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

SCN9A Gene

protein-coding   GIFtS: 63
GCID: GC02M167051

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

(Previous names: sodium channel, voltage-gated, type IX, 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)
About This Section

Aliases
Sodium Channel, Voltage-Gated, Type IX, Alpha Subunit1 2     FEB3B2 5
NENA2 3 5     ETHA2
PN12 3 5     GEFSP72
Sodium Channel, Voltage-Gated, Type IX, Alpha Polypeptide1 2     NE-NA2
Neuroendocrine Sodium Channel2 3     Nav1.72
Peripheral Sodium Channel 12 3     SFNP2
Sodium Channel Protein Type IX Subunit Alpha2 3     Sodium Channel Protein Type 9 Subunit Alpha2
Voltage-Gated Sodium Channel Subunit Alpha Nav1.72 3     Voltage-Gated Sodium Channel Alpha Subunit Nav1.72
hNE-Na2 3     

External Ids:    HGNC: 105971   Entrez Gene: 63352   Ensembl: ENSG000001694327   OMIM: 6034155   UniProtKB: Q158583   

Export aliases for SCN9A gene to outside databases

Previous GC identifers: GC02M165109 GC02M165596 GC02M167018 GC02M167257 GC02M166880 GC02M166763 GC02M158932


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SCN9A Gene:
This gene encodes a voltage-gated sodium channel which plays a significant role in nociception signaling.
Mutations in this gene have been associated with primary erythermalgia, channelopathy-associated insensitivity to
pain, and paroxysmal extreme pain disorder. (provided by RefSeq, Aug 2009)

GeneCards Summary for SCN9A Gene: 
SCN9A (sodium channel, voltage-gated, type IX, alpha subunit) is a protein-coding gene. Diseases associated with SCN9A include erythromelalgia, and pain disorder, and among its related super-pathways are Axon guidance and Activation of cAMP-Dependent PKA. GO annotations related to this gene include sodium ion binding and voltage-gated sodium channel activity. An important paralog of this gene is SCN5A.

UniProtKB/Swiss-Prot: SCN9A_HUMAN, Q15858
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. It is a
tetrodotoxin-sensitive Na(+) channel isoform. Plays a role in pain mechanisms, especially in the development of
inflammatory pain (By similarity)

summary for SCN9A 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 SCN9A (Nav1.7) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NT_005403.17  NC_018913.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SCN9A gene promoter:
         Oct-B1   Sox5   oct-B3   POU3F2 (N-Oct-5b)   POU3F2 (N-Oct-5a)   POU3F2   MEF-2A   POU2F1   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCN9A promoter sequence
   Search SABiosciences Chromatin IP Primers for SCN9A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SCN9A


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

SCN9A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCN9A gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M167051:  view genomic region     (about GC identifiers)

Start:
167,051,695 bp from pter      End:
167,232,503 bp from pter
Size:
180,809 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SCN9A_HUMAN, Q15858 (See protein sequence)
Recommended Name: Sodium channel protein type 9 subunit alpha  
Size: 1988 amino acids; 226372 Da
Subunit: The sodium channel consists of a large polypeptide and 2-3 smaller ones. This sequence represents a large
polypeptide. Interacts with NEDD4 and NEDD4L (By similarity)
Subcellular location: Membrane; Multi-pass membrane protein. Note=In neurite terminals (By similarity)
Secondary accessions: A1BUH5 Q6B4R9 Q6B4S0 Q6B4S1 Q70HX1 Q70HX2 Q8WTU1 Q8WWN4
Alternative splicing: 3 isoforms:  Q15858-1   Q15858-2   Q15858-3   

Explore the universe of human proteins at neXtProt for SCN9A: NX_Q15858

Explore proteomics data for SCN9A at MOPED 

Post-translational modifications:

  • UniProtKB: Ubiquitinated by NEDD4L; which may promote its endocytosis. Does not seem to be ubiquitinated by NEDD4 (By
    similarity)
  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q15858

