SCN1A Gene

SCN1A (Sodium Channel, Voltage Gated, Type I Alpha Subunit) is a Protein Coding gene. Diseases associated with SCN1A include migraine, familial hemiplegic, 3 and epilepsy, generalized, with febrile seizures plus, type 2. Among its related pathways are L1CAM interactions and Activation of cAMP-Dependent PKA. GO annotations related to this gene include voltage-gated sodium channel activity. An important paralog of this gene is CACNA1D.

UniProtKB/Swiss-Prot for SCN1A Gene

  • Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient

Tocris Summary for SCN1A Gene

  • Voltage-gated sodium channels (NaV) are responsible for action potential initiation and propagation in excitable cells, including nerve, muscle, and neuroendocrine cell types. They are also expressed at low levels in non-excitable cells, where their physiological role is unclear. Structurally, Nav channels are composed of one pore-forming alpha-subunit, which may be associated with either one or more beta-subunits. alpha-subunits are composed for four homologous domains, each of which contains six transmembrane segments. The fourth transmembrane loop (S4) acts as the 'voltage sensor' and is activated by changes in membrane potential. S4 is also involved in channel gating.

Gene Wiki entry for SCN1A Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCN1A Gene

Genomics for SCN1A Gene

Regulatory Elements for SCN1A Gene

Genomic Location for SCN1A Gene

165,989,160 bp from pter
166,149,132 bp from pter
159,973 bases
Minus strand

Genomic View for SCN1A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SCN1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCN1A Gene

Proteins for SCN1A Gene

  • Protein details for SCN1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sodium channel protein type 1 subunit alpha
    Protein Accession:
    Secondary Accessions:
    • E9PG49
    • Q16172
    • Q585T7
    • Q8IUJ6
    • Q96LA3
    • Q9C008

    Protein attributes for SCN1A Gene

    2009 amino acids
    Molecular mass:
    228972 Da
    Quaternary structure:
    • The sodium channel consists of a large polypeptide and 2-3 smaller ones. This sequence represents a large polypeptide. Interacts with FGF13; may regulate SCN1A activity.

    Alternative splice isoforms for SCN1A Gene


neXtProt entry for SCN1A Gene

Proteomics data for SCN1A Gene at MOPED

Post-translational modifications for SCN1A Gene

  • Phosphorylation at Ser-1516 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents.
  • Glycosylation at Asn211, Asn284, Asn295, Asn301, Asn306, Asn338, Asn1378, Asn1392, and Asn1403
  • Modification sites at PhosphoSitePlus

Other Protein References for SCN1A Gene

No data available for DME Specific Peptides for SCN1A Gene

Domains for SCN1A Gene

Gene Families for SCN1A Gene

  • SC :Sodium channels
  • SCN :Voltage-gated ion channels / Sodium channels

Graphical View of Domain Structure for InterPro Entry



  • P35498
  • The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1,S2,S3,S5,S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position
  • Contains 1 IQ domain.
  • Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.1/SCN1A subfamily.
genes like me logo Genes that share domains with SCN1A: view

Function for SCN1A Gene

Molecular function for SCN1A Gene

GENATLAS Biochemistry: sodium voltage-gated channel,type I,alpha polypeptide,expressed in brain
UniProtKB/Swiss-Prot Function: Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient

Gene Ontology (GO) - Molecular Function for SCN1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity --
GO:0005248 voltage-gated sodium channel activity NAS 10742094
genes like me logo Genes that share ontologies with SCN1A: view
genes like me logo Genes that share phenotypes with SCN1A: view

Animal Models for SCN1A Gene

MGI Knock Outs for SCN1A:

miRNA for SCN1A Gene

miRTarBase miRNAs that target SCN1A

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for SCN1A Gene

Localization for SCN1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCN1A Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Jensen Localization Image for SCN1A Gene COMPARTMENTS Subcellular localization image for SCN1A gene
Compartment Confidence
plasma membrane 3
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SCN1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001518 voltage-gated sodium channel complex IEA --
GO:0005886 plasma membrane IBA --
GO:0014704 intercalated disc IEA --
GO:0016020 membrane --
GO:0030018 Z disc ISS --
genes like me logo Genes that share ontologies with SCN1A: view

