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SCN3A Gene

protein-coding   GIFtS: 65
GCID: GC02M165908

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

(Previous names: sodium channel, voltage-gated, type III, alpha polypeptide)
  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 III, Alpha Subunit1 2     NAC32 3
Sodium Channel, Voltage-Gated, Type III, Alpha Polypeptide1 2     Nav1.32
Sodium Channel Protein Brain III Subunit Alpha2 3     Brain III Voltage-Gated Sodium Channel2
Sodium Channel Protein Type III Subunit Alpha2 3     Sodium Channel Protein Type 3 Subunit Alpha2
Voltage-Gated Sodium Channel Subtype III2 3     KIAA13563
Voltage-Gated Sodium Channel Subunit Alpha Nav1.32 3     

External Ids:    HGNC: 105901   Entrez Gene: 63282   Ensembl: ENSG000001532537   OMIM: 1823915   UniProtKB: Q9NY463   

Export aliases for SCN3A gene to outside databases

Previous GC identifers: GC02M163999 GC02M164485 GC02M166146 GC02M165769 GC02M165652 GC02M157826


(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 SCN3A 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, and is found in a cluster of five alpha subunit genes on chromosome 2. Multiple transcript
variants encoding different isoforms have been found for this gene. (provided by RefSeq, Jul 2008)

GeneCards Summary for SCN3A Gene:
SCN3A (sodium channel, voltage-gated, type III, alpha subunit) is a protein-coding gene. Diseases associated with SCN3A include trigeminal neuralgia, and pain disorder. GO annotations related to this gene include voltage-gated sodium channel activity. An important paralog of this gene is SCN5A.

UniProtKB/Swiss-Prot: SCN3A_HUMAN, Q9NY46
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 SCN3A 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 SCN3A 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 SCN3A gene promoter:
         GR   Sox5   GR-beta   E47   AREB6   NRF-2   POU2F1   POU2F1a   Sox9   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCN3A promoter sequence
   Search Chromatin IP Primers for SCN3A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SCN3A


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

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

SCN3A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCN3A gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M165908:  view genomic region     (about GC identifiers)

Start:
165,944,030 bp from pter      End:
166,060,577 bp from pter
Size:
116,548 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, 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: SCN3A_HUMAN, Q9NY46 (See protein sequence)
Recommended Name: Sodium channel protein type 3 subunit alpha  
Size: 2000 amino acids; 226294 Da
Subunit: The sodium channel consists of a large polypeptide and 2-3 smaller ones. This sequence represents a large
polypeptide. Interacts with NEDD4L
Secondary accessions: Q16142 Q53SX0 Q9BZB3 Q9C006 Q9NYK2 Q9P2J1 Q9UPD1 Q9Y6P4
Alternative splicing: 4 isoforms:  Q9NY46-1   Q9NY46-2   Q9NY46-3   Q9NY46-4   

Explore the universe of human proteins at neXtProt for SCN3A: NX_Q9NY46

Explore proteomics data for SCN3A at MOPED

Post-translational modifications: 

  • May be ubiquitinated by NEDD4L; which would promote its endocytosis1
  • Phosphorylation at Ser-1501 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, Asn290, Asn296, Asn302, Asn307, Asn339, Asn1366, Asn1380
  • Modification sites at PhosphoSitePlus

  • See SCN3A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_001075145.1  NP_001075146.1  NP_008853.3  

    ENSEMBL proteins: 
     ENSP00000283254   ENSP00000386726   ENSP00000403348   ENSP00000391569   ENSP00000353206  
     ENSP00000439920  
    Reactome Protein details: Q9NY46

    SCN3A Human Recombinant Protein Products:

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    Novus Biologicals SCN3A Protein
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

    SCN3A Antibody Products:

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    Abcam antibodies for SCN3A
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    SCN3A Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.


    (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: Nav1.3
    Voltage-gated sodium channels

    Selected InterPro protein domains (see all 7):
     IPR010526 Na_trans_assoc
     IPR005821 Ion_trans_dom
     IPR027359 Channel_four-helix_dom
     IPR028808 Na_channel_a3su
     IPR001696 Na_channel_asu

    Graphical View of Domain Structure for InterPro Entry Q9NY46

    ProtoNet protein and cluster: Q9NY46

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


    UniProtKB/Swiss-Prot: SCN3A_HUMAN, Q9NY46
    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. Nav1.3/SCN3A subfamily
    Similarity: Contains 1 IQ domain


    SCN3A 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: SCN3A_HUMAN, Q9NY46
    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 SCN3A:
    sodium voltage-gated channel,type III,alpha polypeptide,expressed in brain,encoding two isoforms (neonatal and
    adult)

         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 NAS9589372
    GO:0005515protein binding ----
         