  • SCN9A Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SCN9A Protein Expression
    REFSEQ proteins: NP_002968.1  
    ENSEMBL proteins: 
     ENSP00000386306   ENSP00000386330   ENSP00000413212   ENSP00000393141   ENSP00000364536  
     ENSP00000304748  
    Reactome Protein details: Q15858
    Human Recombinant Protein Products for SCN9A: 
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    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001518voltage-gated sodium channel complex IEA--
    GO:0016020membrane ----
    GO:0016021integral to membrane ----

    SCN9A for ontologies           About GeneDecksing



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

    IUPHAR Guide to PHARMACOLOGY protein family classification: Nav1.7 
    Voltage-gated sodium channels

    5/6 InterPro protein domains (see all 6):
     IPR027359 K_channel_four-helix_dom
     IPR001696 Na_channel_asu
     IPR010526 Na_trans_assoc
     IPR000048 IQ_motif_EF-hand-BS
     IPR005821 Ion_trans_dom

    Graphical View of Domain Structure for InterPro Entry Q15858

    ProtoNet protein and cluster: Q15858

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


    UniProtKB/Swiss-Prot: SCN9A_HUMAN, Q15858
    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. Nav1.7/SCN9A subfamily
    Similarity: Contains 1 IQ domain


    SCN9A 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,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SCN9A_HUMAN, Q15858
    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. It is a
    tetrodotoxin-sensitive Na(+) channel isoform. Plays a role in pain mechanisms, especially in the development of
    inflammatory pain (By similarity)

         Genatlas biochemistry entry for SCN9A:
    sodium channel voltage-gated,type IX,alpha polypeptide,tetradotoxin sensitive,solely expressed in neuroendocrine
    cells

         Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005216ion channel activity ----
    GO:0005248voltage-gated sodium channel activity IEA--
    GO:0005515protein binding ----
    GO:0031402sodium ion binding IEA--
         
    SCN9A for ontologies           About GeneDecksing


    Phenotypes:
         4 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Scn9a):
     behavior/neurological  integument  mortality/aging  nervous system 

    SCN9A for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Scn9atm1.1Jnw for SCN9A

       inGenious Targeting Laboratory - Custom generated mouse model solutions for SCN9A 
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    Inhib. RNA
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for SCN9A About   (see all 7)                                                                                              See pathways by source

    SuperPathContained pathways About
    1Axon guidance
    Axon guidance0.69
    L1CAM interactions0.39
    Developmental Biology0.69
    2Activation of cAMP-Dependent PKA
    Activation of cAMP-Dependent PKA0.77
    PKA Signaling0.56
    cAMP Pathway0.77
    3Neuropathic Pain-Signaling in Dorsal Horn Neurons
    Neuropathic Pain-Signaling in Dorsal Horn Neurons0.47
    Cholera Infection0.40
    Aldosterone Signaling in Epithelial Cells0.47
    4G-Beta Gamma Signaling
    GHRH Signaling0.46
    5Synaptic transmission: ion currents
    Synaptic transmission: ion currents

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    2 EMD Millipore Pathways for SCN9A
        Synaptic transmission- ion currents
    Sodium channels and transporters- inward current

    5/7 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for SCN9A (see all 7)
        Cholera Infection
    Neuropathic Pain-Signaling in Dorsal Horn Neurons
    PKA Signaling
    cAMP Pathway
    Aldosterone Signaling in Epithelial Cells

    4        Reactome Pathways for SCN9A
        L1CAM interactions
    Developmental Biology
    Interaction between L1 and Ankyrins
    Axon guidance



    SCN9A for pathways           About GeneDecksing

    Interactions:

        SABiosciences Gene Network CentralTM Interacting Genes and Proteins Network for SCN9A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 13)

