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SCN5A Gene

protein-coding   GIFtS: 67
GCID: GC03M038589

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

(Previous names: sodium channel, voltage-gated, type V, alpha (long QT syndrome...)
(Previous symbol: CMD1E)
  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 V, Alpha Subunit1 2     Sodium Channel, Voltage-Gated, Type V, Alpha (Long QT Syndrome 3)1
CMD1E1 2 5     CMPD22
Sodium Channel Protein Cardiac Muscle Subunit Alpha2 3     HB22
Voltage-Gated Sodium Channel Subunit Alpha Nav1.52 3     HBBD2
HH12 3     ICCD2
CDCD22 5     IVF2
HB12 5     Nav1.52
LQT32 5     PFHB12
SSS12 5     Cardiac Tetrodotoxin-Insensitive Voltage-Dependent Sodium Channel Alpha
Subunit2
VF12 5     Sodium Channel Protein Type 5 Subunit Alpha2
Long QT Syndrome 31     Sodium Channel Protein Type V Subunit Alpha3

External Ids:    HGNC: 105931   Entrez Gene: 63312   Ensembl: ENSG000001838737   OMIM: 6001635   UniProtKB: Q145243   

Export aliases for SCN5A gene to outside databases

Previous GC identifers: GC03U990070 GC03M038402 GC03M038550 GC03M038565


(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 SCN5A Gene:
The protein encoded by this gene is an integral membrane protein and tetrodotoxin-resistant voltage-gated sodium
channel subunit. This protein is found primarily in cardiac muscle and is responsible for the initial upstroke of
the action potential in an electrocardiogram. Defects in this gene are a cause of long QT syndrome type 3 (LQT3),
an autosomal dominant cardiac disease. Alternative splicing results in several transcript variants encoding
different isoforms. (provided by RefSeq, Jul 2008)

GeneCards Summary for SCN5A Gene:
SCN5A (sodium channel, voltage-gated, type V, alpha subunit) is a protein-coding gene. Diseases associated with SCN5A include right bundle branch block, and heart block, nonprogressive. GO annotations related to this gene include enzyme binding and ubiquitin protein ligase binding. An important paralog of this gene is SCN9A.

UniProtKB/Swiss-Prot: SCN5A_HUMAN, Q14524
Function: This protein 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. It
is a tetrodotoxin-resistant Na(+) channel isoform. This channel is responsible for the initial upstroke of the
action potential. Channel inactivation is regulated by intracellular calcium levels

summary for SCN5A 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 SCN5A (Nav1.5) Gene

PharmGKB "VIP" summary for SCN5A


(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_000003.12  NT_022517.19  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SCN5A gene promoter:
         AP-2alpha isoform 3   AP-2alpha isoform 2   AP-2alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCN5A promoter sequence
   Search Chromatin IP Primers for SCN5A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SCN5A


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

Entrez Gene cytogenetic band: 3p21   Ensembl cytogenetic band:  3p22.2   HGNC cytogenetic band: 3p21

SCN5A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCN5A gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M038589:  view genomic region     (about GC identifiers)

Start:
38,589,548 bp from pter      End:
38,691,164 bp from pter
Size:
101,617 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, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SCN5A_HUMAN, Q14524 (See protein sequence)
Recommended Name: Sodium channel protein type 5 subunit alpha  
Size: 2016 amino acids; 226940 Da
Subunit: Interacts with the PDZ domain of the syntrophin SNTA1, SNTB1 and SNTB2 (By similarity). Interacts with
NEDD4, NEDD4L, WWP2 and GPD1L. Interacts with CALM. Interacts with FGF13; the interaction is direct and may
regulate SNC5A density at membranes and function
Miscellaneous: Na(+) channels in mammalian cardiac membrane have functional properties quite distinct from Na(+)
channels in nerve and skeletal muscle
4 PDB 3D structures from and Proteopedia for SCN5A:
2KBI (3D)        2L53 (3D)        4DCK (3D)        4DJC (3D)    
Secondary accessions: A5H1P8 A6N922 A6N923 B2RTU0 E7ET19 E9PEF3 E9PEK2 E9PFW7 Q59H93 Q75RX9
Q75RY0 Q86UR3 Q8IZC9 Q96J69
Alternative splicing: 6 isoforms:  Q14524-1   Q14524-2   Q14524-3   Q14524-4   Q14524-5   Q14524-6   (High expression in brain where it accounts for nearly 50% of the total transcripts. Non-functional channel, may exist to limit the number of undesired functional Nav1.5 channels)

