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SCN1A Gene

protein-coding   GIFtS: 64
GCID: GC02M166809

Sodium Channel, Voltage-Gated, Type I, Alpha Subunit

(Previous name: febrile convulsions 3)
(Previous symbols: SCN1, FEB3)
  See SCN1A-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Sodium Channel, Voltage-Gated, Type I, Alpha Subunit1 2     SMEI2 5
SCN11 2 3     Febrile Convulsions 31
FEB31 2     HBSCI2
Sodium Channel Protein Type I Subunit Alpha2 3     Nav1.12
Voltage-Gated Sodium Channel Subunit Alpha Nav1.12 3     Sodium Channel Protein Type 1 Subunit Alpha2
NAC12 3     Sodium Channel Protein, Brain I Alpha Subunit2
EIEE62 5     Sodium Channel Voltage Gated Type 1 Alpha Subunit2
FEB3A2 5     Sodium Channel, Voltage-Gated, Type I, Alpha Polypeptide2
FHM32 5     Sodium Channel Protein Brain I Subunit Alpha3
GEFSP22 5     

External Ids:    HGNC: 105851   Entrez Gene: 63232   Ensembl: ENSG000001442857   OMIM: 1823895   UniProtKB: P354983   

Export aliases for SCN1A gene to outside databases

Previous GC identifers: GC02M164900 GC02M165387 GC02M167048 GC02M166671 GC02M166553 GC02M158727


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 febrile seizures, familial, 3a, and epilepsy, generalized, with febrile seizures plus, type 2. GO annotations related to this gene include voltage-gated sodium channel activity. An important paralog of this gene is SCN5A.

UniProtKB/Swiss-Prot: SCN1A_HUMAN, P35498
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

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 (Nav1.1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NC_018913.2  NT_005403.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the SCN1A gene promoter:
         Oct-B1   oct-B3   oct-B2   AML1a   Cdc5   E47   MEF-2A   FOXJ2 (long isoform)   FOXJ2   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCN1A promoter sequence
   Search Chromatin IP Primers for SCN1A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SCN1A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2q24.3   Ensembl cytogenetic band:  2q24.3   HGNC cytogenetic band: 2q24.3

SCN1A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCN1A gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M166809:  view genomic region     (about GC identifiers)

Start:
166,845,670 bp from pter      End:
167,005,642 bp from pter
Size:
159,973 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SCN1A_HUMAN, P35498 (See protein sequence)
Recommended Name: Sodium channel protein type 1 subunit alpha  
Size: 2009 amino acids; 228972 Da
Subunit: 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
Secondary accessions: E9PG49 Q16172 Q585T7 Q8IUJ6 Q96LA3 Q9C008
Alternative splicing: 3 isoforms:  P35498-1   P35498-2   P35498-3   

Explore the universe of human proteins at neXtProt for SCN1A: NX_P35498

Explore proteomics data for SCN1A at MOPED

Post-translational modifications: 

  • Phosphorylation at Ser-1516 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel
    and reduces peak sodium currents (By similarity)1
  • Glycosylation2 at Asn211, Asn284, Asn295, Asn301, Asn306, Asn338, Asn1378, Asn1392, Asn1403
  • Modification sites at PhosphoSitePlus

  • See SCN1A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (4 alternative transcripts): 
    NP_001159435.1  NP_001159436.1  NP_008851.3  NP_001189364.1  

    ENSEMBL proteins: 
     ENSP00000303540   ENSP00000364554   ENSP00000386312   ENSP00000407030  
    Reactome Protein details: P35498

    SCN1A Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    Browse OriGene Protein Over-expression Lysates
    OriGene Custom MassSpec
    OriGene Custom Protein Services for SCN1A
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    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

     
    Search eBioscience for Proteins for SCN1A 

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    Search for Antibodies for SCN1A at Abcam
    Browse Antibodies at Cloud-Clone Corp.
    ThermoFisher Antibodies for SCN1A
    LSBio Antibodies in human, mouse, rat for SCN1A

    SCN1A Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for SCN1A 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    SC: Sodium channels
    SCN: Voltage-gated ion channels / Sodium channels

    IUPHAR Guide to PHARMACOLOGY protein family classification: Nav1.1
    Voltage-gated sodium channels

