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    SCN1A sodium channel, voltage-gated, type I, alpha subunit [ Homo sapiens (human) ]

    Gene ID: 6323, updated on 22-May-2013
    Official Symbol
    SCN1Aprovided by HGNC
    Official Full Name
    sodium channel, voltage-gated, type I, alpha subunitprovided by HGNC
    Primary source
    HGNC:10585
    See related
    Ensembl:ENSG00000144285; HPRD:01669; MIM:182389; Vega:OTTHUMG00000044173
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    FEB3; FHM3; NAC1; SCN1; SMEI; EIEE6; FEB3A; HBSCI; GEFSP2; Nav1.1
    Summary
    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]
    Location :
    2q24.3
    Sequence :
    Chromosome: 2; NC_000002.11 (166845670..167005642, complement)
    See SCN1A in Epigenomics, MapViewer

    Chromosome 2 - NC_000002.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100506124 Neighboring gene tetratricopeptide repeat domain 21B Neighboring gene uncharacterized LOC100506134 Neighboring gene sodium channel, voltage-gated, type IX, alpha subunit Neighboring gene sodium channel, voltage-gated, type VII, alpha subunit

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details

    Related articles in PubMed

    1. Dravet syndrome, what is new? Al-Baradie RS. Neurosciences (Riyadh), 2013 Jan. PMID 23291792.
    2. [Genetic and phenotypic characteristics of SCN1A mutations in Dravet syndrome]. Xu XJ, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2012 Dec. PMID 23225037.
    3. Prevalence of SCN1A mutations in children with suspected Dravet syndrome and intractable childhood epilepsy. Wang JW, et al. Epilepsy Res, 2012 Dec. PMID 23195492.
    4. [Phenotype and SCN1A gene mutation screening in 39 families with generalized epilepsy with febrile seizures plus]. Xu XJ, et al. Zhonghua Er Ke Za Zhi, 2012 Aug. PMID 23158734.
    5. Nontruncating SCN1A mutations associated with severe myoclonic epilepsy of infancy impair cell surface expression. Thompson CH, et al. J Biol Chem, 2012 Dec 7. PMID 23086956.

    See all (190) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. Our study indicates that the prevalence of SCN1A mutation in patients with suspected myoclonic epilepsy of infancy, borderline phenotype and intractable epilepsy is 56.2%, 41.9% and 28.9% respectively
      Title: Prevalence of SCN1A mutations in children with suspected Dravet syndrome and intractable childhood epilepsy.
    2. Ths results of this study suggested that genetic defects of the SCN1A gene are likely to play a role in the etiology of GEFS+ in our Malaysian patients.
      Title: De-novo mutations and genetic variation in the SCN1A gene in Malaysian patients with generalized epilepsy with febrile seizures plus (GEFS+).
    3. Most of the cases of Dravet syndrome have the SCN1A mutation.
      Title: Dravet syndrome, what is new?
    4. SCN1A and PCDH19 mutations in Chinese children with Dravet syndrome
      Title: Identification of SCN1A and PCDH19 mutations in Chinese children with Dravet syndrome.
    5. Characterization of SCN1A gene mutations and their inheritance in patients with Dravet syndrome.
      Title: [Genetic and phenotypic characteristics of SCN1A mutations in Dravet syndrome].
    6. SCN1A IVS5N+5 polymorphism was genotyped in 583 Malaysian and Hong Kong Chinese epilepsy patients receiving sodium valproate monotherapy. We did not demonstrate an association between antiepileptic responsiveness and this polymorphism.
      Title: SCN1A IVS5N+5 polymorphism and response to sodium valproate: a multicenter study.
    7. Missense mutations in SCN1A were common in generalized epilepsy with febrile seizures plus families, few with truncation mutations.
      Title: [Phenotype and SCN1A gene mutation screening in 39 families with generalized epilepsy with febrile seizures plus].
    8. the present results suggest that the SCN1A polymorphism has modulatory effects on brain morphology and vulnerability to age-related alterations in brain activity of cortical regions that subserve working memory.
      Title: SCN1A affects brain structure and the neural activity of the aging brain.
    9. We conclude that in the population studied, although rs3812718 polymorphism increases the susceptibility to medial temporal lobe epilepsy, this is not by increasing the susceptibility to febrile seizures.
      Title: Failure to find association between febrile seizures and SCN1A rs3812718 polymorphism in south Indian patients with mesial temporal lobe epilepsy and hippocampal sclerosis.
    10. certain nontruncating SCN1A mutations associated with SMEI have impaired cell surface expression and that some alleles may be amenable to pharmacological rescue of this defect.
      Title: Nontruncating SCN1A mutations associated with severe myoclonic epilepsy of infancy impair cell surface expression.
    Submit: New GeneRIF Correction See all (160)