Explore the universe of human proteins at neXtProt for SCN5A: NX_Q14524

Explore proteomics data for SCN5A at MOPED

Post-translational modifications: 

  • Regulated through phosphorylation by CaMK2D (By similarity)1
  • Ubiquitinated by NEDD4L; which promotes its endocytosis. Does not seem to be ubiquitinated by NEDD4 or WWP21
  • Phosphorylation at Ser-1503 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel
    and reduces peak sodium currents (By similarity)1
  • Glycosylation2 at Asn214, Asn283, Asn288, Asn291, Asn318, Asn328, Asn740, Asn803, Asn864, Asn1365,
                                 Asn1374, Asn1380, Asn1388, Asn1736
  • Modification sites at PhosphoSitePlus

  • See SCN5A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (6 alternative transcripts): 
    NP_000326.2  NP_001092874.1  NP_001092875.1  NP_001153632.1  NP_001153633.1  NP_932173.1  

    ENSEMBL proteins: 
     ENSP00000398962   ENSP00000398266   ENSP00000410257   ENSP00000328968   ENSP00000399524  
     ENSP00000403355   ENSP00000413996   ENSP00000333674   ENSP00000388797   ENSP00000397915  
     ENSP00000416634  
    Reactome Protein details: Q14524

    SCN5A Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    Novus Biologicals SCN5A Protein
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp.

    SCN5A Antibody Products:

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    ThermoFisher Antibodies for SCN5A
    LSBio Antibodies in human, mouse, rat for SCN5A

    SCN5A 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: Nav1.5
    Voltage-gated sodium channels

    Selected InterPro protein domains (see all 7):
     IPR010526 Na_trans_assoc
     IPR005821 Ion_trans_dom
     IPR008053 Na_channel_a5su
     IPR027359 Channel_four-helix_dom
     IPR001696 Na_channel_asu

    Graphical View of Domain Structure for InterPro Entry Q14524

    ProtoNet protein and cluster: Q14524

    3 Blocks protein domains:
    IPB000048 IQ calmodulin-binding region
    IPB001696 Voltage-gated Na+ channel alpha subunit signature
    IPB008053 Voltage-gated Na+ channel alpha 5 subunit signature


    UniProtKB/Swiss-Prot: SCN5A_HUMAN, Q14524
    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
    Domain: The IQ domain mediates association with calmodulin
    Similarity: Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.5/SCN5A subfamily
    Similarity: Contains 1 IQ domain


    SCN5A 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: SCN5A_HUMAN, Q14524
    Function: This protein 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. It
    is a tetrodotoxin-resistant Na(+) channel isoform. This channel is responsible for the initial upstroke of the
    action potential. Channel inactivation is regulated by intracellular calcium levels

         Genatlas biochemistry entry for SCN5A:
    sodium voltage-gated channel,type V,alpha polypeptide,tetradotoxin-resistant,heart

         Gene Ontology (GO): Selected molecular function terms (see all 13):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005216ion channel activity ----
    GO:0005248voltage-gated sodium channel activity IDA14500339
    GO:0005515protein binding IPI11807557
    GO:0005516calmodulin binding IPI--
    GO:0017134fibroblast growth factor binding IPI12401812
         
    SCN5A for ontologies           About GeneDecksing


    Phenotypes:
         9 MGI mutant phenotypes (inferred from 8 alleles(MGI details for Scn5a):
     behavior/neurological  cardiovascular system  cellular  embryogenesis  growth/size/body 
     mortality/aging  muscle  nervous system  normal 

    SCN5A for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SCN5A
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SCN5A

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SCN5A
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SCN5A

    miRNA
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    Block miRNA regulation of human, mouse, rat SCN5A using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SCN5A (see all 67):
    hsa-miR-520e hsa-miR-1307 hsa-miR-3146 hsa-miR-219-5p hsa-miR-374a hsa-miR-200b hsa-miR-3148 hsa-miR-761
    SwitchGear 3'UTR luciferase reporter plasmidSCN5A 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for SCN5A
    Predesigned siRNA for gene silencing in human, mouse, rat SCN5A

