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SCN2A Gene

protein-coding   GIFtS: 60
GCID: GC02P166095

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

(Previous names: sodium channel, voltage-gated, type II, alpha 2 polypeptide,...)
(Previous symbols: SCN2A1, SCN2A2)
  See 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 II, Alpha Subunit1 2     BFIS32 5
SCN2A11 2 3 5     BFNIS2 5
SCN2A21 2 3     EIEE112 5
Sodium Channel, Voltage-Gated, Type II, Alpha 1 Polypeptide1 2     HBA2
Sodium Channel, Voltage-Gated, Type II, Alpha 2 Polypeptide1 2     HBSCI2
Sodium Channel Protein Brain II Subunit Alpha2 3     HBSCII2
Sodium Channel Protein Type II Subunit Alpha2 3     Na(v)1.22
Voltage-Gated Sodium Channel Subunit Alpha Nav1.22 3     Nav1.22
NAC22 3     Sodium Channel Protein Type 2 Subunit Alpha2
HBSC II2 3     Sodium Channel Protein, Brain Type 2 Alpha Subunit2
BFIC32 5     Voltage-Gated Sodium Channel Subtype II2

External Ids:    HGNC: 105881   Entrez Gene: 63262   Ensembl: ENSG000001365317   OMIM: 1823905   UniProtKB: Q992503   

Export aliases for SCN2A gene to outside databases

Previous GC identifers: GC02P165805 GC02P157978


(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 SCN2A Gene:
Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24
transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and
propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha
subunit gene family. It is heterogeneously expressed in the brain, and mutations in this gene have been linked to
several seizure disorders. Several alternatively spliced transcript variants of this gene have been described,
but the full-length nature of some of these variants has not been determined. (provided by RefSeq, Jul 2008)

GeneCards Summary for SCN2A Gene:
SCN2A (sodium channel, voltage-gated, type II, alpha subunit) is a protein-coding gene. Diseases associated with SCN2A include epileptic encephalopathy, early infantile, 11, and benign familial neonatal-infantile seizures. GO annotations related to this gene include voltage-gated sodium channel activity. An important paralog of this gene is SCN5A.

UniProtKB/Swiss-Prot: SCN2A_HUMAN, Q99250
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 SCN2A 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 SCN2A (Nav1.2) 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:
NC_000002.12  NT_005403.18  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SCN2A gene promoter:
         E2F-3a   E2F-5   E2F-1   E2F   HOXA5   E2F-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCN2A promoter sequence
   Search Chromatin IP Primers for SCN2A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SCN2A


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

SCN2A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCN2A gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P166095:  view genomic region     (about GC identifiers)

Start:
166,095,912 bp from pter      End:
166,248,820 bp from pter
Size:
152,909 bases      Orientation:
plus 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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: SCN2A_HUMAN, Q99250 (See protein sequence)
Recommended Name: Sodium channel protein type 2 subunit alpha  
Size: 2005 amino acids; 227975 Da
Subunit: Interacts with NEDD4L. Interacts with CALM (By similarity). Heterooligomer of a large alpha subunit and a
smaller beta subunit. Heterooligomer with SCN4B; disulfide-linked
Sequence caution: Sequence=CAA46438.1; Type=Frameshift; Positions=1953; Sequence=CAA46438.1; Type=Miscellaneous
discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the C-terminal part;
1 PDB 3D structure from and Proteopedia for SCN2A:
2KAV (3D)    
Secondary accessions: A6NC14 A6NIQ5 Q14472 Q53T77 Q9BZC9 Q9BZD0
Alternative splicing: 2 isoforms:  Q99250-1   Q99250-2   

Explore the universe of human proteins at neXtProt for SCN2A: NX_Q99250

Explore proteomics data for SCN2A at MOPED

Post-translational modifications: 

