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GIFtS

SCN9A Gene

protein-coding   GIFtS: 61
GCID: GC02M167051

sodium channel, voltage-gated, type IX, alpha subunit

(Previous names: sodium channel, voltage-gated, type IX, alpha polypeptide...)
 Explore 32 diseases affiliated with
SCN9A via
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SCN9A    

Aliases
for SCN9A gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Sodium Channel, Voltage-Gated, Type IX, Alpha Subunit1 2     Sodium Channel Protein Type IX Subunit Alpha2 3
NENA1 2 3 5     Voltage-Gated Sodium Channel Subunit Alpha Nav1.72 3
PN11 2 3 5     HNE-Na1
ETHA1 2     FEB3B2 5
NE-NA1 2     GEFSP72
Nav1.71 2     SFNP2
Sodium Channel, Voltage-Gated, Type IX, Alpha Polypeptide1 2     Sodium Channel Protein Type 9 Subunit Alpha2
Neuroendocrine Sodium Channel2 3     Voltage-Gated Sodium Channel Alpha Subunit Nav1.72
Peripheral Sodium Channel 12 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


Summaries
for SCN9A gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for SCN9A:
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)

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:
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)


Genomic Views
for SCN9A 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NC_018913.1  NT_005403.17  
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 plasmid: SCN9A 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

Proteins
for SCN9A gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
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

Post-translational modifications:

  • Ubiquitinated by NEDD4L; which may promote its endocytosis. Does not seem to be ubiquitinated by NEDD4 (By similarity)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q15858

    • SCN9A Protein expression data from MOPED and PaxDb:    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 Proteins at Uscn

    Gene Ontology (GO): 2 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:0016021integral to membrane ----

    SCN9A for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for SCN9A gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    SCN9A for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR001696 Na_channel_asu
     IPR010526 Na_trans_assoc
     IPR000048 IQ_motif_EF-hand-BS
     IPR005821 Ion_trans_dom
     IPR024583 DUF3451

    Graphical View of Domain Structure for InterPro Entry Q15858

    ProtoNet protein and cluster: Q15858

    2 Blocks protein families:
    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


    Function
    for SCN9A gene

    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, 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, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 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): 3 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: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:
         Mouse knock-out Scn9atm1.1Jnw for SCN9A
       inGenious Targeting Laboratory - Customizable classic, inducible, and humanized mouse model solutions for SCN9A 

    miRNA
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    hsa-miR-411* hsa-miR-4317 hsa-miR-100* hsa-miR-3607-3p hsa-miR-379* hsa-miR-376b hsa-miR-429 hsa-miR-513a-5p
    SwitchGear 3'UTR luciferase reporter plasmid: SCN9A 3' UTR sequence
    Inhib. RNA
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    Gene Editing
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    Clone
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    In Situ Assay
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    Pathways & Interactions
    for SCN9A gene

    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section

    Unified GeneCards pathways - 5/7 super-pathways (see all 7) About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1Axon guidance
    		Axon guidance1.00
    		L1CAM interactions0.39
    		Developmental Biology0.69
    2Activation of cAMP-Dependent PKA
    		Activation of cAMP-Dependent PKA1.00
    		PKA Signaling0.56
    		cAMP Pathway0.77
    3Neuropathic Pain-Signaling in Dorsal Horn Neurons
    		Neuropathic Pain-Signaling in Dorsal Horn Neurons1.00
    		Cholera Infection0.40
    		Aldosterone Signaling in Epithelial Cells0.47
    4Interaction between L1 and Ankyrins
    		Interaction between L1 and Ankyrins1.00
    5Synaptic transmission: ion currents
    		Synaptic transmission: ion currents1.00

    Pathway sources
    See GeneCards unified pathways
    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): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006814sodium ion transport TAS7720699
    GO:0006954inflammatory response IEA--
    GO:0009636response to toxin IEA--
    GO:0009791post-embryonic development IEA--
    GO:0019228regulation of action potential in neuron IEA--

