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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SCN1A Gene

protein-coding   GIFtS: 63
GCID: GC02M166809

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

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

Aliases
for SCN1A gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section
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


Summaries
for SCN1A gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
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 dravet syndrome, and myoclonic astatic epilepsy, and among its related super-pathways are Axon guidance 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 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


Genomic Views
for SCN1A 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.2  NT_005403.17  
Regulatory elements:
   SABiosciences 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 plasmid: SCN1A promoter sequence
   Search SABiosciences Chromatin IP Primers for SCN1A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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

Proteins
for SCN1A gene

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section
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
Subcellular location: Membrane; Multi-pass membrane protein
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:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P35498

    • SCN1A Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SCN1A Protein Expression
    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
    Human Recombinant Protein Products 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. 

    Gene Ontology (GO): 5/11 cellular component terms (GO ID links to tree view) (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 to membrane NAS--
    GO:0030018Z disc ISS--

    SCN1A for ontologies           About GeneDecksing



    SCN1A Antibody Products: 
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    Assay Products for SCN1A: 
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    Protein Domains /
    Families
    for SCN1A gene

    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    		 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

    5/7 InterPro protein domains (see all 7):
     IPR008051 Na_channel_a1su
     IPR027359 K_channel_four-helix_dom
     IPR001696 Na_channel_asu
     IPR010526 Na_trans_assoc
     IPR000048 IQ_motif_EF-hand-BS

    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


    SCN1A for domains           About GeneDecksing


    Function
    for SCN1A gene

    (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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section
    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 (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005216ion channel activity ----
    GO:0005248voltage-gated sodium channel activity NAS10742094
         
    SCN1A for ontologies           About GeneDecksing


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

         5 MGI mutant phenotypes (inferred from 4 alleles) (MGI details for Scn1a):
     behavior/neurological  growth/size  mortality/aging  nervous system  reproductive system 

    SCN1A for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for SCN1A: Scn1atm1Kzy Scn1atm1Wac

       inGenious Targeting Laboratory - Custom generated mouse model solutions for SCN1A 
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SCN1A 
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    miRNA
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    8/75 QIAGEN miScript miRNA 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 plasmid: SCN1A 3' UTR sequence
    Inhib. RNA
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    Gene Editing
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    Sirion Biotech Customized adenovirus for overexpression of SCN1A

    Clone
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    Pathways & Interactions
    for SCN1A gene

    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for SCN1A About   (see all 8)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Axon guidance
    		Axon guidance0.69
    		L1CAM interactions0.39
    		Developmental Biology0.69
    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

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 EMD Millipore Pathways for SCN1A
        Synaptic transmission- ion currents
    Sodium channels and transporters- inward current

    5/7 Downloadable PowerPoint Slides of QIAGEN 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

    4        Reactome Pathways for SCN1A
        L1CAM interactions
    Developmental Biology
    Interaction between L1 and Ankyrins
    Axon guidance


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


    SCN1A for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SCN1A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 16)

    5/22 Interacting proteins for SCN1A (P354983 ENSP000003645544) via UniProtKB, MINT, STRING, and/or I2D (see all 22)
    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): 5/9 biological process terms (GO ID links to tree view) (see all 9):    About this table

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

    SCN1A for ontologies           About GeneDecksing



    Drugs & Compounds
    for SCN1A gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    SCN1A for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    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  

    Search CenterWatch for drugs/clinical trials and news about SCN1A

    Transcripts
    for SCN1A gene

    (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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    About This Section
    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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    SwitchGear 3'UTR luciferase reporter plasmid: SCN1A 3' UTR sequence
    Inhib. RNA
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    Primer
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    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 

    24/32 AceView cDNA sequences (see all 32):

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

    GeneLoc Exon Structure


    Expression
    for SCN1A gene

    (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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SCN1A expression in normal human tissues (normalized intensities)      SCN1A embryonic expression: see
    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 
     5/1 selected tissues (see all 1) fully expand
     
     Brain (Nervous System)
             Oligodendrocyte Precursor Cells Forebrain White Matter

    See SCN1A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SCN1A

    SOURCE GeneReport for Unigene cluster: Hs.22654
        SABiosciences Expression via Pathway-Focused PCR Array including SCN1A: 
              Neuronal Ion Channels in human mouse rat

    Primer
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    In Situ
    Assay Products:     
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    Orthologs
    for SCN1A gene

    (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)
    About This Section
    This gene was present in the common ancestor of chordates.