  • May be ubiquitinated by NEDD4L; which would promote its endocytosis (By similarity)1
  • Phosphorylation at Ser-1506 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel
    and reduces peak sodium currents (By similarity)1
  • Glycosylation2 at Asn212, Asn285, Asn291, Asn297, Asn303, Asn308, Asn340, Asn1368, Asn1382, Asn1393
  • Modification sites at PhosphoSitePlus

  • See SCN2A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001035232.1  NP_001035233.1  NP_066287.2  

    ENSEMBL proteins: 
     ENSP00000406454   ENSP00000283256   ENSP00000364576   ENSP00000364586   ENSP00000349973  
    Reactome Protein details: Q99250

    SCN2A Human Recombinant Protein Products:

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    SCN2A Assay Products:

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    (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: Nav1.2
    Voltage-gated sodium channels

    Selected InterPro protein domains (see all 7):
     IPR010526 Na_trans_assoc
     IPR005821 Ion_trans_dom
     IPR027359 Channel_four-helix_dom
     IPR001696 Na_channel_asu
     IPR000048 IQ_motif_EF-hand-BS

    Graphical View of Domain Structure for InterPro Entry Q99250

    ProtoNet protein and cluster: Q99250

    2 Blocks protein domains:
    IPB000048 IQ calmodulin-binding region
    IPB001696 Voltage-gated Na+ channel alpha subunit signature


    UniProtKB/Swiss-Prot: SCN2A_HUMAN, Q99250
    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. Nav1.2/SCN2A subfamily
    Similarity: Contains 1 IQ domain


    SCN2A for domains           About GeneDecksing


    (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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SCN2A_HUMAN, Q99250
    Function: Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed
    conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective
    channel through which Na(+) ions may pass in accordance with their electrochemical gradient

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005216ion channel activity ----
    GO:0005248voltage-gated sodium channel activity ISS--
    GO:0005515protein binding ----
         
    SCN2A for ontologies           About GeneDecksing


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SCN2A
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    miRNA
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    miRTarBase miRNAs that target SCN2A:
    hsa-mir-26b-5p (MIRT029544)

    Block miRNA regulation of human, mouse, rat SCN2A using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SCN2A (see all 87):
    hsa-miR-100* hsa-miR-520e hsa-miR-3607-3p hsa-miR-106a hsa-miR-374a hsa-miR-30d hsa-miR-371-5p hsa-miR-502-3p
    SwitchGear 3'UTR luciferase reporter plasmidSCN2A 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SCN2A

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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCN2A


    (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
    SCN2A_HUMAN, Q99250: Cell membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane4
    cytosol2
    extracellular1
    nucleus1

    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:0005887integral component of plasma membrane TAS1325650
    GO:0014704intercalated disc IEA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane ----

    SCN2A for ontologies           About GeneDecksing


    (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 SCN2A About    
    See pathways by source

    SuperPathContained pathways About
    1L1CAM interactions
    Axon guidance0.63
    L1CAM interactions0.36
    Developmental Biology0.63
    2Synaptic transmission ion currents
    Synaptic transmission ion currents
    3Sodium channels and transporters inward current
    Sodium channels and transporters inward current
    4Interaction between L1 and Ankyrins
    Interaction between L1 and Ankyrins

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for SCN2A (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 SCN2A
        Interaction between L1 and Ankyrins



    SCN2A for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including SCN2A: 
              Neuronal Ion Channels in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for SCN2A

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

    Selected Interacting proteins for SCN2A (Q992502, 3 ENSP000002832564) via UniProtKB, MINT, STRING, and/or I2D (see all 36)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ARHGEF10LQ9HCE62, 3MINT-64955 I2D: score=3 
    MPP3Q133682, 3MINT-64795 I2D: score=3 
    RNF130Q86XS82, 3MINT-64837 I2D: score=3 
    CALM1P621583I2D: score=1 
    CALM2P621583I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006811ion transport ----
    GO:0006814sodium ion transport TAS1325650
    GO:0006915apoptotic process ----
    GO:0007399nervous system development ----
    GO:0008627intrinsic apoptotic signaling pathway in response to osmotic stress IEA--