    SCN9A for ontologies           About GeneDecksing



    Drugs & Compounds
    for SCN9A gene

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 #
    TC-N 1752Selective NaV1.7 blocker[1211866-85-1]

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

    3 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

    3 Novoseek 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 

    Transcripts
    for SCN9A gene

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, Sirion Biotech, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    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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    hsa-miR-411* hsa-miR-4317 hsa-miR-100* hsa-miR-3607-3p hsa-miR-379* hsa-miR-376b hsa-miR-429 hsa-miR-513a-5p
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    Inhib. RNA
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    Clone
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    Additional cDNA 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 AA298508 BM993170 AJ310883 CB146297 NM_002977 AJ310882 BG253038 
    AJ277393 BX100638 X82835 BX409894 AY682086 CK005041 AY682085 AI091722 
    AY682084 AL517958 BX409895 AL517957 BG483641 AA620400 BG227970 BG183871 

    GeneLoc Exon Structure


    Expression
    for SCN9A gene

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SCN9A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --
    SCN9A Expression
    About this image

    SCN9A expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    4 LifeMap In Vivo Development Anatomical Compartments/Cells 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BoneMaxillary ProcessBone
    BoneZeugopod Epiphyseal EndBone
    BoneZeugopod Growth PlateBone
    Head MesenchymeFrontonasal ProcessHead Mesenchyme
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 2 LifeMap Cells 
    NameCategory
    PureStem™ progenitor T42 (Embryonic Progenitor Cell)
    PureStem™ progenitor Z1 (Embryonic Progenitor Cell)

    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

    Primer
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    In Situ
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    Orthologs
    for SCN9A gene

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

    Orthologs for SCN9A gene from 4/17 species (see all 17)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    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
    		 --
    		 72(a)
    		 1 ↔ 1
    		 GL343214.1(789958-867035)
    zebrafish
    (Danio rerio)    		 Actinopterygii scn1lab6
    scn1a6
    		 sodium channel, voltage-gated, type I, alpha
    		 73(a)
    65(a)
    		 many ↔ many
    many ↔ many
    		 6(10158986-10231330)
    9(50902616-50972365)
    fruit fly
    (Drosophila melanogaster)    		 Insecta NaCP60E3 sodium ion transport voltage-gated sodium
    channel    		 64(a)
    (best of 3)    		   60E5   --


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

    Paralogs
    for SCN9A gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SCN9A gene
    CACNA1A2  SCN5A2  CACNA1D2  CACNA1I2  SCN7A2  CACNA1F2  SCN8A2  CACNA1G2  
    SCN10A2  SCN3A2  CACNA1E2  SCN2A2  CACNA1S2  CACNA1C2  CACNA1H2  SCN11A2  
    SCN4A2  SCN1A2  CACNA1B2  
    17 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    CACNA1D    CACNA1E    CACNA1C    CACNA1I

    SCN9A for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for SCN9A
    PGOHUM00000240414


    Genomic Variants
    for SCN9A gene

    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/3932 NCBI SNPs in SCN9A are shown (see all 3932)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 2 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs803564651,2
    		Cnon-pathogenic167160835(-) GGTATG/TTAACA 2 V L mis10--------
    rs803564781,2
    		Cpathogenic167083097(-) ATAATG/TTCAAC 2 V F mis10--------
    rs1219089101,2
    		Cpathogenic167129241(-) CCTTAC/TGTGAA 2 R C mis10--------
    rs803564771,2
    		Cpathogenic167133747(-) TGTTGC/G/TCCATC 3 P A S mis10--------
    rs803564751,2
    		Cpathogenic167133761(-) TAACCA/TCACCT 2 H L mis10--------
    rs803564761,2
    		Cpathogenic167133762(-) GTAACC/TTCACC 2 L F mis10--------
    rs803564741,2
    		Cpathogenic167133791(-) GATCAC/TTGGTA 2 T I mis10--------
    rs1219089191,2
    		Cpathogenic167138296(-) ACACAA/GGAAAA 2 K R mis10--------
    rs1219089181,2
    		Cpathogenic167141016(-) TCCCCA/TATGGA 2 N Y mis10--------
    rs412686731,2
    		C,Fpathogenic167141109(+) CATTGG/TTGGGG 2 T P mis12Minor allele frequency- T:0.03NA EU 595