    Gene Editing
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    Clone
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    OriGene clones in human, mouse for SCN5A (see all 25)
    OriGene ORF clones in mouse, rat for SCN5A
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    GenScript: all cDNA clones in your preferred vector (see all 6): SCN5A (NM_001099404)
    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SCN5A

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCN5A


    (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
    SCN5A_HUMAN, Q14524: Membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum4
    plasma membrane4
    cytoskeleton1
    extracellular1

    Gene Ontology (GO): Selected cellular component terms (see all 12):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001518voltage-gated sodium channel complex IDA19808477
    GO:0005783endoplasmic reticulum IDA--
    GO:0005886plasma membrane IDA16728661
    GO:0005901colocalizes with caveola TAS17060380
    GO:0009986cell surface IDA14500339

    SCN5A 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 SCN5A About   (see all 10)  
    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 SCN5A (see all 7)
        Cholera Infection
    Neuropathic Pain-Signaling in Dorsal Horn Neurons
    PKA Signaling
    cAMP Pathway
    Aldosterone Signaling in Epithelial Cells

    2 BioSystems Pathways for SCN5A
        SIDS Susceptibility Pathways
    Cardiac Progenitor Differentiation

    1 Reactome Pathway for SCN5A
        Interaction between L1 and Ankyrins

    1 PharmGKB Pathway for SCN5A
        Antiarrhythmic Pathway, Pharmacodynamics

    1 Kegg Pathway  (Kegg details for SCN5A):
        Adrenergic signaling in cardiomyocytes


    SCN5A for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SCN5A
    Interactions:

        GeneGlobe Interaction Network for SCN5A

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

    Selected Interacting proteins for SCN5A (Q145241, 2, 3 ENSP000003289684) via UniProtKB, MINT, STRING, and/or I2D (see all 92)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HIST1H4AP628053I2D: score=1 
    HIST1H4BP628053I2D: score=1 
    HIST1H4CP628053I2D: score=1 
    HIST1H4DP628053I2D: score=1 
    HIST1H4EP628053I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 33):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0002027regulation of heart rate IMP10471492
    GO:0003231cardiac ventricle development ISS--
    GO:0003360brainstem development ISS--
    GO:0006811ion transport ----
    GO:0006814sodium ion transport IDA19074138

    SCN5A 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 SCN5A 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 SCN5A    About this table
    CompoundSynonyms CAS #PubMed Ids
    SodiumSodium (see all 2)7440-23-5--
    VerapamilAkilen (see all 107)52-53-9--

    Selected DrugBank Compounds for SCN5A (see all 29)    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    FlecainideFlecainida [INN-Spanish] (see all 2)54143-55-4targetinhibitor10758053 10617684 15272045 10961955 12601084 11752352 11196553 11535580 11307783
    Quinidine-- 56-54-2targetinhibitor16138883 16972995 17023504 9476974 17556186 11752352 15877619 20685573
    Quinidine barbiturate-- --targetinhibitor16138883 16972995 17023504 9476974 17556186 11752352 15877619 20685573
    MexiletineMexiletina [INN-Spanish] (see all 4)31828-71-4targetinhibitor12650887 16168489 12123767 12604879 12676070 11752352 11196553
    ZonisamideZonisamida [Spanish] (see all 2)68291-97-4targetinhibitor20025128 14704463 19557119 18433351 20001433 15511691 19948168
    Ajmaline-- 4360-12-7targetinhibitor20022821 18599870 20174578 6088360 20870038 21126620
    Dibucaine-- 85-79-0targetinhibitor9742684 17139284 11752352 17016423 12354567 8798723
    Indecainide9-(3-(Isopropylamino)propyl)-9-fluorenylcarboxamid (see all 6)74517-78-5targetinhibitor17139284 2688391 6206315 11752352 17016423 2476626
    LidocaineDilocaine (see all 2)137-58-6targetinhibitor16686685 17016511 20585544 19088384 16840798 17445919
    Procainamide-- 51-06-9targetinhibitor11155778 11752352 10662748 11839626 10443304 11225790