    SCN3A for ontologies           About GeneDecksing


    Phenotypes:
         6 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Scn3a):
     behavior/neurological  growth/size/body  homeostasis/metabolism  mortality/aging  no phenotypic analysis 
     normal 

    SCN3A for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Scn3atm1.2Jwo for SCN3A

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SCN3A
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SCN3A

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SCN3A
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SCN3A

    miRNA
    Products:
        
    miRTarBase miRNAs that target SCN3A:
    hsa-mir-124-3p (MIRT022759), hsa-mir-335-5p (MIRT018072), hsa-mir-1 (MIRT023856)

    Block miRNA regulation of human, mouse, rat SCN3A using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SCN3A (see all 51):
    hsa-miR-548j hsa-miR-4291 hsa-miR-3607-3p hsa-miR-4328 hsa-miR-15a hsa-miR-30d hsa-miR-507 hsa-miR-223
    SwitchGear 3'UTR luciferase reporter plasmidSCN3A 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for SCN3A
    Predesigned siRNA for gene silencing in human, mouse, rat SCN3A

    Gene Editing
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    Clone
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    OriGene ORF clones in mouse, rat for SCN3A
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    GenScript: all cDNA clones in your preferred vector (see all 3): SCN3A (NM_001081676)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SCN3A
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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCN3A


    (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
    SCN3A_HUMAN, Q9NY46: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    cytoskeleton1
    extracellular1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001518voltage-gated sodium channel complex IEA--
    GO:0005737cytoplasm IEA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane ----

    SCN3A 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 SCN3A About   (see all 6)  
    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
    5Sodium channels and transporters inward current
    Sodium channels and transporters inward current

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    Selected Downloadable PowerPoint Slides of GeneGlobe Pathway Central Maps for SCN3A (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 SCN3A
        Interaction between L1 and Ankyrins



    SCN3A for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including SCN3A: 
              Neuronal Ion Channels in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for SCN3A

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

    Selected Interacting proteins for SCN3A (Q9NY463 ENSP000002832544) via UniProtKB, MINT, STRING, and/or I2D (see all 30)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CALM1P621583I2D: score=1 
    CALM2P621583I2D: score=1 
    CALM3P621583I2D: score=1 
    LRP1Q079543, ENSP000002430774I2D: score=2 STRING: ENSP00000243077
    LRP2P981643, ENSP000002638164I2D: score=1 STRING: ENSP00000263816
    About this table

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006811ion transport ----
    GO:0006814sodium ion transport NAS9589372
    GO:0035725sodium ion transmembrane transport NAS9589372
    GO:0055085transmembrane transport ----

    SCN3A 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 SCN3A 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 SCN3A    About this table
    CompoundSynonyms CAS #PubMed Ids
    SodiumSodium (see all 2)7440-23-5--

    2 DrugBank Compounds for SCN3A    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    ZonisamideZonisamida [Spanish] (see all 2)68291-97-4targetinhibitor20025128 14704463 19557119 18433351 20001433 15511691 19948168
    LacosamideErlosamide (see all 4)175481-36-4target--10592235

    7 IUPHAR Ligands for SCN3A (Nav1.3)    About this table
    LigandTypeActionAffinityPubmed IDs
    tetrodotoxin
    Pore BlockerAntagonist8.411122339
    AFT-II
    Gating inhibitorAntagonist6.315169781
    ATX-II
    Gating inhibitorAntagonist6.115169781
    Bc-III
    Gating inhibitorAntagonist5.815169781
    saxitoxin
    Channel blockerNone5.8--
    veratridine
    ActivatorNone5.8--
    batrachotoxin
    ActivatorNone5.8--

    1 Novoseek inferred chemical compound relationship for SCN3A gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sodium 54.6 4 8159690 (1), 8015391 (1), 11122339 (1), 16550174 (1)



    SCN3A 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 SCN3A gene (3 alternative transcripts): 
    NM_001081676.1  NM_001081677.1  NM_006922.3  

    Unigene Cluster for SCN3A:

    Sodium channel, voltage-gated, type III, alpha subunit
    Hs.435274  [show with all ESTs]
    Unigene Representative Sequence: NM_006922
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000283254(uc002ucx.3 uc002ucy.3) ENST00000409101(uc002udb.1)
    ENST00000465043 ENST00000471697 ENST00000440431(uc002uda.1) ENST00000484898
    ENST00000453007 ENST00000360093(uc010zcy.2 uc002ucz.3) ENST00000540861

    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate SCN3A (see all 51):
    hsa-miR-548j hsa-miR-4291 hsa-miR-3607-3p hsa-miR-4328 hsa-miR-15a hsa-miR-30d hsa-miR-507 hsa-miR-223
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    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 3): SCN3A (NM_001081676)
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    Primer
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    Additional mRNA sequence: 