    Orthologs for SCN1A gene from 5/11 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 83.34(n)
    91.55(a)    		   771555  XM_003641586.1  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)


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

    Paralogs
    for SCN1A gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SCN1A gene
    SCN5A2  SCN9A2  CACNA1D2  SCN7A2  CACNA1I2  CACNA1F2  CACNA1G2  SCN8A2  
    SCN10A2  SCN3A2  SCN2A2  CACNA1H2  CACNA1C2  CACNA1S2  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

    SCN1A for paralogs           About GeneDecksing



    Genomic Variants
    for SCN1A gene

    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/3773 SNPs in SCN1A are shown (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
    ----------
    VAR_0643224
    		Familial hemiplegic migraine 3 (FHM3)4--see VAR_0643222 L Q mis40--------
    VAR_0642494
    		Severe myoclonic epilepsy in infancy (SMEI)4--see VAR_0642492 V E mis40--------
    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
    		CFamilial hemiplegic migraine 3 (FHM3)4 pathogenic1166249686(-) ACATCC/TTTATG 8 L F 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
    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing SCN1A
    DNA2.0 Custom Variant and Variant Library Synthesis for SCN1A

    Disorders / Diseases
    for SCN1A gene

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    		 OMIM gene information: 182389   
    OMIM disorders: 604233  607208  609634  604403  
    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
  • Familial hemiplegic migraine 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
  • Familial febrile convulsions 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

    • 20/43 diseases for SCN1A (see all 43):    About MalaCards
    dravet syndrome    myoclonic astatic epilepsy    epilepsy with generalized tonic-clonic seizures    scn1a-related seizure disorders
    epilepsy, generalized, with febrile seizures plus, type 2    familial hemiplegic migraine type 3    lennox-gastaut syndrome    febrile convulsions, familial, 3a
    febrile infection-related epilepsy syndrome    seizure disorder    epileptic encephalopathy lennox-gastaut type    febrilel, convulsions, familial, 8
    epileptic encephalopathy, early infantile, 12    generalized epilepsy with febrile seizures plus    migraine    hemiplegic migraine
    familial hemiplegic migraine    hepatic coma    febrile seizures    rasmussen encephalitis

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

    SCN1A for disorders           About GeneDecksing

    10/19 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

    Publications
    for SCN1A gene

    (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)
    About This Section

    PubMed articles for SCN1A gene, integrated from 9 sources (see all 314):
    (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. (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. (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. (1994)
    4. The spectrum of SCN1A-related infantile epileptic encephalopathies. (PubMed id 17347258)1, 2, 4, 9 Harkin L.A.... Scheffer I.E. (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. (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. (2004)
    7. Differential role of sodium channels SCN1A and SCN2A gene polymorphisms with epilepsy and multiple drug resistance in the north Indi an population. (PubMed id 19694741)1, 2, 4 Lakhan R....Mittal B. (2009)
    8. Physicochemical property changes of amino acid residu es that accompany missense mutations in SCN1A affect epilepsy phenotype severit y. (PubMed id 19586930)1, 4, 9 Kanai K....Kaneko S. (2009)
    9. Cryptogenic epileptic syndromes related to SCN1A: twelve novel mutations identified. (PubMed id 18413471)1, 2, 9 Zucca C.... Bassi M.T. (2008)
    10. Novel SCN1A mutations in Indonesian patients with sev ere myoclonic epilepsy in infancy. (PubMed id 19563458)1, 2, 9 Herini E.S....Nishio H. (2010)

    External Searches for SCN1A gene

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  
      Query String
    		PubMed
    OMIM
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      (Note: In FireFox, select the above section and copy using Ctrl-C)

    Genome Databases showing SCN1A gene

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

    Other Databases showing SCN1A gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing SCN1A gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SCN1A Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SCN1A

    Intellectual Property
    for SCN1A gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		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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    About This Section

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