Pathways for SCN1A Gene

genes like me logo Genes that share pathways with SCN1A: view

Gene Ontology (GO) - Biological Process for SCN1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001508 action potential --
GO:0002230 positive regulation of defense response to virus by host IMP 22020285
GO:0006811 ion transport --
GO:0006814 sodium ion transport NAS 10742094
GO:0007628 adult walking behavior IEA --
genes like me logo Genes that share ontologies with SCN1A: view

Compounds for SCN1A Gene

(5) Tocris Compounds for SCN1A Gene

Compound Action Cas Number
Flecainide acetate Cardiac Na+ channel blocker. Antiarrhythmic [54143-56-5]
QX 314 bromide Na+ channel blocker [24003-58-5]
QX 314 chloride Na+ channel blocker [5369-03-9]
Tetrodotoxin Na+ channel blocker [4368-28-9]
Tetrodotoxin citrate Na+ channel blocker; citrate salt of tetrodotoxin (Cat. No. 1078) [18660-81-6]

(2) HMDB Compounds for SCN1A Gene

Compound Synonyms Cas Number PubMed IDs
  • Sodium
  • Epitomax

(8) Drugbank Compounds for SCN1A Gene

Compound Synonyms Cas Number Type Actions PubMed IDs
141626-36-0 target inhibitor
  • 1, 3-Dihydro-7-nitro-5-phenyl-2H-1,4-benzodiazepin-2-one
146-22-5 target other/unknown
52645-53-1 target inhibitor
  • Carbamide phenylacetate
63-98-9 target inhibitor
94-78-0 target inhibitor

(7) IUPHAR Ligand for SCN1A Gene

Ligand Type Action Affinity Pubmed IDs
tetrodotoxin Pore Blocker Antagonist 7.6
AFT-II Gating inhibitor Antagonist 7.5
ATX-II Gating inhibitor Antagonist 7.3
Bc-III Gating inhibitor Antagonist 6.1
saxitoxin Channel blocker None
veratridine Activator None
batrachotoxin Activator None

(5) Novoseek inferred chemical compound relationships for SCN1A Gene

Compound -log(P) Hits PubMed IDs
sodium 80.2 83
phenytoin 36.5 6
lamotrigine 30.3 3
carbamazepine 16.3 7
potassium 8.38 1

(2) PharmGKB related drug/compound annotations for SCN1A Gene

Drug/compound Annotation
carbamazepine CA
phenytoin CA
genes like me logo Genes that share compounds with SCN1A: view

Transcripts for SCN1A Gene

Unigene Clusters for SCN1A Gene

Sodium channel, voltage-gated, type I, alpha subunit:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SCN1A Gene

No ASD Table

Relevant External Links for SCN1A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCN1A Gene

mRNA expression in normal human tissues for SCN1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCN1A Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (9.2), Brain - Cortex (5.9), and Brain - Anterior cingulate cortex (BA24) (5.7).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for SCN1A Gene

SOURCE GeneReport for Unigene cluster for SCN1A Gene Hs.22654

genes like me logo Genes that share expressions with SCN1A: view

No data available for mRNA Expression by UniProt/SwissProt for SCN1A Gene

Orthologs for SCN1A Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCN1A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SCN1A 35
  • 99.57 (n)
  • 99.9 (a)
SCN1A 36
  • 100 (a)
(Bos Taurus)
Mammalia SCN1A 35
  • 93.63 (n)
  • 98.25 (a)
SCN1A 36
  • 98 (a)
(Canis familiaris)
Mammalia SCN1A 35
  • 94.09 (n)
  • 98.56 (a)
SCN1A 36
  • 98 (a)
(Mus musculus)
Mammalia Scn1a 35
  • 90.44 (n)
  • 98.15 (a)
Scn1a 16
Scn1a 36
  • 98 (a)
(Monodelphis domestica)
Mammalia SCN1A 36
  • 96 (a)
(Ornithorhynchus anatinus)
Mammalia SCN1A 36
  • 89 (a)
(Rattus norvegicus)
Mammalia Scn1a 35
  • 89.96 (n)
  • 98.16 (a)
(Gallus gallus)
Aves SCN1A 35
  • 83.09 (n)
  • 91.2 (a)
(Anolis carolinensis)
Reptilia SCN1A 36
  • 89 (a)
(Danio rerio)
Actinopterygii scn1lab 36
  • 78 (a)
Species with no ortholog for SCN1A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCN1A Gene