    Selected InterPro protein domains (see all 7):
     IPR008051 Na_channel_a1su
     IPR010526 Na_trans_assoc
     IPR005821 Ion_trans_dom
     IPR027359 Channel_four-helix_dom
     IPR001696 Na_channel_asu

    Graphical View of Domain Structure for InterPro Entry P35498

    ProtoNet protein and cluster: P35498

    4 Blocks protein domains:
    IPB000048 IQ calmodulin-binding region
    IPB000100 Bacterial ribonuclease P protein
    IPB001696 Voltage-gated Na+ channel alpha subunit signature
    IPB008051 Voltage-gated Na+ channel alpha 1 subunit signature


    UniProtKB/Swiss-Prot: SCN1A_HUMAN, P35498
    Domain: 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
    Similarity: Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.1/SCN1A subfamily
    Similarity: Contains 1 IQ domain


    Find genes that share domains with SCN1A           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SCN1A_HUMAN, P35498
    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

         Genatlas biochemistry entry for SCN1A:
    sodium voltage-gated channel,type I,alpha polypeptide,expressed in brain

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005216ion channel activity ----
    GO:0005248voltage-gated sodium channel activity NAS10742094
         
    Find genes that share ontologies with SCN1A           About GenesLikeMe


    Phenotypes:
         2 GenomeRNAi human phenotypes for SCN1A:
     Elongated cells  Synthetic lethal with c-Myc af 

         6 MGI mutant phenotypes (inferred from 8 alleles(MGI details for Scn1a):
     behavior/neurological  growth/size/body  mortality/aging  nervous system  normal 
     reproductive system 

    Find genes that share phenotypes with SCN1A           About GenesLikeMe

    Animal Models:
         MGI mouse knock-outs for SCN1A: Scn1atm1Kea Scn1atm2.2Kzy Scn1atm1Kzy Scn1atm1Wac

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SCN1A
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SCN1A

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SCN1A
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SCN1A

    miRNA
    Products:
        
    miRTarBase miRNAs that target SCN1A:
    hsa-mir-93-3p (MIRT038738)

    Block miRNA regulation of human, mouse, rat SCN1A using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SCN1A (see all 75):
    hsa-miR-548j hsa-miR-100* hsa-miR-3607-3p hsa-miR-106a hsa-miR-30d hsa-miR-371-5p hsa-miR-519a hsa-miR-30a
    SwitchGear 3'UTR luciferase reporter plasmidSCN1A 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for SCN1A
    Predesigned siRNA for gene silencing in human, mouse, rat SCN1A

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for SCN1A

    Clone
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    OriGene clones in human, mouse for SCN1A (see all 14)
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    GenScript: all cDNA clones in your preferred vector (see all 4): SCN1A (NM_001202435)
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCN1A


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SCN1A_HUMAN, P35498: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    cytoskeleton1
    mitochondrion1

    Gene Ontology (GO): Selected cellular component terms (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001518voltage-gated sodium channel complex IEA--
    GO:0014704intercalated disc IEA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane ----
    GO:0030018Z disc ISS--

    Find genes that share ontologies with SCN1A           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SCN1A About   (see all 8)  
    See pathways by source

    SuperPathContained pathways About
    1L1CAM interactions
    Axon guidance0.63
    L1CAM interactions0.36
    Developmental Biology0.63
    2Activation of cAMP-Dependent PKA
    Activation of cAMP-Dependent PKA0.77
    PKA Signaling0.56
    cAMP Pathway0.77
    3Neuropathic Pain-Signaling in Dorsal Horn Neurons
    Neuropathic Pain-Signaling in Dorsal Horn Neurons0.47
    Cholera Infection0.40
    Aldosterone Signaling in Epithelial Cells0.47
    4G-Beta Gamma Signaling
    GHRH Signaling0.46
    5Circadian entrainment
    Dopaminergic synapse0.37


    Find genes that share SuperPaths with SCN1A           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for SCN1A (see all 7)
        Cholera Infection
    Neuropathic Pain-Signaling in Dorsal Horn Neurons
    PKA Signaling
    cAMP Pathway
    Aldosterone Signaling in Epithelial Cells

