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

Gene ID: 6335, updated on 13-Mar-2020

Summary

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
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

Genomic context

See SCN9A in Genome Data Viewer
Location:
2q24.3
Exon count:
30
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 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 SCN1A and SCN9A antisense RNA 1 Neighboring gene RN7SK pseudogene 152 Neighboring gene sodium voltage-gated channel alpha subunit 7 Neighboring gene uncharacterized LOC107985958

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon ISS
Inferred from Sequence or Structural Similarity
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001365536.1NP_001352465.1  sodium channel protein type 9 subunit alpha isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC074101, AC107082, AC108146
    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:11911466
    Ion_trans; Ion transport protein
    pfam06512
    Location:9821187
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488681
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17741837
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  2. NM_002977.3NP_002968.1  sodium channel protein type 9 subunit alpha isoform 1

    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, ENST00000409672.5
    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 Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. 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
    Conserved Domains (5) summary
    cd13433
    Location:14581510
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11911466
    Ion_trans; Ion transport protein
    pfam06512
    Location:9821187
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488681
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17741837
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  2. 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
  3. 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
  4. XM_017004668.1XP_016860157.1  sodium channel protein type 9 subunit alpha isoform X4

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

  6. 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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