    5/16 Interacting proteins for SCN9A (Q158583 ENSP000003863064) via UniProtKB, MINT, STRING, and/or I2D (see all 16)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CALM1P621583I2D: score=1 
    CALM2P621583I2D: score=1 
    CALM3P621583I2D: score=1 
    SCN10AENSP000003906004STRING: ENSP00000390600
    SCN11AENSP000003075994STRING: ENSP00000307599
    About this table

    Gene Ontology (GO): 5/8 biological process terms (GO ID links to tree view) (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006811ion transport ----
    GO:0006814sodium ion transport TAS7720699
    GO:0006954inflammatory response IEA--
    GO:0009636response to toxic substance IEA--
    GO:0009791post-embryonic development IEA--

    SCN9A for ontologies           About GeneDecksing



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

    SCN9A for compounds           About GeneDecksing

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

    Compounds for SCN9A 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 SCN9A    About this table
    CompoundSynonyms CAS #PubMed Ids
    SodiumSodium (see all 2)7440-23-5--

    5 DrugBank Compounds for SCN9A    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    ZonisamideZonisamida [Spanish] (see all 2)68291-97-4targetinhibitor20025128 14704463 19557119 18433351 20001433 15511691 19948168
    LidocaineDilocaine (see all 2)137-58-6targetinhibitor17430993 20585544 19088384
    Ranolazine(-)-Ranolazine (see all 3)142387-99-3targetinhibitor11752352 19077543
    RufinamideCGP 33101 (see all 4)106308-44-5targetmodulator23221868
    LacosamideErlosamide (see all 4)175481-36-4target----

    8 IUPHAR Ligands for SCN9A (Nav1.7)    About this table 
    LigandTypeActionAffinityPubmed IDs
    XEN907
    Pore BlockerInhibition8.5221570288
    tetrodotoxin
    Pore BlockerAntagonist7.67720699
    N-Me-aminopyrimidinone 9
    Gating inhibitorInhibition7.122209205
    pyrrolopyrimidine 48
    Pore BlockerInhibition6.9622318156
    Cd2+
    Pore BlockerAntagonist37720699
    veratridine
    ActivatorNone3--
    saxitoxin
    Channel blockerNone3--
    batrachotoxin
    ActivatorNone3--

    3 Novoseek inferred chemical compound relationships for SCN9A gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    sodium 73.2 39 9169448 (3), 17167479 (2), 14985375 (2), 18347287 (2) (see all 24)
    carrageenan 44 1 15030943 (1)
    tetrodotoxin 26.6 2 9169448 (2)

    Search CenterWatch for drugs/clinical trials and news about SCN9A

    (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,
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    About This Section

    REFSEQ mRNAs for SCN9A gene: 
    NM_002977.3  

    Unigene Cluster for SCN9A:

    Sodium channel, voltage-gated, type IX, alpha subunit
    Hs.439145  [show with all ESTs]
    Unigene Representative Sequence: NM_002977
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000409672(uc010fpl.3) ENST00000409435(uc002udr.1) ENST00000454569
    ENST00000452182 ENST00000472119 ENST00000375387(uc002uds.1 uc002udt.1)
    ENST00000303354
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    Additional mRNA sequence: 

    AJ277393.1 AJ310882.1 AJ310883.1 AJ310897.1 AK307549.1 AY682084.1 AY682085.1 AY682086.1 
    BC113079.1 BC113080.1 DQ857292.1 X82835.1 

    6 DOTS entries:

    DT.203056  DT.310741  DT.120960101  DT.100740641  DT.75152923  DT.92420091 

    24/26 AceView cDNA sequences (see all 26):

    AJ310897 BM993170 AJ310882 AJ310883 X82835 NM_002977 BX100638 CB146297 
    AA298508 AJ277393 BG253038 CK005041 AY682086 BX409894 BX409895 AI091722 
    AL517958 AY682085 AY682084 BG483641 AL517957 AA620400 BG227970 BG183871 