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Familial hemiplegic migraine type 3

    Summary from GeneReviews: Familial Hemiplegic Migraine Go to GeneReviews

    Disease Characteristics
    Familial hemiplegic migraine (FHM) falls within the category of migraine with aura. In migraine with aura (including familial hemiplegic migraine) the neurologic symptoms of aura are unequivocally localizable to the cerebral cortex or brain stem and include visual disturbance (most common), sensory loss (e.g., numbness or paresthesias of the face or an extremity), and dysphasia (difficulty with speech); FHM must include motor involvement, i.e., hemiparesis (weakness of an extremity). Hemiparesis occurs with at least one other symptom during FHM aura. Neurologic deficits with FHM attacks can be prolonged for hours to days and may outlast the associated migrainous headache. FHM is often earlier in onset than typical migraine, frequently beginning in the first or second decade; the frequency of attacks tends to decrease with age. Approximately 40%-50% of families with FHM1 have cerebellar signs ranging from nystagmus to progressive, usually late-onset mild ataxia. Cerebral infarction and death have rarely been associated with hemiplegic migraine.
    Diagnosis Testing
    Diagnostic criteria for FHM: (1) fulfills criteria for migraine with aura; (2) aura includes some degree of hemiparesis and may be prolonged; (3) at least one first-degree relative (i.e., parent, sib, offspring) has identical attacks. Molecular genetic testing is available for the three genes known to be associated with FHM: CACNA1A (FHM1), ATP1A2 (FHM2), and SCN1A (FHM3).
    Genetic Counseling
    Because the diagnosis of FHM requires at least one affected first-degree relative, most individuals diagnosed with familial hemiplegic migraine have an affected parent. The proportion of cases caused by de novo gene mutations is unknown. Each child of an individual with familial hemiplegic migraine has a 50% chance of inheriting the mutation. Prenatal testing for pregnancies at increased risk is possible if the disease-causing mutation in the family has been identified.
    References

    Generalized epilepsy with febrile seizures plus, type 2

    Summary from GeneReviews: SCN1A-Related Seizure Disorders Go to GeneReviews

    Disease Characteristics
    SCN1A-related seizure disorders encompass a spectrum that ranges from simple febrile seizures (FS) and generalized epilepsy with febrile seizures plus (GEFS+) at the mild end to Dravet syndrome and intractable childhood epilepsy with generalized tonic-clonic seizures (ICE-GTC) at the severe end. Phenotypes with intractable seizures including Dravet syndrome (also known as severe myoclonic epilepsy in infancy [SMEI] or polymorphic myoclonic epilepsy in infancy [PMEI]) are usually associated with progressive dementia. Less commonly observed phenotypes include myoclonic-astatic epilepsy (MAE or Doose syndrome), Lennox-Gastaut syndrome (LGS), infantile spasms, and vaccine-related encephalopathy and seizures. The phenotype of SCN1A-related seizure disorders can vary even within the same family.
    Diagnosis Testing
    The diagnosis of SCN1A-related seizure disorders relies on molecular genetic testing of SCN1A. Sequence analysis and deletion testing are available on a clinical basis.
    Genetic Counseling
    SCN1A-related seizure disorders are inherited in an autosomal dominant manner. A proband with an SCN1A-related seizure disorder may have an inherited or de novo mutation. The proportion of cases caused by de novo mutations varies by phenotype: the percentage of probands with an SCN1A-related seizure disorder and an affected parent decreases as the severity of the phenotype in the proband increases; thus, most SCN1A-related SMEI and ICE-GTC are the result of a de novo heterozygous mutation. Each child of an individual with an SCN1A-related seizure disorder has a 50% chance of inheriting the mutation; however, the risk of developing seizures is less than 100% because of reduced penetrance. Prenatal diagnosis for pregnancies at increased risk is possible if the disease-causing mutation in the family is known.
    References