    1 Reactome Pathway for SCN1A
        Interaction between L1 and Ankyrins


    1 Kegg Pathway  (Kegg details for SCN1A):
        Dopaminergic synapse

        Pathway & Disease-focused RT2 Profiler PCR Array including SCN1A: 
              Neuronal Ion Channels in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for SCN1A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SCN1A (P354983 ENSP000003645544) via UniProtKB, MINT, STRING, and/or I2D (see all 33)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CALM1P621583I2D: score=1 
    CALM2P621583I2D: score=1 
    CALM3P621583I2D: score=1 
    ESR2Q927313, ENSP000003439254I2D: score=1 STRING: ENSP00000343925
    SNTA1Q134243, ENSP000002173814I2D: score=1 STRING: ENSP00000217381
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001508action potential ----
    GO:0006811ion transport ----
    GO:0006814sodium ion transport NAS10742094
    GO:0007628adult walking behavior IEA--
    GO:0019227neuronal action potential propagation IEA--

    Find genes that share ontologies with SCN1A           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Compounds for SCN1A available from Tocris Bioscience    About this table
    CompoundAction CAS #
    Phrixotoxin 3 Potent modulator of NaV1.2, NaV1.3 and NaV1.5 channels [880886-00-0]
    QX 314 chlorideNa+ channel blocker[5369-03-9]
    VeratridineVoltage-gated Na+ channel opener[71-62-5]
    TetrodotoxinNa+ channel blocker[4368-28-9]
    Tetrodotoxin citrateNa+ channel blocker. Citrate salt of tetrodotoxin (Cat. No. 1078)[18660-81-6]

    2 HMDB Compounds for SCN1A    About this table
    CompoundSynonyms CAS #PubMed Ids
    SodiumSodium (see all 2)7440-23-5--
    TopiramateEpitomax (see all 5)97240-79-4--

    8 DrugBank Compounds for SCN1A    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    ZonisamideZonisamida [Spanish] (see all 2)68291-97-4targetinhibitor20025128 14704463 19557119 11752352 18433351 20001433 15511691 19948168
    Permethrin-- 52645-53-1targetinhibitor19766671 19960691 14651650 19171193 20881019
    TopiramateTipiramate [French] (see all 3)97240-79-4targetinhibitor15526956 15508261 17621480 12861512 11948006
    PhenacemideCarbamide phenylacetate (see all 5)63-98-9targetinhibitor17139284 3959032 11752352 17016423
    Phenytoin5,5-diphenylhydantoin (see all 13)57-41-0targetinhibitor15805193 17001291 20298965
    Phenazopyridine-- 94-78-0targetinhibitor20976818 8799190
    Dronedarone-- 141626-36-0targetinhibitor12890054
    Nitrazepam1, 3-Dihydro-7-nitro-5-phenyl-2H-1,4-benzodiazepin-2-one (see all 8)146-22-5targetother/unknown2450203

    7 IUPHAR Ligands for SCN1A (Nav1.1)    About this table
    LigandTypeActionAffinityPubmed IDs
    ATX-II
    Gating inhibitorAntagonist8.215169781
    Bc-III
    Gating inhibitorAntagonist6.515169781
    AFT-II
    Gating inhibitorAntagonist6.415169781
    saxitoxin
    Channel blockerNone6.4--
    veratridine
    ActivatorNone6.4--
    batrachotoxin
    ActivatorNone6.4--
    tetrodotoxin
    Channel blockerNone6.4--

    5 Novoseek inferred chemical compound relationships for SCN1A gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sodium 80.2 92 17054685 (3), 12566275 (2), 14672992 (2), 17544618 (2) (see all 71)
    phenytoin 36.5 6 17001291 (3), 19087113 (1), 15805193 (1), 18489610 (1)
    lamotrigine 30.3 3 20037572 (2), 19087113 (1)
    carbamazepine 16.3 2 18489610 (3), 19087113 (1), 17001291 (1), 18554361 (1) (see all 5)
    potassium 8.38 2 11579435 (1)

    2 PharmGKB related drug/compound annotations for SCN1A gene    About this table
    Drug/compound PharmGKB Annotation
    carbamazepineCA  
    phenytoinCA  