    8 IUPHAR Ligands for SCN5A (Nav1.5)    About this table
    LigandTypeActionAffinityPubmed IDs
    ATX-II
    Gating inhibitorAntagonist7.315169781
    AFT-II
    Gating inhibitorAntagonist7.215169781
    Bc-III
    Gating inhibitorAntagonist6.515169781
    lidocaine
    Pore BlockerAntagonist4.88786356
    aconitine
    ActivatorAgonist4.811826163 2433183
    veratridine
    ActivatorNone4.8--
    tetrodotoxin
    Channel blockerNone4.8--
    batrachotoxin
    ActivatorNone4.8--

    Selected Novoseek inferred chemical compound relationships for SCN5A gene (see all 22)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sodium 87 288 18436145 (4), 14753626 (3), 18591664 (3), 20042427 (3) (see all 99)
    ajmaline 83.4 5 15520322 (1), 20022821 (1), 15028074 (1), 10662748 (1) (see all 5)
    mexiletine 83.1 9 17698727 (2), 9556090 (1), 18071303 (1), 18060054 (1) (see all 6)
    flecainide 82 13 11333173 (4), 10758053 (2), 11535580 (1), 18071303 (1) (see all 8)
    pilsicainide 78.6 2 17916151 (1)
    lidocaine 51.1 16 8785328 (4), 18599870 (2), 1309946 (1), 10758053 (1) (see all 10)
    potassium 49.9 23 8873679 (2), 10613047 (2), 9570196 (1), 11259355 (1) (see all 15)
    procainamide 46.7 1 10662748 (1)
    cisapride 34.1 1 16301357 (1)
    tetrodotoxin 29.5 7 1309946 (2), 9694861 (1), 1375397 (1)



    SCN5A 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,
    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 SCN5A gene (6 alternative transcripts): 
    NM_000335.4  NM_001099404.1  NM_001099405.1  NM_001160160.1  NM_001160161.1  NM_198056.2  

    Unigene Cluster for SCN5A:

    Sodium channel, voltage-gated, type V, alpha subunit
    Hs.517898  [show with all ESTs]
    Unigene Representative Sequence: NM_198056
    14 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000414099 ENST00000423572(uc021wvn.1 uc021wvo.1) ENST00000413689(uc021wvi.1 uc021wvk.1 uc021wvp.1 uc021wvs.1 uc021wvt.1)
    ENST00000333535 ENST00000455624(uc021wvw.1) ENST00000450102(uc010hhl.1)
    ENST00000449557 ENST00000464652 ENST00000491944 ENST00000476683 ENST00000327956(uc021wvx.1)
    ENST00000451551(uc021wvj.1 uc021wvl.1 uc021wvu.1) ENST00000443581(uc021wvq.1 uc021wvr.1)
    ENST00000425664(uc021wvm.1 uc021wvv.1)
    miRNA
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    Block miRNA regulation of human, mouse, rat SCN5A using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SCN5A (see all 67):
    hsa-miR-520e hsa-miR-1307 hsa-miR-3146 hsa-miR-219-5p hsa-miR-374a hsa-miR-200b hsa-miR-3148 hsa-miR-761
    SwitchGear 3'UTR luciferase reporter plasmidSCN5A 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for SCN5A
    Predesigned siRNA for gene silencing in human, mouse, rat SCN5A
    Clone
    Products:
         
    OriGene clones in human, mouse for SCN5A (see all 25)
    OriGene ORF clones in mouse, rat for SCN5A
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 6): SCN5A (NM_001099404)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SCN5A
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SCN5A
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for SCN5A
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      QuantiTect SYBR Green Assays in human, mouse, rat SCN5A
      QuantiFast Probe-based Assays in human, mouse, rat SCN5A

    Additional mRNA sequence: 

    AB158469.2 AB158470.2 AB208866.1 AF482988.1 AJ310886.1 AJ310887.1 AJ310888.1 AJ310889.1 
    AJ310890.1 AJ310891.1 AJ310892.1 AJ310893.1 AJ310894.1 AJ310895.1 AJ310896.1 AY038064.1 
    AY148488.1 BC051374.1 BC140813.1 BC144621.1 EF092292.1 EF092293.1 EF092294.1 EF092295.1 
    EF629346.1 EF629347.1 