    AB037777.1 AF035685.1 AF035686.1 AF225986.1 AF225987.1 AF239921.1 AJ251507.1 AJ276139.1 
    AJ276140.1 AJ277394.1 AK299757.1 AK301853.1 DQ993536.1 DQ993537.1 DQ993538.1 

    4 DOTS entries:

    DT.202774  DT.100742352  DT.65285907  DT.40122710 

    Selected AceView cDNA sequences (see all 40):

    BX281223 AW341281 AI457246 AB037777 AF239921 AA973965 H23297 AJ277394 
    AW341288 BM681920 BE327347 AJ276140 AJ251507 AJ276139 BE173197 AV702029 
    AF035685 CD623433 AF225986 BM728972 AF225987 NM_006922 AW341282 BP348889 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SCN3A (see all 9)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^
    SP1:                                                                                                  -                 -                                       
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 20 ^ 21 ^ 22 ^ 23 ^ 24a · 24b · 24c ^ 25a · 25b ^ 26a · 26b · 26c ^ 27 ^ 28 ^ 29
    SP1:                          -                                                               
    SP2:                          -           -                                                   
    SP3:                                                                                          
    SP4:                                                                                          
    SP5:                                                                                          


    ECgene alternative splicing isoforms for SCN3A

    (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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    SCN3A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TTCCAACTTT
    SCN3A Expression
    About this image


    SCN3A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     Blood (Cardiovascular System)    fully expand to see all 2 entries
             Mature B-Cells Peripheral Blood
     
     Thymus (Hematopoietic System)
             T Helper Cells Thymus
     
     Fibroblasts
             Detroit 551
     
     Epidermis (Integumentary System)
             Detroit 551
     
     Brain (Nervous System)
    SCN3A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SCN3A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.435274
        Pathway & Disease-focused RT2 Profiler PCR Array including SCN3A: 
              Neuronal Ion Channels in human mouse rat

    Primer
    Products:
    OriGene qSTAR qPCR primer pairs in human, mouse for SCN3A
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCN3A

    (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 SCN3A gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Scn3a1 , 5 sodium channel, voltage-gated, type III, alpha1, 5 89.57(n)1
    97.43(a)1
      2 (38.55 cM)5
    202691  NM_018732.31  NP_061202.31 
     654582635 
    chicken
    (Gallus gallus)
    Aves SCN3A1 sodium channel, voltage-gated, type III, alpha subunit 83.02(n)
    89.89(a)
      424180  XM_004942809.1  XP_004942866.1 
    lizard
    (Anolis carolinensis)
    Reptilia SCN3A6
    sodium channel, voltage-gated, type III, alpha sub...
    87(a)
    1 ↔ 1
    GL343214.1(1520472-1611131)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004886211 sodium channel protein type 2 subunit alpha-like 77.26(n)
    84.46(a)
      100488621  XM_002936749.2  XP_002936795.2 
    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 SCN3A (if available)
    TreeFam Gene Tree for SCN3A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SCN3A gene
    SCN5A2  SCN9A2  CACNA1D2  SCN7A2  CACNA1I2  CACNA1F2  CACNA1G2  SCN8A2  
    SCN10A2  SCN2A2  CACNA1S2  CACNA1C2  CACNA1H2  SCN11A2  SCN4A2  SCN1A2  
    Selected SIMAP similar genes for SCN3A using alignment to 7 protein entries:     SCN3A_HUMAN (see all proteins) (see all similar genes):
    SCN2A    SCN2A2    SCN1A    SCN9A    SCN8A    SCN4A
    SCN5A    SCN10A    CACNA1I    SCN7A    CACNA1E    CACNA1S
    CACNA1B    CACNA1C    SCN11A    CACNA1G    CACNA1A    CACNA1D

    SCN3A 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 SCN3A (see all 2191)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1837447671,2
    C--165943669(+) GCCACA/C/TGCGCC 3 -- ds50010--------
    rs1445847071,2
    --165943671(+) CACCGC/TGCCCA 3 -- ds50010--------
    rs1872450051,2
    --165943734(+) GGAAGA/TAGTTA 3 -- ds50010--------
    rs1925216431,2
    --165944032(+) GAATTC/TCAATT 3 -- ut310--------
    rs1475390711,2
    --165944098(+) ATTGTC/GTTTAA 3 -- ut310--------
    rs739691731,2
    C,F--165944376(+) GAAAGC/GTATTG 3 -- ut312Minor allele frequency- G:0.04WA 120
    rs1165817531,2
    C,F--165944558(+) AATGTC/AAGATC 3 -- ut311Minor allele frequency- A:0.05NA 120
    rs1401410541,2
    --165944640(+) GGCCAA/GTAAGT 3 -- ut310--------
    rs765761641,2
    C,F--165944939(+) CATACG/ATAAAT 3 -- ut311Minor allele frequency- A:0.01WA 118
    rs1141198681,2
    F--165944992(+) TTATAT/CTGAGG 3 -- ut311Minor allele frequency- C:0.01NA 120