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

    SCN9A expression in normal human tissues (normalized intensities)      SCN9A embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    SCN9A Expression
    About this image


    SCN9A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/7 selected tissues (see all 7) fully expand
     
     Bone (Muscoskeletal System)    fully expand to see all 2 entries
             Zeugopod Growth Plate
     
     Smooth Muscle (Extraembryonic Tissues)
             Human umbilical Smooth Muscle (HUSM)   
     
     Peripheral Nervous System (Nervous System)
             dorsal root ganglia   
     
     Umbilical Cord (Extraembryonic Tissues)
             Human umbilical Smooth Muscle (HUSM)   
     
     Liver (Hepatobiliary System)
             Fetal Liver Stromal Cells   

    See SCN9A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SCN9A

    SOURCE GeneReport for Unigene cluster: Hs.439145

    UniProtKB/Swiss-Prot: SCN9A_HUMAN, Q15858
    Tissue specificity: Expressed strongly in dorsal root ganglion, with only minor levels elsewhere in the body,
    smooth muscle cells, MTC cell line and C-cell carcinoma. Isoform 1 is expressed preferentially in the central and
    peripheral nervous system. Isoform 2 is expressed preferentially in the dorsal root ganglion

        SABiosciences Expression via Pathway-Focused PCR Array including SCN9A: 
              Neuronal Ion Channels in human mouse rat

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for SCN9A gene from 4/11 species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Scn9a1 , 5 sodium channel, voltage-gated, type IX, alpha1, 5 86.5(n)1
    92.35(a)1
      2 (39.13 cM)5
    202741  NM_018852.21  NP_061340.21 
     664800805 
    chicken
    (Gallus gallus)
    Aves SCN9A1 sodium channel, voltage-gated, type IX, alpha subunit 75.37(n)
    76.55(a)
      395946  XM_422021.3  XP_422021.3 
    lizard
    (Anolis carolinensis)
    Reptilia SCN9A6
    sodium channel, voltage-gated, type IX, alpha subu...
    72(a)
    1 ↔ 1
    GL343214.1(737315-867044)
    zebrafish
    (Danio rerio)
    Actinopterygii scn1lab6
    sodium channel, voltage-gated, type I like, alpha ...
    73(a)
    1 → many
    6(10158986-10231330)


    ENSEMBL Gene Tree for SCN9A (if available)
    TreeFam Gene Tree for SCN9A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SCN9A gene
    SCN5A2  CACNA1D2  SCN7A2  CACNA1I2  CACNA1F2  CACNA1G2  SCN8A2  SCN10A2  
    SCN3A2  SCN2A2  CACNA1H2  CACNA1C2  CACNA1S2  SCN11A2  SCN4A2  SCN1A2  
    16 SIMAP similar genes for SCN9A using alignment to 7 protein entries:     SCN9A_HUMAN (see all proteins):
    SCN3A    SCN1A    SCN2A    SCN2A2    SCN8A    SCN5A
    SCN4A    SCN10A    TPCN1    SCN7A    SCN11A    CACNA1B
    CACNA1A    CACNA1C    CACNA1E    CACNA1I

    SCN9A for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for SCN9A
    PGOHUM00000240414


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

    10/4593 SNPs in SCN9A are shown (see all 4593)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0646014
    Primary erythermalgia (PERYTHM)4--see VAR_0646012 E K mis40--------
    VAR_0320214
    Paroxysmal extreme pain disorder (PEPD)4--see VAR_0320212 F V mis40--------
    VAR_0320174
    Paroxysmal extreme pain disorder (PEPD)4--see VAR_0320172 V F mis40--------
    VAR_0645964
    Familial febrile convulsions 3B (FEB3B)4--see VAR_0645962 I V mis40--------
    VAR_0320184
    Paroxysmal extreme pain disorder (PEPD)4--see VAR_0320182 V F mis40--------
    VAR_0646044
    Generalized epilepsy with febrile seizures plus 7 (GEFS+7)4--see VAR_0646042 N Y mis40--------
    VAR_0320194
    Primary erythermalgia (PERYTHM)4--see VAR_0320192 F V mis40--------
    VAR_0199484
    Primary erythermalgia (PERYTHM)4--see VAR_0199482 L H mis40--------
    VAR_0199474
    Primary erythermalgia (PERYTHM)4--see VAR_0199472 I T mis40--------
    VAR_0320234
    Paroxysmal extreme pain disorder (PEPD)4--see VAR_0320232 M K mis40--------