    SCN2A for ontologies           About GeneDecksing



    (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 SCN2A 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]

    1 HMDB Compound for SCN2A    About this table
    CompoundSynonyms CAS #PubMed Ids
    SodiumSodium (see all 2)7440-23-5--

    3 DrugBank Compounds for SCN2A    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    ZonisamideZonisamida [Spanish] (see all 2)68291-97-4targetinhibitor20025128 14704463 19557119 18433351 20001433 15511691 19948168
    LamotrigineGW 273293 (see all 3)84057-84-1targetinhibitor17139284 17016423 16174788
    Propofol2,6-Diisopropylphenol (see all 2)2078-54-8targetinhibitor18574460

    8 IUPHAR Ligands for SCN2A (Nav1.2)    About this table
    LigandTypeActionAffinityPubmed IDs
    ATX-II
    Gating inhibitorAntagonist8.115169781
    Bc-III
    Gating inhibitorAntagonist5.815169781
    AFT-II
    Gating inhibitorAntagonist5.715169781
    phenytoin
    Pore BlockerNone4.91658608
    veratridine
    ActivatorNone4.9--
    tetrodotoxin
    Channel blockerNone4.9--
    saxitoxin
    Channel blockerNone4.9--
    batrachotoxin
    ActivatorNone4.9--

    1 Novoseek inferred chemical compound relationship for SCN2A gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sodium 54.6 1 11166117 (1)



    SCN2A for compounds           About GeneDecksing



    (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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SCN2A gene (3 alternative transcripts): 
    NM_001040142.1  NM_001040143.1  NM_021007.2  

    Unigene Cluster for SCN2A:

    Sodium channel, voltage-gated, type II, alpha subunit
    Hs.93485  [show with all ESTs]
    Unigene Representative Sequence: NM_021007
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000424833 ENST00000283256 ENST00000480032 ENST00000375427 ENST00000486878
    ENST00000375437(uc002udc.3 uc002udd.3) ENST00000357398(uc002ude.3 uc021vry.1)

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    hsa-miR-100* hsa-miR-520e hsa-miR-3607-3p hsa-miR-106a hsa-miR-374a hsa-miR-30d hsa-miR-371-5p hsa-miR-502-3p
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      QuantiFast Probe-based Assays in human, mouse, rat SCN2A

    Additional mRNA sequence: 

    AK289656.1 AL137498.1 DQ993531.1 JF437648.1 M91804.1 M94055.1 X65361.1 

    4 DOTS entries:

    DT.100740790  DT.108731  DT.210911  DT.92417535 

    Selected AceView cDNA sequences (see all 44):

    BX094575 N49273 BX488957 AW292894 F04027 M94055 BX478689 BU618561 
    BM680946 NM_021007 BI752826 BC047398 BI488967 M91804 BX508621 BX505276 
    F07776 X65361 BC048417 BC029489 CK003057 AW771930 AL120392 AI796228 

    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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    SCN2A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CAGGAAAATG
    SCN2A Expression
    About this image

    SCN2A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SCN2A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.93485
        Pathway & Disease-focused RT2 Profiler PCR Array including SCN2A: 
              Neuronal Ion Channels in human mouse rat

    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCN2A

    (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 animals.

    Orthologs for SCN2A gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Scn2a11 sodium channel, voltage-gated, type II, alpha 1 89.46(n)
    98.1(a)
      110876  NM_001099298.2  NP_001092768.1 
    chicken
    (Gallus gallus)
    Aves SCN2A1 sodium channel, voltage-gated, type II, alpha subunit 83.59(n)
    92.27(a)
      395945  XM_004942787.1  XP_004942844.1 
    lizard
    (Anolis carolinensis)
    Reptilia SCN2A6
    sodium channel, voltage-gated, type II, alpha subu...
    91(a)
    1 ↔ 1
    GL343214.1(1332766-1396213)
    African clawed frog
    (Xenopus laevis)
    Amphibia scn2a2-A2 sodium channel, voltage-gated, type II, alpha 2 80.24(n)    AY121368.1 
    zebrafish
    (Danio rerio)
    Actinopterygii scn1lab1 sodium channel, voltage-gated, type I like, alpha b 71.88(n)
    80.42(a)
      559447  NM_001044895.1  NP_001038360.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta para1 paralytic 54.47(n)
    49.34(a)
      32619  NM_001201695.2  NP_001188624.1 