    Find genes that share compounds with SCN1A           About GenesLikeMe



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SCN1A gene (4 alternative transcripts): 
    NM_001165963.1  NM_001165964.1  NM_006920.4  NM_001202435.1  

    Unigene Cluster for SCN1A:

    Sodium channel, voltage-gated, type I, alpha subunit
    Hs.22654  [show with all ESTs]
    Unigene Representative Sequence: NM_001202435
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000303395 ENST00000375405 ENST00000409050 ENST00000473295 ENST00000491429
    ENST00000507401 ENST00000423058(uc010fpk.3 uc021vsb.1 uc002udo.4)

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    Selected qRT-PCR Assays for microRNAs that regulate SCN1A (see all 75):
    hsa-miR-548j hsa-miR-100* hsa-miR-3607-3p hsa-miR-106a hsa-miR-30d hsa-miR-371-5p hsa-miR-519a hsa-miR-30a
    SwitchGear 3'UTR luciferase reporter plasmidSCN1A 3' UTR sequence
    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat SCN1A
      QuantiFast Probe-based Assays in human, mouse, rat SCN1A

    Additional mRNA sequence: 

    AB093548.1 AB093549.1 AB098335.1 AK094487.1 AK293759.1 AK294900.1 AY043484.1 HQ726795.1 
    HQ726796.1 HQ726798.1 HQ726799.1 M91803.1 X65362.1 

    4 DOTS entries:

    DT.211707  DT.100012777  DT.100735345  DT.97774887 

    Selected AceView cDNA sequences (see all 32):

    BX116162 AA297746 AB093548 BM718214 F03961 AB093549 AB098335 X65362 
    BX507999 AY043484 F04010 BX477644 AK094487 AL565167 AF225985 NM_006920 
    BX432053 AL533359 AL707423 M91803 F07763 BI667397 F07703 BP359985 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SCN1A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGGAAAATG
    SCN1A Expression
    About this image


    SCN1A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Brain (Nervous System)
             Oligodendrocyte Precursor Cells Forebrain White Matter
    SCN1A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SCN1A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.22654
        Pathway & Disease-focused RT2 Profiler PCR Array including SCN1A: 
              Neuronal Ion Channels in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of chordates.

    Orthologs for SCN1A gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Scn1a1 , 5 sodium channel, voltage-gated, type I, alpha1, 5 90.44(n)1
    98.15(a)1
      2 (39.13 cM)5
    202651  NM_018733.21  NP_061203.21 
     662707815 
    chicken
    (Gallus gallus)
    Aves SCN1A1 sodium channel, voltage-gated, type I, alpha subunit 83.09(n)
    91.2(a)
      771555  XM_003641586.2  XP_003641634.1 
    lizard
    (Anolis carolinensis)
    Reptilia SCN1A6
    sodium channel, voltage-gated, type I, alpha subun...
    89(a)
    1 ↔ 1
    GL343214.1(901340-1055970)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia BX735435.12   -- 76.51(n)    BX735435.1 
    zebrafish
    (Danio rerio)
    Actinopterygii scn1lab6
    sodium channel, voltage-gated, type I like, alpha ...
    78(a)
    1 → many
    6(10158986-10231330) ENSDARG00000062744


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SCN1A gene
    SCN5A2  SCN9A2  CACNA1D2  SCN7A2  CACNA1I2  CACNA1F2  CACNA1G2  SCN8A2  
    SCN10A2  SCN3A2  SCN2A2  CACNA1S2  CACNA1C2  CACNA1H2  SCN11A2  SCN4A2  
    17 SIMAP similar genes for SCN1A using alignment to 6 protein entries:     SCN1A_HUMAN (see all proteins):
    SCN2A    SCN2A2    SCN3A    SCN9A    SCN4A    SCN5A
    SCN8A    SCN10A    CACNA1D    SCN11A    CACNA1H    SCN7A
    CACNA1A    CACNA1B    TPCN1    CACNA1E    CACNA1C