    Severe myoclonic epilepsy in infancy

    Summary from GeneReviews: SCN1A-Related Seizure Disorders Go to GeneReviews

    Disease Characteristics
    SCN1A-related seizure disorders encompass a spectrum that ranges from simple febrile seizures (FS) and generalized epilepsy with febrile seizures plus (GEFS+) at the mild end to Dravet syndrome and intractable childhood epilepsy with generalized tonic-clonic seizures (ICE-GTC) at the severe end. Phenotypes with intractable seizures including Dravet syndrome (also known as severe myoclonic epilepsy in infancy [SMEI] or polymorphic myoclonic epilepsy in infancy [PMEI]) are usually associated with progressive dementia. Less commonly observed phenotypes include myoclonic-astatic epilepsy (MAE or Doose syndrome), Lennox-Gastaut syndrome (LGS), infantile spasms, and vaccine-related encephalopathy and seizures. The phenotype of SCN1A-related seizure disorders can vary even within the same family.
    Diagnosis Testing
    The diagnosis of SCN1A-related seizure disorders relies on molecular genetic testing of SCN1A. Sequence analysis and deletion testing are available on a clinical basis.
    Genetic Counseling
    SCN1A-related seizure disorders are inherited in an autosomal dominant manner. A proband with an SCN1A-related seizure disorder may have an inherited or de novo mutation. The proportion of cases caused by de novo mutations varies by phenotype: the percentage of probands with an SCN1A-related seizure disorder and an affected parent decreases as the severity of the phenotype in the proband increases; thus, most SCN1A-related SMEI and ICE-GTC are the result of a de novo heterozygous mutation. Each child of an individual with an SCN1A-related seizure disorder has a 50% chance of inheriting the mutation; however, the risk of developing seizures is less than 100% because of reduced penetrance. Prenatal diagnosis for pregnancies at increased risk is possible if the disease-causing mutation in the family is known.
    References
    Products Interactant Other Gene Complex Source Pubs Description
    BioGRID:112228 BioGRID:110815 NEDD8    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:112228 BioGRID:111642 PSEN1    BioGRID  PubMed Two-hybrid 
    BioGRID:112228 BioGRID:112523 SNTA1    BioGRID  PubMed Affinity Capture-Western; Protein-peptide 
    • Axon guidance, organism-specific biosystem (from REACTOME)
      Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • Dopaminergic synapse, organism-specific biosystem (from KEGG)
      Dopaminergic synapse, organism-specific biosystemDopamine (DA) is an important and prototypical slow neurotransmitter in the mammalian brain, where it controls a variety of functions including locomotor activity, motivation and reward, learning an...
    • Dopaminergic synapse, conserved biosystem (from KEGG)
      Dopaminergic synapse, conserved biosystemDopamine (DA) is an important and prototypical slow neurotransmitter in the mammalian brain, where it controls a variety of functions including locomotor activity, motivation and reward, learning an...
    • Interaction between L1 and Ankyrins, organism-specific biosystem (from REACTOME)
      Interaction between L1 and Ankyrins, organism-specific biosystemAnkyrins are a family of adaptor proteins that couple membrane proteins such as voltage gated Na+ channels and the Na+/K+ anion exchanger to the spectrin actin cytoskeleton. Ankyrins are encoded by t...
    • L1CAM interactions, organism-specific biosystem (from REACTOME)
      L1CAM interactions, organism-specific biosystemThe L1 family of cell adhesion molecules (L1CAMs) are a subfamily of the immunoglobulin superfamily of transmembrane receptors, comprised of four structurally related proteins: L1, Close Homolog of L...