    HapMap Linkage Disequilibrium report for SCN9A (167051695 - 167232503 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/11 variations for SCN9A (see all 11):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2721082CNV Deletion23290073
    esv2127014CNV Deletion18987734
    esv1764654CNV Deletion17803354
    esv2721083CNV Deletion23290073
    esv2666983CNV Deletion23128226
    esv2658860CNV Deletion23128226
    nsv507046CNV Insertion20534489
    esv23265CNV Loss19812545
    nsv834448CNV Loss17160897
    nsv459937CNV Loss19166990


    Human Gene Mutation Database (HGMD): SCN9A
    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 603415   
    OMIM disorders: 133020  243000  167400  604403  
    UniProtKB/Swiss-Prot: SCN9A_HUMAN, Q15858
  • Primary erythermalgia (PERYTHM) [MIM:133020]: Autosomal dominant disease characterized by recurrent
    episodes of severe pain associated with redness and warmth in the feet or hands. Note=The disease is caused by
    mutations affecting the gene represented in this entry
  • Congenital indifference to pain autosomal recessive (CIPAR) [MIM:243000]: A disorder characterized by
    congenital inability to perceive any form of pain, in any part of the body. All other sensory modalities are
    preserved and the peripheral and central nervous systems are apparently intact. Patients perceive the sensations
    of touch, warm and cold temperature, proprioception, tickle and pressure, but not painful stimuli. There is no
    evidence of a motor or sensory neuropathy, either axonal or demyelinating. Note=The disease is caused by
    mutations affecting the gene represented in this entry
  • Paroxysmal extreme pain disorder (PEPD) [MIM:167400]: Autosomal dominant paroxysmal disorder of pain and
    autonomic dysfunction. The distinctive features are paroxysmal episodes of burning pain in the rectal, ocular,
    and mandibular areas accompanied by autonomic manifestations such as skin flushing. Note=The disease is caused by
    mutations affecting the gene represented in this entry
  • Generalized epilepsy with febrile seizures plus 7 (GEFS+7) [MIM:613863]: A rare autosomal dominant,
    familial condition with incomplete penetrance and large intrafamilial variability. Patients display febrile
    seizures persisting sometimes beyond the age of 6 years and/or a variety of afebrile seizure types. This disease
    combines febrile seizures, generalized seizures often precipitated by fever at age 6 years or more, and partial
    seizures, with a variable degree of severity. Note=The disease is caused by mutations affecting the gene
    represented in this entry
  • Familial febrile convulsions 3B (FEB3B) [MIM:613863]: Seizures associated with febrile episodes in
    childhood without any evidence of intracranial infection or defined pathologic or traumatic cause. It is a common
    condition, affecting 2-5% of children aged 3 months to 5 years. The majority are simple febrile seizures
    (generally defined as generalized onset, single seizures with a duration of less than 30 minutes). Complex
    febrile seizures are characterized by focal onset, duration greater than 30 minutes, and/or more than one seizure
    in a 24 hour period. The likelihood of developing epilepsy following simple febrile seizures is low. Complex
    febrile seizures are associated with a moderately increased incidence of epilepsy. Note=The disease is caused by
    mutations affecting the gene represented in this entry