    ENSEMBL Gene Tree for SCN2A (if available)
    TreeFam Gene Tree for SCN2A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SCN2A gene
    SCN5A2  SCN9A2  CACNA1D2  SCN7A2  CACNA1I2  CACNA1F2  CACNA1G2  SCN8A2  
    SCN10A2  SCN3A2  CACNA1S2  CACNA1C2  CACNA1H2  SCN11A2  SCN4A2  SCN1A2  
    11 SIMAP similar genes for SCN2A using alignment to 2 protein entries:     SCN2A_HUMAN (see all proteins):
    SCN2A2    SCN3A    SCN1A    SCN9A    SCN8A    SCN5A
    SCN4A    SCN10A    SCN7A    SCN11A    TPCN1

    SCN2A for paralogs           About GeneDecksing



    (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 SCN2A (see all 3021)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0700064
    Epileptic encephalopathy, early infantile, 11 (EIEE11)4--see VAR_0700062 S Y mis40--------
    VAR_0699974
    Epileptic encephalopathy, early infantile, 11 (EIEE11)4--see VAR_0699972 N D mis40--------
    VAR_0700004
    Epileptic encephalopathy, early infantile, 11 (EIEE11)4--see VAR_0700002 A T mis40--------
    VAR_0700054
    Epileptic encephalopathy, early infantile, 11 (EIEE11)4--see VAR_0700052 V L mis40--------
    VAR_0700014
    Epileptic encephalopathy, early infantile, 11 (EIEE11)4--see VAR_0700012 R Q mis40--------
    VAR_0297404
    Seizures, benign familial infantile 3 (BFIS3)4--see VAR_0297402 L F mis40--------
    VAR_0700094
    Epileptic encephalopathy, early infantile, 11 (EIEE11)4--see VAR_0700092 T N mis40--------
    VAR_0651814
    Epileptic encephalopathy, early infantile, 11 (EIEE11)4--see VAR_0651812 I M mis40--------
    VAR_0297344
    Seizures, benign familial infantile 3 (BFIS3)4--see VAR_0297342 R Q mis40--------
    VAR_0700034
    Epileptic encephalopathy, early infantile, 11 (EIEE11)4--see VAR_0700032 E K mis40--------

    HapMap Linkage Disequilibrium report for SCN2A (166095912 - 166248820 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for SCN2A:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv875368CNV Loss21882294
    nsv526967CNV Loss19592680
    dgv4354n71CNV Loss21882294
    nsv528928CNV Loss19592680
    esv5728CNV Gain19470904

    Human Gene Mutation Database (HGMD): SCN2A
    Site Specific Mutation Identification with PCR Assays
    1 Copy Number PCR Panel containing SCN2A:
    Intellectual Disability
    SeqTarget long-range PCR primers for resequencing SCN2A
    DNA2.0 Custom Variant and Variant Library Synthesis for SCN2A

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 182390   
    OMIM disorders: 607745  613721  
    UniProtKB/Swiss-Prot: SCN2A_HUMAN, Q99250
  • Seizures, benign familial infantile 3 (BFIS3) [MIM:607745]: An autosomal dominant disorder in which
    afebrile seizures occur in clusters during the first year of life, without neurologic sequelae. Note=The disease
    is caused by mutations affecting the gene represented in this entry
  • Epileptic encephalopathy, early infantile, 11 (EIEE11) [MIM:613721]: An autosomal dominant seizure
    disorder characterized by neonatal or infantile onset of refractory seizures with resultant delayed neurologic
    development and persistent neurologic abnormalities. Patients may progress to West syndrome, which is
    characterized by tonic spasms with clustering, arrest of psychomotor development, and hypsarrhythmia on EEG.
    Note=The disease is caused by mutations affecting the gene represented in this entry