    Find genes that share paralogs with SCN1A           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SCN1A (see all 3773)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1219186291,2,,4
    CIntractable childhood epilepsy with generalized tonic-clonic seizures (ICEGTC)4 pathogenic1166245737(-) TGAGAC/TCTTTG 8 T I mis10--------
    rs1219187441,2,,4
    CGeneralized epilepsy with febrile seizures plus 2 (GEFS+2)4 untested1166245809(-) CTACGA/C/TCATCT 12 D A V mis10--------
    rs1219179221,2,,4
    CSevere myoclonic epilepsy in infancy (SMEI)4 untested1166245890(-) CCGCAC/G/TGCTGC 12 T R M mis10--------
    rs1219179551,2,,4
    CGeneralized epilepsy with febrile seizures plus 2 (GEFS+2)4 pathogenic1166245895(-) GGGATC/GCGCAC 8 I M mis10--------
    rs1219186221,2,,4
    CSevere myoclonic epilepsy in infancy (SMEI)4 pathogenic1166245920(-) CCTACA/GTCTGA 8 H R mis10--------
    rs1219186301,2,,4
    CIntractable childhood epilepsy with generalized tonic-clonic seizures (ICEGTC)4 pathogenic1166247758(-) TTGTGG/TTTGTC 8 V F mis10--------
    rs1219187421,2,,4
    CSevere myoclonic epilepsy in infancy (SMEI)4 untested1166247832(-) TACTGA/GAGAGT 8 E G mis10--------
    rs1219186321,2,,4
    CMigraine, familial hemiplegic, 3 (FHM3)4 pathogenic1166249686(-) ACATCC/TTTATG 8 L F mis10--------
    rs1219186331,2,,4
    CMigraine, familial hemiplegic, 3 (FHM3)4 pathogenic1166251634(-) CAGCAC/GAAAAA 8 H Q mis10--------
    rs1219186281,2,,4
    CMigraine, familial hemiplegic, 3 (FHM3)4 pathogenic1166251636(-) ACCAGA/CAGAAA 8 K Q mis10--------

    HapMap Linkage Disequilibrium report for SCN1A (166845670 - 167005642 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for SCN1A:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2721078CNV Deletion23290073
    esv2721076CNV Deletion23290073
    esv2357676CNV Deletion18987734
    esv2721077CNV Deletion23290073
    esv2721079CNV Deletion23290073
    esv2721080CNV Deletion23290073
    nsv459936CNV Loss19166990
    dgv63n17CNV Loss16327808
    dgv4355n71CNV Gain21882294
    nsv834445CNV Gain+Loss17160897

    Human Gene Mutation Database (HGMD): SCN1A
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SCN1A
    DNA2.0 Custom Variant and Variant Library Synthesis for SCN1A

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 182389   
    OMIM disorders: 604403  607208  609634  
    UniProtKB/Swiss-Prot: SCN1A_HUMAN, P35498
  • 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. Note=The disease is caused by mutations affecting the gene
    represented in this entry
  • Severe myoclonic epilepsy in infancy (SMEI) [MIM:607208]: A rare disorder 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 SMEI.
    SMEI is considered to be the most severe phenotype within the spectrum of generalized epilepsies with febrile
    seizures-plus. 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. 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. 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. Note=The disease is caused by
    mutations affecting the gene represented in this entry

  • Selected diseases for SCN1A (see all 27):    
    About MalaCards
    febrile seizures, familial, 3a    epilepsy, generalized, with febrile seizures plus, type 2    myoclonic astatic epilepsy    familial hemiplegic migraine type 3
    scn1a-related seizure disorders    dravet syndrome    lennox-gastaut syndrome    epilepsy with generalized tonic-clonic seizures
    myoclonic epilepsy of infancy    familial hemiplegic migraine    dravet syndrome, modifier of    malignant migrating partial seizures of infancy
    epilepsy, generalized, with febrile seizures plus, type 3    sporadic hemiplegic migraine    febrile infection-related epilepsy syndrome    hemiplegic migraine
    familial hemiplegic migraine type 1    epileptic encephalopathy, early infantile, 12    migraine    temporal lobe epilepsy

    1 disease from the University of Copenhagen DISEASES database for SCN1A:
    Brain disease