    Markers

    Genotypes

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    voltage-gated sodium channel activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    adult walking behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    neuromuscular process controlling posture IEA
    Inferred from Electronic Annotation
    more info
    		  
    neuronal action potential propagation IEA
    Inferred from Electronic Annotation
    more info
    		  
    regulation of action potential in neuron IEA
    Inferred from Electronic Annotation
    more info
    		  
    sodium ion transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    T-tubule IEA
    Inferred from Electronic Annotation
    more info
    		  
    Z disc ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    axon initial segment IEA
    Inferred from Electronic Annotation
    more info
    		  
    integral to membrane NAS
    Non-traceable Author Statement
    more info
    		  
    intercalated disc IEA
    Inferred from Electronic Annotation
    more info
    		  
    neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
    		  
    node of Ranvier IEA
    Inferred from Electronic Annotation
    more info
    		  
    voltage-gated sodium channel complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    Preferred Names
    sodium channel protein type 1 subunit alpha
    Names
    sodium channel protein type 1 subunit alpha
    sodium channel protein type I subunit alpha
    sodium channel protein, brain I alpha subunit
    sodium channel voltage gated type 1 alpha subunit
    voltage-gated sodium channel subunit alpha Nav1.1
    sodium channel, voltage-gated, type I, alpha polypeptide

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_011906.1 RefSeqGene

      Range
      820..89480
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_8

    mRNA and Protein(s)

    1. NM_001165963.1 → NP_001159435.1  sodium channel protein type 1 subunit alpha isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes encodes the longest isoform (1).
      Source sequence(s)
      AB093548, AC010127
      Consensus CDS
      CCDS54413.1
      UniProtKB/Swiss-Prot
      P35498
      Related
      ENSP00000303540, OTTHUMP00000041051, ENST00000303395, OTTHUMT00000102661
      Conserved Domains (3) summary
      pfam00520
      Location:1254 – 1482
      Blast Score: 357
      Ion_trans; Ion transport protein
      pfam06512
      Location:1006 – 1228
      Blast Score: 560
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:520 – 719
      Blast Score: 554
      DUF3451; Domain of unknown function (DUF3451)

    2. NM_001165964.1 → NP_001159436.1  sodium channel protein type 1 subunit alpha isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AB098335, AC010127
      Consensus CDS
      CCDS54414.1
      UniProtKB/Swiss-Prot
      P35498
      Conserved Domains (3) summary
      pfam00520
      Location:1226 – 1454
      Blast Score: 355
      Ion_trans; Ion transport protein
      pfam06512
      Location:978 – 1200
      Blast Score: 560
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:520 – 691
      Blast Score: 546
      DUF3451; Domain of unknown function (DUF3451)

    3. NM_001202435.1 → NP_001189364.1  sodium channel protein type 1 subunit alpha isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) represents a transcript with 5' untranslated exons, compared to variant 1. The RefSeq Project created this record to better support clinical studies but the exact combination of exons and splice sites still needs to be experimentally confirmed. Variants 1 and 4 encode the same isoform.
      Source sequence(s)
      AC010127, AC107082
      Consensus CDS
      CCDS54413.1
      UniProtKB/Swiss-Prot
      P35498
      Conserved Domains (3) summary
      pfam00520
      Location:1254 – 1482
      Blast Score: 357
      Ion_trans; Ion transport protein
      pfam06512
      Location:1006 – 1228
      Blast Score: 560
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:520 – 719
      Blast Score: 554
      DUF3451; Domain of unknown function (DUF3451)