Gene Tree for SCN1A (if available)
Gene Tree for SCN1A (if available)

Paralogs for SCN1A Gene

genes like me logo Genes that share paralogs with SCN1A: view

Variants for SCN1A Gene

Sequence variations from dbSNP and Humsavar for SCN1A Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs490317 -- 166,039,668(+) TAGAA(C/T)ATAAT intron-variant
rs492299 -- 166,065,188(+) CTGGA(A/G)GTCAG intron-variant
rs506933 -- 166,039,711(-) ATTTA(A/G)GTTAG intron-variant
rs509727 -- 166,039,401(-) AAAGC(A/C)CCAAA intron-variant
rs531143 -- 166,050,999(-) TACAC(A/C)ATGTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SCN1A Gene

Variant ID Type Subtype PubMed ID
nsv834445 CNV Gain+Loss 17160897
dgv4355n71 CNV Gain 21882294
dgv63n17 CNV Loss 16327808
esv2721076 CNV Deletion 23290073
esv2721077 CNV Deletion 23290073
nsv459936 CNV Loss 19166990
esv2721078 CNV Deletion 23290073
esv2357676 CNV Deletion 18987734
esv2721079 CNV Deletion 23290073
esv2721080 CNV Deletion 23290073

Relevant External Links for SCN1A Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCN1A Gene

Disorders for SCN1A Gene

(3) OMIM Diseases for SCN1A Gene (182389)


