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SCN9A sodium voltage-gated channel alpha subunit 9 [ Homo sapiens (human) ]

Gene ID: 6335, updated on 23-May-2018
Official Symbol
SCN9Aprovided by HGNC
Official Full Name
sodium voltage-gated channel alpha subunit 9provided by HGNC
Primary source
HGNC:HGNC:10597
See related
Ensembl:ENSG00000169432 MIM:603415; Vega:OTTHUMG00000154044
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PN1; ETHA; NENA; SFNP; FEB3B; NE-NA; GEFSP7; HSAN2D; Nav1.7
Summary
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]
Expression
Broad expression in testis (RPKM 3.8), placenta (RPKM 2.0) and 20 other tissues See more
Orthologs
See SCN9A in Genome Data Viewer
Location:
2q24.3
Exon count:
30
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (166195185..166375987, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (167051695..167232497, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724058 Neighboring gene sodium voltage-gated channel alpha subunit 1 Neighboring gene uncharacterized LOC101929680 Neighboring gene RNA, 7SK small nuclear pseudogene 152 Neighboring gene sodium voltage-gated channel alpha subunit 7 Neighboring gene uncharacterized LOC107985958

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • Axon guidance, organism-specific biosystem (from REACTOME)
    Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
  • Cardiac conduction, organism-specific biosystem (from REACTOME)
    Cardiac conduction, organism-specific biosystemThe normal sequence of contraction of atria and ventricles of the heart require activation of groups of cardiac cells. The mechanism must elicit rapid changes in heart rate and respond to changes in ...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • Interaction between L1 and Ankyrins, organism-specific biosystem (from REACTOME)
    Interaction between L1 and Ankyrins, organism-specific biosystemAnkyrins are a family of adaptor proteins that couple membrane proteins such as voltage gated Na+ channels and the Na+/K+ anion exchanger to the spectrin actin cytoskeleton. Ankyrins are encoded by t...
  • L1CAM interactions, organism-specific biosystem (from REACTOME)
    L1CAM interactions, organism-specific biosystemThe L1 family of cell adhesion molecules (L1CAMs) are a subfamily of the immunoglobulin superfamily of transmembrane receptors, comprised of four structurally related proteins: L1, Close Homolog of L...
  • Muscle contraction, organism-specific biosystem (from REACTOME)
    Muscle contraction, organism-specific biosystemIn this module, the processes by which calcium binding triggers actin - myosin interactions and force generation in smooth and striated muscle tissues are annotated.
  • Phase 0 - rapid depolarisation, organism-specific biosystem (from REACTOME)
    Phase 0 - rapid depolarisation, organism-specific biosystemPhase 0 is the rapid depolarisation phase in which electrical stimulation of a cell initiates events involving the influx and efflux of ions resulting in the production of a cell's action potential. ...
  • Taste transduction, organism-specific biosystem (from KEGG)
    Taste transduction, organism-specific biosystemFive basic tastes are recognized by humans and most other animals - bitter, sweet, sour, salty and umami. In vertebrates, taste stimuli are detected by taste receptor cells (TRCs). At least three dis...
  • Taste transduction, conserved biosystem (from KEGG)
    Taste transduction, conserved biosystemFive basic tastes are recognized by humans and most other animals - bitter, sweet, sour, salty and umami. In vertebrates, taste stimuli are detected by taste receptor cells (TRCs). At least three dis...

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cation channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium ion binding IEA
Inferred from Electronic Annotation
more info
 
voltage-gated ion channel activity IEA
Inferred from Electronic Annotation
more info
 
voltage-gated sodium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
voltage-gated sodium channel activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
behavioral response to pain IEA
Inferred from Electronic Annotation
more info
 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
membrane depolarization during action potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuronal action potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
post-embryonic development IEA
Inferred from Electronic Annotation
more info
 
regulation of ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
response to toxic substance IEA
Inferred from Electronic Annotation
more info
 
sensory perception of pain IMP
Inferred from Mutant Phenotype
more info
PubMed 
sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
sodium ion transport TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cell projection IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
voltage-gated sodium channel complex IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
sodium channel protein type 9 subunit alpha
Names
hNE-Na
neuroendocrine sodium channel
peripheral sodium channel 1
sodium channel protein type IX subunit alpha
sodium channel, voltage-gated, type IX, alpha polypeptide
sodium channel, voltage-gated, type IX, alpha subunit
voltage-gated sodium channel alpha subunit Nav1.7
voltage-gated sodium channel subunit alpha Nav1.7

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012798.1 RefSeqGene

    Range
    5001..185803
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_369

mRNA and Protein(s)

  1. NM_002977.3NP_002968.1  sodium channel protein type 9 subunit alpha

    See identical proteins and their annotated locations for NP_002968.1

    Status: REVIEWED

    Source sequence(s)
    AC107082, AC108146, AK307549, AL517958, BU742924, DQ857292, X82835
    Consensus CDS
    CCDS46441.1
    UniProtKB/Swiss-Prot
    Q15858
    Related
    ENSP00000386306.1, OTTHUMP00000204933, ENST00000409672.5, OTTHUMT00000333636
    Conserved Domains (5) summary
    cd13433
    Location:14471499
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11981455
    Ion_trans; Ion transport protein
    pfam06512
    Location:9711176
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488607
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17711826
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    166195185..166375987 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005246757.2XP_005246814.1  sodium channel protein type 9 subunit alpha isoform X1

    See identical proteins and their annotated locations for XP_005246814.1

    UniProtKB/Swiss-Prot
    Q15858
    Related
    ENSP00000495601.1, ENST00000642356.1
    Conserved Domains (5) summary
    cd13433
    Location:14581510
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12091466
    Ion_trans; Ion transport protein
    pfam06512
    Location:9821187
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488607
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17821837
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  2. XM_011511616.3XP_011509918.1  sodium channel protein type 9 subunit alpha isoform X1

    See identical proteins and their annotated locations for XP_011509918.1

    UniProtKB/Swiss-Prot
    Q15858
    Related
    OTTHUMP00000204936
    Conserved Domains (5) summary
    cd13433
    Location:14581510
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12091466
    Ion_trans; Ion transport protein
    pfam06512
    Location:9821187
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488607
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17821837
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  3. XM_011511618.2XP_011509920.1  sodium channel protein type 9 subunit alpha isoform X3

    UniProtKB/Swiss-Prot
    Q15858
    Related
    ENSP00000495983.1, ENST00000645907.1
    Conserved Domains (5) summary
    cd13433
    Location:14471499
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11981455
    Ion_trans; Ion transport protein
    pfam06512
    Location:9711176
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488607
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17711826
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  4. XM_011511617.2XP_011509919.1  sodium channel protein type 9 subunit alpha isoform X2

    UniProtKB/Swiss-Prot
    Q15858
    Related
    ENSP00000386330.2, ENST00000409435.6
    Conserved Domains (5) summary
    cd13433
    Location:14581510
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12091466
    Ion_trans; Ion transport protein
    pfam06512
    Location:9821187
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488607
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17821837
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  5. XM_017004668.1XP_016860157.1  sodium channel protein type 9 subunit alpha isoform X4

  6. XM_017004669.1XP_016860158.1  sodium channel protein type 9 subunit alpha isoform X5

  7. XM_011511619.2XP_011509921.1  sodium channel protein type 9 subunit alpha isoform X6

    Conserved Domains (4) summary
    cd13433
    Location:14581504
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12091466
    Ion_trans; Ion transport protein
    pfam06512
    Location:9821187
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488607
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

RNA

  1. XR_001738886.1 RNA Sequence

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