    5 DOTS entries:

    DT.100745286  DT.75174024  DT.99955208  DT.120884034  DT.100697400 

    Selected AceView cDNA sequences (see all 27):

    AJ310891 AJ310896 AJ310893 AJ310889 AJ310886 AF482988 NM_000335 AJ310888 
    AJ310887 AJ310890 AY148488 NM_198056 AB158469 AY038064 BU845010 M77235 
    AJ310894 BC051374 AJ310895 BM917024 AJ310892 AB158470 BU846317 BE391214 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for SCN5A    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8
    SP1:                          -                                                   
    SP2:                                                  -                 -         
    SP3:                                                  -     -     -               
    SP4:                                            -     -                 -         
    SP5:                                                                              


    ECgene alternative splicing isoforms for SCN5A

    (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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    SCN5A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SCN5A Expression
    About this image


    SCN5A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Heart (Cardiovascular System)    fully expand to see all 3 entries
             Early cardiomyocytes
     
     NULL (Cardiovascular System)    fully expand to see all 2 entries
             Early cardiomyocytes
     
     Eye (Sensory Organs)    fully expand to see all 2 entries
             GABAergic Amacrine Cells Inner Nuclear Layer
             Retina
     
     Epidermis (Integumentary System)
             Stratified Epidermis
     
     Neurons
             GABAergic Amacrine Cells Inner Nuclear Layer
    SCN5A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SCN5A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.517898

    UniProtKB/Swiss-Prot: SCN5A_HUMAN, Q14524
    Tissue specificity: Found in jejunal circular smooth muscle cells (at protein level). Expressed in human atrial
    and ventricular cardiac muscle but not in adult skeletal muscle, brain, myometrium, liver, or spleen. Isoform 4
    is expressed in brain

        Custom PCR Arrays for SCN5A
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    QuantiFast Probe-based Assays in human, mouse, rat SCN5A
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SCN5A

    (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 SCN5A gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Scn5a1 , 5 sodium channel, voltage-gated, type V, alpha1, 5 89.1(n)1
    94.39(a)1
      9 (71.33 cM)5
    202711  NM_021544.41  NP_067519.21 
     1194834105 
    chicken
    (Gallus gallus)
    Aves SCN5A1 sodium channel, voltage-gated, type V, alpha subunit 72.41(n)
    78.06(a)
      395947  XM_001232817.3  XP_001232818.3 
    lizard
    (Anolis carolinensis)
    Reptilia SCN5A6
    sodium channel, voltage-gated, type V, alpha subun...
    68(a)
    1 ↔ 1
    GL343530.1(7110-146192)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia scn5a1 sodium channel, voltage-gated, type V, alpha subunit 69.23(n)
    72.32(a)
      100485924  XM_002932488.2  XP_002932534.2 
    zebrafish
    (Danio rerio)
    Actinopterygii scn12aa1 sodium channel, voltage gated, type XII, alpha a 67.12(n)
    69.39(a)
      795688  NM_001044922.1  NP_001038387.1 


    ENSEMBL Gene Tree for SCN5A (if available)
    TreeFam Gene Tree for SCN5A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SCN5A gene
    SCN9A2  CACNA1D2  SCN7A2  CACNA1I2  CACNA1F2  CACNA1G2  SCN8A2  SCN10A2  
    SCN3A2  SCN2A2  CACNA1S2  CACNA1C2  CACNA1H2  SCN11A2  SCN4A2  SCN1A2  
    Selected SIMAP similar genes for SCN5A using alignment to 17 protein entries:     SCN5A_HUMAN (see all proteins) (see all similar genes):
    SCN1A    SCN2A    SCN10A    SCN3A    SCN9A    SCN4A
    CACNA1F    SCN8A    SCN2A2    SCN11A    CACNA1A    CACNA1I
    CACNA1S    CACNA1B    CACNA1C    CACNA1D    CACNA1H    TPCN1