    Find genes that share disorders with SCN1A           About GenesLikeMe

    Selected Novoseek inferred disease relationships for SCN1A gene (see all 19)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    dravet syndrome 98.4 43 19673951 (3), 19087113 (2), 19763161 (2), 18076640 (2) (see all 23)
    epilepsies myoclonic 97 62 16458823 (3), 17030758 (3), 12821740 (2), 18479393 (2) (see all 45)
    epilepsy generalized 95.6 40 11254445 (2), 14738422 (2), 19339291 (2), 11579434 (1) (see all 35)
    seizures febrile 95.4 66 19292758 (4), 11254445 (3), 12742596 (2), 15087100 (2) (see all 48)
    hemiplegic migraine familial 91 9 19332696 (2), 18357670 (1), 19673951 (1), 18451712 (1) (see all 8)
    myoclonic seizure 84.7 1 17507202 (1)
    epilepsy 83.5 95 19586930 (3), 17561957 (3), 18413471 (3), 19666879 (3) (see all 53)
    seizure febrile simple 79.4 2 17565594 (1), 16326807 (1)
    familial benign neonatal convulsions 76.4 2 17181426 (1), 11579435 (1)
    myoclonic astatic epilepsy 76.2 2 15944908 (2)

    GeneTests: SCN1A
    GeneReviews: SCN1A
    Genetic Association Database (GAD): SCN1A
    Human Genome Epidemiology (HuGE) Navigator: SCN1A (31 documents)

    Export disorders for SCN1A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SCN1A gene, integrated from 10 sources (see all 323):
    (articles sorted by number of sources associating them with SCN1A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Spectrum of SCN1A mutations in severe myoclonic epilepsy of infancy. (PubMed id 12821740)1, 2, 4, 9 Nabbout R....Zara F. (Neurology 2003)
    2. A novel SCN1A mutation associated with generalized epilepsy with febrile seizures plus -- and prevalence of variants in patients with epilepsy. (PubMed id 11254445)1, 2, 4, 9 Escayg A.... Meisler M.H. (Am. J. Hum. Genet. 2001)
    3. Localization of a putative human brain sodium channel gene (SCN1A) to chromosome band 2q24. (PubMed id 8062593)1, 2, 3, 9 Malo M.S.... Ingram V.M. (Cytogenet. Cell Genet. 1994)
    4. The spectrum of SCN1A-related infantile epileptic encephalopathies. (PubMed id 17347258)1, 2, 4, 9 Harkin L.A.... Scheffer I.E. (Brain 2007)
    5. A common polymorphism in the SCN1A gene associates with phenytoin serum levels at maintenance dose. (PubMed id 17001291)1, 4, 7, 9 Tate S.K....Liou H.H. (Pharmacogenet. Genomics 2006)
    6. Mutations of neuronal voltage-gated Na+ channel alpha 1 subunit gene SCN1A in core severe myoclonic epilepsy in infancy (SMEI) and in borderline SMEI (SMEB). (PubMed id 14738421)1, 2, 4, 9 Fukuma G.... Hirose S. (Epilepsia 2004)
    7. Differential role of sodium channels SCN1A and SCN2A gene polymorphisms with epilepsy and multiple drug resistance in the north Indian population. (PubMed id 19694741)1, 2, 4 Lakhan R.... Mittal B. (Br. J. Clin. Pharmacol. 2009)
    8. Physicochemical property changes of amino acid residues that accompany missense mutations in SCN1A affect epilepsy phenotype severity. (PubMed id 19586930)1, 4, 9 Kanai K....Kaneko S. (J. Med. Genet. 2009)
    9. Cryptogenic epileptic syndromes related to SCN1A: twelve novel mutations identified. (PubMed id 18413471)1, 2, 9 Zucca C.... Bassi M.T. (Arch. Neurol. 2008)
    10. Novel SCN1A mutations in Indonesian patients with severe myoclonic epilepsy in infancy. (PubMed id 19563458)1, 2, 9 Herini E.S.... Nishio H. (Pediatr. Int. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6323 HGNC: 10585 AceView: SCN1A Ensembl:ENSG00000144285 euGenes: HUgn6323
    ECgene: SCN1A Kegg: 6323 H-InvDB: SCN1A

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SCN1A Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SCN1A[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SCN1A gene:
    Search GeneIP for patents involving SCN1A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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