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

Gene ID: 6335, updated on 11-Apr-2024

Summary

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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; AllianceGenome:HGNC:10597
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
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Genomic context

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Location:
2q24.3
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (166195185..166375987, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (166652733..166833467, complement)
105.20220307 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 small nucleolar RNA U13 Neighboring gene sodium voltage-gated channel alpha subunit 7 Neighboring gene uncharacterized LOC124906087 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:167367421-167367674

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Novel SCN9A variant associated with congenital insensitivity to pain. Yammine T, et al. Mol Biol Rep, 2023 Jul. PMID 37231219
  2. SCN9A rs6746030 Polymorphism and Pain Perception in Combat Athletes and Non-Athletes. Leźnicka K, et al. Genes (Basel), 2023 Mar 16. PMID 36981004, Free PMC Article
  3. Na(V)1.7 channels are expressed in the lower airways of the human respiratory tract. Hernández-Plata E, et al. Respir Physiol Neurobiol, 2023 May. PMID 36792043
  4. Integrative miRNA-mRNA profiling of human epidermis: unique signature of SCN9A painful neuropathy. Andelic M, et al. Brain, 2023 Jul 3. PMID 36730021, Free PMC Article
  5. Nav1.7 P610T mutation in two siblings with persistent ocular pain after corneal axon transection: impaired slow inactivation and hyperexcitable trigeminal neurons. Ghovanloo MR, et al. J Neurophysiol, 2023 Mar 1. PMID 36722722, Free PMC Article

See all (187) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Identification and In-Silico study of non-synonymous functional SNPs in the human SCN9A gene.
    Title: Identification and In-Silico study of non-synonymous functional SNPs in the human SCN9A gene.
  2. COMT and SCN9A gene variants do not contribute to chronic low back pain in Mexican-Mestizo patients.
    Title: COMT and SCN9A gene variants do not contribute to chronic low back pain in Mexican-Mestizo patients.
  3. A novel mutation in the SCN9A gene associated with congenital insensitivity to pain, anhidrosis, and mild cognitive impairment.
    Title: A novel mutation in the SCN9A gene associated with congenital insensitivity to pain, anhidrosis, and mild cognitive impairment.
  4. Erythromelalgia caused by the missense mutation p.Arg220Pro in an alternatively spliced exon of SCN9A (NaV1.7).
    Title: Erythromelalgia caused by the missense mutation p.Arg220Pro in an alternatively spliced exon of SCN9A (NaV1.7).
  5. Genetic, electrophysiological, and pathological studies on patients with SCN9A-related pain disorders.
    Title: Genetic, electrophysiological, and pathological studies on patients with SCN9A-related pain disorders.
  6. Structural basis for severe pain caused by mutations in the voltage sensors of sodium channel NaV1.7.
    Title: Structural basis for severe pain caused by mutations in the voltage sensors of sodium channel NaV1.7.
  7. Integrative miRNA-mRNA profiling of human epidermis: unique signature of SCN9A painful neuropathy.
    Title: Integrative miRNA-mRNA profiling of human epidermis: unique signature of SCN9A painful neuropathy.
  8. Novel SCN9A variant associated with congenital insensitivity to pain.
    Title: Novel SCN9A variant associated with congenital insensitivity to pain.
  9. SCN9A rs6746030 Polymorphism and Pain Perception in Combat Athletes and Non-Athletes.
    Title: SCN9A rs6746030 Polymorphism and Pain Perception in Combat Athletes and Non-Athletes.
  10. NaV1.7 channels are expressed in the lower airways of the human respiratory tract.
    Title: Na(V)1.7 channels are expressed in the lower airways of the human respiratory tract.
Submit: New GeneRIF Correction See all GeneRIFs (176)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association scan of dental caries in the permanent dentition.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables voltage-gated sodium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables voltage-gated sodium channel activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in behavioral response to pain IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac muscle cell action potential involved in contraction IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in circadian rhythm IEA
Inferred from Electronic Annotation
more info
  
involved_in detection of mechanical stimulus involved in sensory perception IEA
Inferred from Electronic Annotation
more info
  
involved_in detection of temperature stimulus involved in sensory perception of pain IEA
Inferred from Electronic Annotation
more info
  
involved_in inflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in post-embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in response to toxic substance IEA
Inferred from Electronic Annotation
more info
  
involved_in sensory perception of pain IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sodium ion transmembrane transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in sodium ion transport TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in axon ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of voltage-gated sodium channel complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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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)