    HapMap Linkage Disequilibrium report for SCN3A (165944030 - 166060577 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SCN3A (see all 13):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2666303CNV Deletion23128226
    nsv435715CNV Deletion17901297
    esv2721067CNV Deletion23290073
    esv2673049CNV Deletion23128226
    esv2585640CNV Deletion19546169
    esv2667791CNV Deletion23128226
    esv2554394CNV Deletion19546169
    esv25924CNV Loss19812545
    esv7053CNV Loss19470904
    nsv821783CNV Loss20364138

    Human Gene Mutation Database (HGMD): SCN3A
    Site Specific Mutation Identification with PCR Assays
    1 Copy Number PCR Panel containing SCN3A:
    Intellectual Disability
    SeqTarget long-range PCR primers for resequencing SCN3A
    DNA2.0 Custom Variant and Variant Library Synthesis for SCN3A

    (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: 182391    OMIM disorders: --

    13 diseases for SCN3A:    
    About MalaCards
    trigeminal neuralgia    pain disorder    epilepsy with generalized tonic-clonic seizures    erythromelalgia
    dravet syndrome    epilepsy syndrome    focal epilepsy    long qt syndrome
    idiopathic generalized epilepsy    spinal cord injury    brain disease    cholera
    neuronitis

    7 diseases from the University of Copenhagen DISEASES database for SCN3A:
    Dravet Syndrome     Idiopathic generalized epilepsy     Erythromelalgia     Pain disorder
    Epilepsy with generalized tonic-clonic seizures     Long QT syndrome     Focal epilepsy

    SCN3A for disorders           About GeneDecksing

    Genetic Association Database (GAD): SCN3A
    Human Genome Epidemiology (HuGE) Navigator: SCN3A (4 documents)

    Export disorders for SCN3A 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 SCN3A gene, integrated from 10 sources (see all 36):
    (articles sorted by number of sources associating them with SCN3A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Isolation of a human-brain sodium-channel gene encoding two isoforms of the subtype III alpha-subunit. (PubMed id 9589372)1, 2, 3 Lu C.M. and Brown G.B. (J. Mol. Neurosci. 1998)
    2. Targeted gene walking by low stringency polymerase chain reaction: assignment of a putative human brain sodium channel gene (SCN3A) to chromosome 2q24-31. (PubMed id 8159690)1, 2, 9 Malo M.S....Ingram V.M. (Proc. Natl. Acad. Sci. U.S.A. 1994)
    3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    4. Multidrug resistance in epilepsy and polymorphisms in the voltage-gated sodium channel genes SCN1A, SCN2A, and SCN3A: correlation among phenotype, genotype, and mRNA expression. (PubMed id 18784617)1, 4 Kwan P....Baum L. (Pharmacogenet. Genomics 2008)
    5. Molecular determinants of voltage-gated sodium channel regulation by the Nedd4/Nedd4-like proteins. (PubMed id 15548568)1, 2 Rougier J.-S....Abriel H. (Am. J. Physiol. 2005)
    6. International Union of Pharmacology. XLVII. Nomenclature and structure-function relationships of voltage-gated sodium channels. (PubMed id 16382098)1, 3 Catterall W.A....Waxman S.G. (Pharmacol. Rev. 2005)
    7. Sodium channels SCN1A, SCN2A and SCN3A in familial autism. (PubMed id 12610651)1, 2 Weiss L.A.... Meisler M.H. (Mol. Psychiatry 2003)
    8. Genomic structures of SCN2A and SCN3A -- candidate genes for deafness at the DFNA16 locus. (PubMed id 11245985)1, 2 Kasai N.... Smith R.J.H. (Gene 2001)
    9. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10718198)1, 2 Nagase T.... Ohara O. (DNA Res. 2000)
    10. Cloning, distribution and functional analysis of the type III sodium channel from human brain. (PubMed id 11122339)1, 9 Chen Y.H....Clare J.J. (Eur. J. Neurosci. 2000)

    (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: 6328 HGNC: 10590 AceView: SCN3A Ensembl:ENSG00000153253 euGenes: HUgn6328
    ECgene: SCN3A H-InvDB: SCN3A

    (According to HUGE)
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    HUGE: KIAA1356

    (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 SCN3A Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SCN3A gene:
    Search GeneIP for patents involving SCN3A

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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