  • 20/34 diseases for SCN9A (see all 34):    About MalaCards
    erythromelalgia    pain disorder    paroxysmal extreme pain disorder    small fiber neuropathy
    scn9a-related dravet syndrome    scn9a-related inherited erythromelalgia    congenital indifference to pain, autosomal recessive    scn9a-related generalized epilepsy with febrile seizures plus
    febrile convulsions, familial, 3b    familial febrile seizures 3b    scn1a-related seizure disorders    burning mouth syndrome
    trigeminal neuralgia    dravet syndrome    febrile seizures    generalized epilepsy with febrile seizures plus
    seizure disorder    borderline personality disorder    hereditary sensory neuropathy    complex regional pain syndrome

    3 diseases from the University of Copenhagen DISEASES database for SCN9A:
    Erythromelalgia     Pain disorder     Neuropathy

    SCN9A for disorders           About GeneDecksing

    2 Novoseek inferred disease relationships for SCN9A gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    erythromelalgia 95 20 14985375 (3), 18347287 (3), 20146699 (2), 15314237 (1) (see all 12)
    prostate cancer 18.2 2 16088330 (1), 18596065 (1)

    GeneTests: SCN9A
    GeneReviews: SCN9A
    Genetic Association Database (GAD): SCN9A
    Human Genome Epidemiology (HuGE) Navigator: SCN9A (6 documents)

    Export disorders for SCN9A 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)
    About This Section

    PubMed articles for SCN9A gene, integrated from 9 sources (see all 130):
    (articles sorted by number of sources associating them with SCN9A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A role of SCN9A in human epilepsies, as a cause of fe brile seizures and as a potential modifier of Dravet syndrome. (PubMed id 19763161)1, 2, 4, 9 Singh N.A....Leppert M.F. (2009)
    2. Structure and functional expression of a new member of the tetrodotoxin-sensitive voltage-activated sodium channel family from human neuroendocrine cells. (PubMed id 7720699)1, 2, 3, 9 Klugbauer N.... Hofmann F. (1995)
    3. Association analysis of SCN9A gene variants with borderline personality disorder. (PubMed id 18439623)1, 4, 9 Tadic A....Dahmen N. (2008)
    4. An SCN9A channelopathy causes congenital inability to experience pain. (PubMed id 17167479)1, 2, 9 Cox J.J.... Woods C.G. (2006)
    5. Mutations in SCN9A, encoding a sodium channel alpha subunit, in patients with primary erythermalgia. (PubMed id 14985375)1, 2, 9 Yang Y.... Shen Y. (2004)
    6. A novel tetrodotoxin-sensitive, voltage-gated sodium channel expressed in rat and human dorsal root ganglia. (PubMed id 9169448)1, 2, 9 Sangameswaran L.... Hunter J.C. (1997)
    7. Pain perception is altered by a nucleotide polymorphi sm in SCN9A. (PubMed id 20212137)1, 4, 9 Reimann F....Woods C.G. (2010)
    8. Electrophysiological properties of mutant Nav1.7 sodium channels in a painful inherited neuropathy. (PubMed id 15385606)1, 2, 9 Cummins T.R.... Waxman S.G. (2004)
    9. Autosomal dominant erythermalgia associated with a novel mutation in the voltage-gated sodium channel alpha subunit Nav1.7. (PubMed id 16216943)1, 2, 9 Michiels J.J.... Drenth J.P.H. (2005)
    10. Congenital insensitivity to pain: novel SCN9A missens e and in-frame deletion mutations. (PubMed id 20635406)1, 2 Cox J.J....Parvari R. (2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 6335 HGNC: 10597 AceView: SCN9A Ensembl:ENSG00000169432 euGenes: HUgn6335
    ECgene: SCN9A H-InvDB: SCN9A

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SCN9A Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SCN9A
    Wikipedia http://en.wikipedia.org/wiki/SCN9A
    Protein Spotlighthttp://web.expasy.org/spotlight/back_issues/sptlt102.shtml

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SCN9A gene:
    Search GeneIP for patents involving SCN9A

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



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    About This Section

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