    SCN5A 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 SCN5A (see all 3104)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs413111171,2,,4
    C,FLong QT syndrome 3 (LQT3)4 untested138524282(+) GGGGAA/C/GGTCGG 18 L V F mis19NS NA EU 1551
    rs413154931,2,,4
    C,FAtrial fibrillation, familial, 10 (ATFB10)4 untested138524441(+) CATCAA/C/TGTAGG 18 M V L mis19NS NA EU 1495
    rs289373161,2,,4
    CLong QT syndrome 3 (LQT3)4 pathogenic138525361(-) GATCCA/GCACGC 12 H R mis1 ese30--------
    rs289373171,2,,4
    CLong QT syndrome 3 (LQT3)4 pathogenic138534373(-) GGTCAA/GTGCCC 12 N S mis1 ese30--------
    rs289373191,2,,4
    CSick sinus syndrome 1 (SSS1)4 pathogenic138536442(-) GGGCCC/TCATCA 12 P L mis1 ese30--------
    rs413111271,2,,4
    CBrugada syndrome 1 (BRGDA1)4 untested138536457(+) CGGCAA/GAGCCC 12 S F mis13Minor allele frequency- G:0.00NS NA 454
    rs455897411,2,,4
    CLong QT syndrome 3 (LQT3)4 untested138540459(-) ATGTCT/CTCGTG 12 /L /F mis12Minor allele frequency- C:0.00NA 642
    rs412613441,2,,4
    C,FLong QT syndrome 3 (LQT3)4 pathogenic138549343(+) GCAACC/TGCCAC 12 Q R mis110Minor allele frequency- T:0.01NA NS EA EU 1559
    rs127204521,2,,4
    CLong QT syndrome 3 (LQT3)4 untested138577718(-) CCCAGG/AAAGCC 12 /E /G mis1 ese31Minor allele frequency- A:0.00--638
    rs362104231,2,,4
    CLong QT syndrome 3 (LQT3)4 untested138577847(-) CAGTGA/C/G/
            
    CCAGG
    18 D A V mis112NA NS 1682

    HapMap Linkage Disequilibrium report for SCN5A (38589548 - 38691164 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10 variations for SCN5A:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2725164CNV Deletion23290073
    nsv3770CNV Insertion18451855
    esv267664CNV Insertion20981092
    nsv508912CNV Insertion20534489
    esv272685CNV Insertion20981092
    nsv819980CNV Loss19587683
    nsv876708CNV Loss21882294
    nsv517802CNV Loss19592680
    nsv876709CNV Gain21882294
    nsv876710CNV Gain21882294

    Human Gene Mutation Database (HGMD): SCN5A
    Locus Specific Mutation Databases (LSDB): SCN5A

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SCN5A
    DNA2.0 Custom Variant and Variant Library Synthesis for SCN5A