  • Generalized epilepsy with febrile seizures plus 2 (GEFS+2) [MIM:604403]: A rare autosomal dominant, familial condition with incomplete penetrance and large intrafamilial variability. Patients display febrile seizures persisting sometimes beyond the age of 6 years and/or a variety of afebrile seizure types. This disease combines febrile seizures, generalized seizures often precipitated by fever at age 6 years or more, and partial seizures, with a variable degree of severity. {ECO:0000269 PubMed:10742094, ECO:0000269 PubMed:11254444, ECO:0000269 PubMed:11254445, ECO:0000269 PubMed:11524484, ECO:0000269 PubMed:11756608, ECO:0000269 PubMed:12919402, ECO:0000269 PubMed:14672992, ECO:0000269 PubMed:15525788, ECO:0000269 PubMed:15694566, ECO:0000269 PubMed:15715999, ECO:0000269 PubMed:16525050, ECO:0000269 PubMed:17507202, ECO:0000269 PubMed:17561957, ECO:0000269 PubMed:18413471, ECO:0000269 PubMed:19464195, ECO:0000269 PubMed:20117752, ECO:0000269 PubMed:20600615, ECO:0000269 PubMed:20729507}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Epileptic encephalopathy, early infantile, 6 (EIEE6) [MIM:607208]: A severe form of epileptic encephalopathy characterized by generalized tonic, clonic, and tonic-clonic seizures that are initially induced by fever and begin during the first year of life. Later, patients also manifest other seizure types, including absence, myoclonic, and simple and complex partial seizures. Psychomotor development delay is observed around the second year of life. Some patients manifest a borderline disease phenotype and do not necessarily fulfill all diagnostic criteria for core EIEE6. EIEE6 is considered to be the most severe phenotype within the spectrum of generalized epilepsies with febrile seizures-plus. {ECO:0000269 PubMed:11359211, ECO:0000269 PubMed:12083760, ECO:0000269 PubMed:12566275, ECO:0000269 PubMed:12754708, ECO:0000269 PubMed:12821740, ECO:0000269 PubMed:14504318, ECO:0000269 PubMed:14738421, ECO:0000269 PubMed:15087100, ECO:0000269 PubMed:15944908, ECO:0000269 PubMed:16122630, ECO:0000269 PubMed:16458823, ECO:0000269 PubMed:16713920, ECO:0000269 PubMed:17054684, ECO:0000269 PubMed:17347258, ECO:0000269 PubMed:17561957, ECO:0000269 PubMed:18413471, ECO:0000269 PubMed:19563458, ECO:0000269 PubMed:19589774, ECO:0000269 PubMed:20110217, ECO:0000269 PubMed:20431604, ECO:0000269 PubMed:20452746, ECO:0000269 PubMed:20522430, ECO:0000269 PubMed:20729507, ECO:0000269 PubMed:22612257}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Intractable childhood epilepsy with generalized tonic-clonic seizures (ICEGTC) [MIM:607208]: A disorder characterized by generalized tonic-clonic seizures beginning usually in infancy and induced by fever. Seizures are associated with subsequent mental decline, as well as ataxia or hypotonia. ICEGTC is similar to SMEI, except for the absence of myoclonic seizures. {ECO:0000269 PubMed:12566275, ECO:0000269 PubMed:17507202}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Migraine, familial hemiplegic, 3 (FHM3) [MIM:609634]: A subtype of migraine associated with transient blindness in some families. Migraine is a disabling symptom complex of periodic headaches, usually temporal and unilateral. Headaches are often accompanied by irritability, nausea, vomiting and photophobia, preceded by constriction of the cranial arteries. The two major subtypes are common migraine (migraine without aura) and classic migraine (migraine with aura). Classic migraine is characterized by recurrent attacks of reversible neurological symptoms (aura) that precede or accompany the headache. Aura may include a combination of sensory disturbances, such as blurred vision, hallucinations, vertigo, numbness and difficulty in concentrating and speaking. {ECO:0000269 PubMed:16054936, ECO:0000269 PubMed:17397047, ECO:0000269 PubMed:18021921, ECO:0000269 PubMed:19332696}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Febrile seizures, familial, 3A (FEB3A) [MIM:604403]: Seizures associated with febrile episodes in childhood without any evidence of intracranial infection or defined pathologic or traumatic cause. It is a common condition, affecting 2-5% of children aged 3 months to 5 years. The majority are simple febrile seizures (generally defined as generalized onset, single seizures with a duration of less than 30 minutes). Complex febrile seizures are characterized by focal onset, duration greater than 30 minutes, and/or more than one seizure in a 24 hour period. The likelihood of developing epilepsy following simple febrile seizures is low. Complex febrile seizures are associated with a moderately increased incidence of epilepsy. {ECO:0000269 PubMed:16326807}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(1) University of Copenhagen DISEASES for SCN1A Gene

(19) Novoseek inferred disease relationships for SCN1A Gene

Disease -log(P) Hits PubMed IDs
dravet syndrome 98.4 32
epilepsies myoclonic 97 58
epilepsy generalized 95.6 38
seizures febrile 95.4 58
hemiplegic migraine familial 91 9

Relevant External Links for SCN1A

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with SCN1A: view

Publications for SCN1A Gene

  1. Localization of a putative human brain sodium channel gene (SCN1A) to chromosome band 2q24. (PMID: 8062593) Malo M.S. … Ingram V.M. (Cytogenet. Cell Genet. 1994) 2 3 4 23
  2. A novel SCN1A mutation associated with generalized epilepsy with febrile seizures plus -- and prevalence of variants in patients with epilepsy. (PMID: 11254445) Escayg A. … Meisler M.H. (Am. J. Hum. Genet. 2001) 3 4 23 48
  3. Spectrum of SCN1A mutations in severe myoclonic epilepsy of infancy. (PMID: 12821740) Nabbout R. … Zara F. (Neurology 2003) 3 4 23 48
  4. The spectrum of SCN1A-related infantile epileptic encephalopathies. (PMID: 17347258) Harkin L.A. … Scheffer I.E. (Brain 2007) 3 4 23 48
  5. A common polymorphism in the SCN1A gene associates with phenytoin serum levels at maintenance dose. (PMID: 17001291) Tate S.K. … Liou H.H. (Pharmacogenet. Genomics 2006) 3 23 25 48

Products for SCN1A Gene

Sources for SCN1A Gene

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