    HapMap Linkage Disequilibrium report for SCN9A (167051695 - 167232503 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 6 variations for SCN9A
         4 CNVs: 90117 90115 63230 90116
         2 Indels: 45897 26485
    Human Gene Mutation Database (HGMD): SCN9A

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing SCN9A
    DNA2.0 Custom Variant and Variant Library Synthesis for SCN9A

    Disorders / Diseases
    for SCN9A gene

    (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
    SCN9A for disorders           About GeneDecksing

    OMIM gene information: 603415   
    OMIM disorders: 133020  243000  167400  604403  
    UniProtKB/Swiss-Prot: SCN9A_HUMAN, Q15858
  • Defects in SCN9A are the cause of primary erythermalgia (PERYTHM) [MIM:133020]. It is an autosomal dominant
    • disease characterized by recurrent episodes of severe pain associated with redness and warmth in the feet or hands
  • Defects in SCN9A are the cause of congenital indifference to pain autosomal recessive (CIPAR) [MIM:243000];
    • also known as channelopathy-associated insensitivity to pain. 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
  • Defects in SCN9A are a cause of paroxysmal extreme pain disorder (PEPD) [MIM:167400]; previously known as
    • familial rectal pain (FRP). PEPD is an 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
  • Defects in SCN9A are a cause of generalized epilepsy with febrile seizures plus type 7 (GEFS+7) [MIM:613863].
    • GEFS+7 is 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
  • Defects in SCN9A are the cause of familial febrile convulsions type 3B (FEB3B) [MIM:613863]. FEB3B consists of
    • 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

    20/32 diseases for SCN9A (see all 32):    About MalaCards
    paroxysmal extreme pain disorder    erythermalgia    insensitivity to pain    pain disorder
    febrile convulsions, familial, 3b    congenital indifference to pain, autosomal recessive    generalized epilepsy with febrile seizures plus    febrile convulsions
    complex regional pain syndrome    trigeminal neuralgia    burning mouth syndrome    borderline personality disorder
    erythromelalgia    febrile seizures    hereditary sensory neuropathy    generalized epilepsy
    convulsions    personality disorder    autonomic dysfunction    dravet syndrome

    4 diseases from the University of Copenhagen DISEASES database for SCN9A:
    Erythromelalgia     Pain disorder     Dravet Syndrome     Neuropathy

    2 Novoseek 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
    SCN9A-Related Inherited Erythromelalgia

    Human Genome Epidemiology (HuGE) Navigator: SCN9A (6 documents)

    Export disorders for SCN9A gene to outside databases

    Publications
    for SCN9A gene

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SCN9A gene, integrated from 9 sources (see all 118):
    (articles sorted by number of sources associating them with SCN9A)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. 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)
    2. 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, 9 Singh N.A....Leppert M.F. (2009)
    3. An SCN9A channelopathy causes congenital inability to experience pain. (PubMed id 17167479)1, 2, 9 Cox J.J.... Woods C.G. (2006)
    4. 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)
    5. 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)
    6. 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)
    7. 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)
    8. Congenital insensitivity to pain: novel SCN9A missens e and in-frame deletion mutations. (PubMed id 20635406)1, 2 Cox J.J....Parvari R. (2010)
    9. A Nav1.7 channel mutation associated with hereditary erythromelalgia contributes to neuronal hyperexcitability and displays reduced lidocaine sensitivity. (PubMed id 17430993)1, 7 Sheets P.L....Cummins T.R. (2007)
    10. Sporadic onset of erythermalgia: a gain-of-function mutation in Nav1.7. (PubMed id 16392115)1, 2 Han C....Waxman S.G. (2006)

    External Searches for SCN9A gene

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

    Genome Databases showing SCN9A gene

    (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

    Other Databases showing SCN9A gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing SCN9A gene

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for 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

    Intellectual Property
    for SCN9A gene

    (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:
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