  • Selected diseases for SCN2A (see all 31):    
    About MalaCards
    epileptic encephalopathy, early infantile, 11    benign familial neonatal-infantile seizures    seizures, benign familial infantile, 3    seizure disorder
    epileptic encephalopathy, early infantile, 4    epilepsy with generalized tonic-clonic seizures    benign familial infantile seizures 2    epilepsy, generalized, with febrile seizures plus, type 3
    dravet syndrome    epileptic encephalopathy, early infantile, 1    myoclonic epilepsy of infancy    febrile seizures
    epileptic encephalopathy, early infantile, 17    generalized epilepsy with febrile seizures plus    episodic ataxia    scrapie
    hemoglobinopathy    epilepsy syndrome    idiopathic generalized epilepsy    myoclonus

    5 diseases from the University of Copenhagen DISEASES database for SCN2A:
    Thalassemia     Scrapie     Epilepsy syndrome     Anemia
    Sickle cell anemia

    SCN2A for disorders           About GeneDecksing

    Genetic Association Database (GAD): SCN2A
    Human Genome Epidemiology (HuGE) Navigator: SCN2A (10 documents)

    Export disorders for SCN2A 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 SCN2A gene, integrated from 10 sources (see all 91):
    (articles sorted by number of sources associating them with SCN2A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Differential expression of two sodium channel subtypes in human brain. (PubMed id 1317301)1, 2, 3 Lu C.-M.... Brown G.B. (FEBS Lett. 1992)
    2. SCN2A mutation is associated with infantile spasms and bitemporal glucose hypometabolism. (PubMed id 23827426)1, 2 Sundaram S.K.... Huq A.H. (Pediatr. Neurol. 2013)
    3. Clinical spectrum of SCN2A mutations expanding to Ohtahara syndrome. (PubMed id 23935176)1, 2 Nakamura K....Saitsu H. (Neurology 2013)
    4. Whole genome sequencing identifies SCN2A mutation in monozygotic twins with Ohtahara syndrome and unique neuropathologic findings. (PubMed id 23550958)1, 2 Touma M....Agrawal P.B. (Epilepsia 2013)
    5. High-density SNP association study and copy number variation analysis of the AUTS1 and AUTS5 loci implicate the IMMP2L-DOCK4 gene region in autism susceptibility. (PubMed id 19401682)1, 4 Maestrini E....Monaco A.P. (Mol. Psychiatry 2010)
    6. Molecular correlates of age-dependent seizures in an inherited neonatal-infantile epilepsy. (PubMed id 20371507)1, 2 Liao Y.... Lerche H. (Brain 2010)
    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, 4 Lakhan R.... Mittal B. (Br. J. Clin. Pharmacol. 2009)
    8. Liability of the voltage-gated sodium channel gene SCN2A R19K polymorphism to oxaliplatin-induced peripheral neuropathy. (PubMed id 19738391)1, 4 Argyriou A.A....Kalofonos H.P. (Oncology 2009)
    9. Gene-to-gene interaction between sodium channel-related genes in determining the risk of antiepileptic drug resistance. (PubMed id 19270815)1, 4 Jang S.Y....Kim Y.S. (J. Korean Med. Sci. 2009)
    10. De novo mutations of voltage-gated sodium channel alphaII gene SCN2A in intractable epilepsies. (PubMed id 19786696)1, 2 Ogiwara I....Yamakawa K. (Neurology 2009)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    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: 6326 HGNC: 10588 AceView: SCN2A2 Ensembl:ENSG00000136531 euGenes: HUgn6326
    ECgene: SCN2A H-InvDB: SCN2A

    (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 SCN2A Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SCN2A[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 SCN2A gene:
    Search GeneIP for patents involving SCN2A

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



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