    4. NM_006920.4 → NP_008851.3  sodium channel protein type 1 subunit alpha isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AB093549, AC010127, AF225985
      Consensus CDS
      CCDS33316.1
      UniProtKB/Swiss-Prot
      P35498
      Related
      ENSP00000364554, OTTHUMP00000041052, ENST00000375405, OTTHUMT00000102662
      Conserved Domains (3) summary
      pfam00520
      Location:1243 – 1471
      Blast Score: 356
      Ion_trans; Ion transport protein
      pfam06512
      Location:995 – 1217
      Blast Score: 560
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:520 – 708
      Blast Score: 541
      DUF3451; Domain of unknown function (DUF3451)

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000002.11 Reference GRCh37.p10 Primary Assembly

      Range
      166845670..167005642, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000134.1 Alternate HuRef

      Range
      158727062..158886965, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018913.1 Alternate CHM1_1.0

      Range
      166242748..166402705, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    genomic ABBA01004927.1 (40898..55490) None
    genomic ABBA01004928.1 None
    genomic AC010127.12 AAX81984.1
    genomic AC107082.3 None
    genomic AMYH01011229.1 (180912..340869) None
    genomic CH471058.2 EAX11318.1
      EAX11319.1
    genomic S71446.1 AAB31605.1
    mRNA AB093548.1 BAC21101.1
    mRNA AB093549.1 BAC21102.1
    mRNA AB098335.1 BAC45228.1
    mRNA AF225985.1 AAK00217.1
    mRNA AK094487.1 None
    mRNA AK293759.1 BAG57178.1
    mRNA AK294900.1 BAG57989.1
    mRNA AY043484.1 AAK95360.1
    mRNA EU368117.1 None
    mRNA EU368119.1 ABY76307.1
    mRNA HQ726795.1 AEJ07962.1
    mRNA HQ726796.1 AEJ07963.1
    mRNA HQ726798.1 AEJ07965.1
    mRNA HQ726799.1 AEJ07966.1
    mRNA M91803.1 None
    mRNA X65362.1 CAA46439.1
    Protein Accession Links
    GenPept Link UniProtKB Link
    P35498.2 GenPept UniProtKB/Swiss-Prot:P35498

    Additional Links

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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    Research Materials
    Tools
    Miscellaneous

      Supplemental Content

      Table of contents

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        BioSystems
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        Conserved Domain Database Links between Entrez Gene and Conserved Domain Database (CDD) are calculated from the domains annotated by the CDD group on Reference Sequence proteins.
      • dbVar
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        Full text in PubMedCentral identified from shared sequence links
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        Related GEO
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        PubChem Substances
      • PubMed
        Links between Gene and PubMed are the result of the following: 1. Manual curation within NCBI. Part of the process of generating a REVIEWED RefSeq is an analysis of the current literature. Papers that are seminal in defining the gene, its sequence, and its function are added to the record at that time. Alert users point out gaps or errors in papers associated with a Gene record. These messages are reviewed and implemented as required. 2. Integration of information from other public databases. Gene integrates gene-citation from resources external to NCBI such as model organism-specific databases, Gene Ontology (GO), groups curating interactions, and sequence databases. The assumption in using these source is that they report citations specific to a gene in a known species. Gene does not process citations from OMIM automatically, because many of citations in OMIM refer to studies of genes in species other than human.
      • PubMed (GeneRIF)
        GeneRIF -- Gene Reference Into Function Staff of the Index Section in the National Library of Medicine review the current literature. When they find articles focused on the structure and function of a gene, they write a brief summary of the impact of the paper and make the connection between the citation (PubMed) and Gene. An interface exists for interested users to submit such data as well. http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html
      • PubMed (OMIM)
        Links are provided when Gene has a link to a record in OMIM, and OMIM explicitly cites these publications in PubMed.
      • PubMed(nucleotide/PMC)
        Citations in PubMed identified from shared sequence and PMC links.
      • RefSeq Proteins
        Link to Protein RefSeqs
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        Link to Nucleotide RefSeq RNAs
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        Link to Nucleotide RefSeqGenes
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        Related SNP records
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