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

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    OMIM gene information: 600163   
    OMIM disorders: 603830  601144  113900  603829  608567  601154  272120  614022  
    UniProtKB/Swiss-Prot: SCN5A_HUMAN, Q14524
  • Progressive familial heart block 1A (PFHB1A) [MIM:113900]: A cardiac bundle branch disorder characterized
    by progressive alteration of cardiac conduction through the His-Purkinje system, with a pattern of a right
    bundle-branch block and/or left anterior hemiblock occurring individually or together. It leads to complete
    atrio-ventricular block causing syncope and sudden death. Note=The disease is caused by mutations affecting the
    gene represented in this entry
  • Long QT syndrome 3 (LQT3) [MIM:603830]: A heart disorder characterized by a prolonged QT interval on the
    ECG and polymorphic ventricular arrhythmias. They cause syncope and sudden death in response to exercise or
    emotional stress, and can present with a sentinel event of sudden cardiac death in infancy. Note=The disease is
    caused by mutations affecting the gene represented in this entry
  • Brugada syndrome 1 (BRGDA1) [MIM:601144]: A tachyarrhythmia characterized by right bundle branch block
    and ST segment elevation on an electrocardiogram (ECG). It can cause the ventricles to beat so fast that the
    blood is prevented from circulating efficiently in the body. When this situation occurs, the individual will
    faint and may die in a few minutes if the heart is not reset. Note=The disease is caused by mutations affecting
    the gene represented in this entry
  • Sick sinus syndrome 1 (SSS1) [MIM:608567]: The term 'sick sinus syndrome' encompasses a variety of
    conditions caused by sinus node dysfunction. The most common clinical manifestations are syncope, presyncope,
    dizziness, and fatigue. Electrocardiogram typically shows sinus bradycardia, sinus arrest, and/or sinoatrial
    block. Episodes of atrial tachycardias coexisting with sinus bradycardia ('tachycardia-bradycardia syndrome') are
    also common in this disorder. SSS occurs most often in the elderly associated with underlying heart disease or
    previous cardiac surgery, but can also occur in the fetus, infant, or child without heart disease or other
    contributing factors. SSS1 onset is in utero, infancy, or early childhood. Note=The disease is caused by
    mutations affecting the gene represented in this entry
  • Familial paroxysmal ventricular fibrillation 1 (VF1) [MIM:603829]: A cardiac arrhythmia marked by
    fibrillary contractions of the ventricular muscle due to rapid repetitive excitation of myocardial fibers without
    coordinated contraction of the ventricle and by absence of atrial activity. Note=The disease is caused by
    mutations affecting the gene represented in this entry
  • Sudden infant death syndrome (SIDS) [MIM:272120]: SIDS is the sudden death of an infant younger than 1
    year that remains unexplained after a thorough case investigation, including performance of a complete autopsy,
    examination of the death scene, and review of clinical history. Pathophysiologic mechanisms for SIDS may include
    respiratory dysfunction, cardiac dysrhythmias, cardiorespiratory instability, and inborn errors of metabolism,
    but definitive pathogenic mechanisms precipitating an infant sudden death remain elusive. Note=Disease
    susceptibility is associated with variations affecting the gene represented in this entry
  • Atrial standstill (ATST) [MIM:108770]: A rare arrhythmia characterized by the absence of electrical and
    mechanical activity in the atria. Electrocardiographically, it is characterized by bradycardia, the absence of P
    waves, and a junctional narrow complex escape rhythm. Note=The disease may be caused by mutations affecting
    distinct genetic loci, including the gene represented in this entry. A mutation in SCN5A has been detected in
    combination with a rare GJA5 genotype in a large family with atrial standstill
  • Cardiomyopathy, dilated 1E (CMD1E) [MIM:601154]: A disorder characterized by ventricular dilation and
    impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of
    premature death. Note=The disease is caused by mutations affecting the gene represented in this entry
  • Atrial fibrillation, familial, 10 (ATFB10) [MIM:614022]: A familial form of atrial fibrillation, a common
    sustained cardiac rhythm disturbance. Atrial fibrillation is characterized by disorganized atrial electrical
    activity and ineffective atrial contraction promoting blood stasis in the atria and reduces ventricular filling.
    It can result in palpitations, syncope, thromboembolic stroke, and congestive heart failure. Note=The disease is
    caused by mutations affecting the gene represented in this entry

  • Selected diseases for SCN5A (see all 68):    
    About MalaCards
    right bundle branch block    heart block, nonprogressive    atrial fibrillation, familial, 10    brugada syndrome 1
    atrioventricular block    heart block, progressive, type ia    scn5a-related brugada syndrome    ventricular fibrillation, familial, 1
    progressive familial heart block type 1a    sudden infant death syndrome    sick sinus syndrome 1, autosomal recessive    long qt syndrome
    paroxysmal ventricular fibrillation    long qt syndrome 3    scn5a-related disorders    sick sinus syndrome 1
    paroxysmal familial ventricular fibrillation 1    scn5a-associated dilated cardiomyopathy    cardiomyopathy, dilated, 1e    scn5a-related dilated cardiomyopathy

    8 diseases from the University of Copenhagen DISEASES database for SCN5A:
    Brugada syndrome     Long QT syndrome     Right bundle branch block     Sick sinus syndrome
    Sudden infant death syndrome     Congenital heart block     Dilated cardiomyopathy     Familial atrial fibrillation

    SCN5A for disorders           About GeneDecksing

    Selected Novoseek inferred disease relationships for SCN5A gene (see all 39)    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    brugada syndrome 98 265 17227473 (7), 16325048 (5), 19100032 (5), 11748104 (4) (see all 99)
    long qt syndrome 94.9 69 8521555 (2), 19083750 (2), 14654377 (2), 10200053 (1) (see all 57)
    long qt syndrome 3 91 6 16707561 (1), 18408010 (1), 19041666 (1), 17110414 (1) (see all 5)
    ventricular fibrillation, idiopathic 90.9 16 10940383 (2), 12693506 (1), 14985827 (1), 20042427 (1) (see all 15)
    death sudden cardiac 85.7 13 19377070 (2), 15890323 (1), 16132053 (1), 16943925 (1) (see all 10)
    death sudden 85.3 29 10590249 (2), 18361072 (2), 11289718 (1), 16707561 (1) (see all 25)
    arrhythmia 83.8 92 18368697 (5), 18708744 (2), 15123648 (2), 19027780 (2) (see all 57)
    romano-ward syndrome 82.6 3 18752142 (1), 10973849 (1), 10508990 (1)
    defect conduction 81.9 23 11748104 (3), 16707561 (2), 16643399 (2), 17897635 (2) (see all 14)
    right bundle branch block 80.9 3 16943925 (1), 10940383 (1), 10662748 (1)

    GeneTests: SCN5A
    GeneReviews: SCN5A
    Genetic Association Database (GAD): SCN5A
    Human Genome Epidemiology (HuGE) Navigator: SCN5A (101 documents)

    Export disorders for SCN5A 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 SCN5A gene, integrated from 10 sources (see all 691):
    (articles sorted by number of sources associating them with SCN5A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. SCN5A variants in Japanese patients with left ventricular noncompaction and arrhythmia. (PubMed id 18368697)1, 2, 4, 9 Shan L.... Towbin J.A. (Mol. Genet. Metab. 2008)
    2. Sodium channel mutation in irritable bowel syndrome: evidence for an ion channelopathy. (PubMed id 19056759)1, 2, 4, 9 Saito Y.A.... Farrugia G. (Am. J. Physiol. 2009)
    3. Type of SCN5A mutation determines clinical severity and degree of conduction slowing in loss-of-function sodium channelopathies. (PubMed id 19251209)1, 2, 4, 9 Meregalli P.G.... Wilde A.A.M. (Heart Rhythm 2009)
    4. Cardiac sodium channel (SCN5A) variants associated with atrial fibrillation. (PubMed id 18378609)1, 2, 4, 9 Darbar D.... Roden D.M. (Circulation 2008)
    5. Genetic analysis of the cardiac sodium channel gene SCN5A in Koreans with Brugada syndrome. (PubMed id 15338453)1, 2, 4, 9 Shin D.-J.... Yoon S.K. (J. Hum. Genet. 2004)
    6. Congenital sick sinus syndrome caused by recessive mutations in the cardiac sodium channel gene (SCN5A). (PubMed id 14523039)1, 2, 4, 9 Benson D.W.... George A.L. Jr. (J. Clin. Invest. 2003)
    7. Allelic variants in long-QT disease genes in patients with drug- associated torsades de pointes. (PubMed id 11997281)1, 2, 4, 9 Yang P.... Roden D.M. (Circulation 2002)
    8. Double SCN5A mutation underlying asymptomatic Brugada syndrome. (PubMed id 15851320)1, 2, 4, 9 Yokoi H.... Tsutsui H. (Heart Rhythm 2005)
    9. SCN5A mutation associated with dilated cardiomyopathy, conduction disorder, and arrhythmia. (PubMed id 15466643)1, 2, 3, 9 McNair W.P....Mestroni L. (Circulation 2004)
    10. SNP S1103Y in the cardiac sodium channel gene SCN5A is associated with cardiac arrhythmias and sudden death in a white family. (PubMed id 12471205)1, 2, 4, 9 Chen S.... Wang Q. (J. Med. Genet. 2002)

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

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

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6331 HGNC: 10593 AceView: SCN5A Ensembl:ENSG00000183873 euGenes: HUgn6331
    ECgene: SCN5A Kegg: 6331 H-InvDB: SCN5A

    (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 SCN5A Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SCN5A[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 SCN5A gene:
    Search GeneIP for patents involving SCN5A

    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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