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

    Status: REVIEWED

    Source sequence(s)
    AC074101, AC107082, AC108146
    Consensus CDS
    CCDS92892.1
    UniProtKB/Swiss-Prot
    A1BUH5, Q15858, Q6B4R9, Q6B4S0, Q6B4S1, Q70HX1, Q70HX2, Q8WTU1, Q8WWN4
    Related
    ENSP00000495601.1, ENST00000642356.2
    Conserved Domains (5) summary
    cd13433
    Location:1458 → 1510
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1191 → 1466
    Ion_trans; Ion transport protein
    pfam06512
    Location:982 → 1187
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488 → 681
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:1774 → 1837
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

  2. NM_002977.4 → NP_002968.2  sodium channel protein type 9 subunit alpha isoform 1

    Status: REVIEWED

    Source sequence(s)
    AC074101, AC107082, AC108146
    Consensus CDS
    CCDS46441.1
    Related
    ENSP00000386306.1, ENST00000409672.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_011511618.3 → XP_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:1447 → 1499
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1198 → 1455
    Ion_trans; Ion transport protein
    pfam06512
    Location:971 → 1176
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488 → 607
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:1771 → 1826
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

  2. XM_011511617.3 → XP_011509919.1  sodium channel protein type 9 subunit alpha isoform X1

    UniProtKB/Swiss-Prot
    Q15858
    Conserved Domains (5) summary
    cd13433
    Location:1458 → 1510
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1209 → 1466
    Ion_trans; Ion transport protein
    pfam06512
    Location:982 → 1187
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488 → 607
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:1782 → 1837
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

  3. XM_011511619.3 → XP_011509921.1  sodium channel protein type 9 subunit alpha isoform X5

    Conserved Domains (4) summary
    cd13433
    Location:1458 → 1504
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1209 → 1466
    Ion_trans; Ion transport protein
    pfam06512
    Location:982 → 1187
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488 → 607
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

  4. XM_011511616.4 → XP_011509918.1  sodium channel protein type 9 subunit alpha isoform X2

    See identical proteins and their annotated locations for XP_011509918.1

    UniProtKB/Swiss-Prot
    A1BUH5, Q15858, Q6B4R9, Q6B4S0, Q6B4S1, Q70HX1, Q70HX2, Q8WTU1, Q8WWN4
    Conserved Domains (5) summary
    cd13433
    Location:1458 → 1510
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1191 → 1466
    Ion_trans; Ion transport protein
    pfam06512
    Location:982 → 1187
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:488 → 681
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:1774 → 1837
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

  5. XM_017004669.2 → XP_016860158.1  sodium channel protein type 9 subunit alpha isoform X4

RNA

  1. XR_001738886.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    166652733..166833467 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343322.1 → XP_054199297.1  sodium channel protein type 9 subunit alpha isoform X3

  2. XM_054343320.1 → XP_054199295.1  sodium channel protein type 9 subunit alpha isoform X1

  3. XM_054343324.1 → XP_054199299.1  sodium channel protein type 9 subunit alpha isoform X5

  4. XM_054343321.1 → XP_054199296.1  sodium channel protein type 9 subunit alpha isoform X2

  5. XM_054343323.1 → XP_054199298.1  sodium channel protein type 9 subunit alpha isoform X4

  6. XM_054343325.1 → XP_054199300.1  sodium channel protein type 9 subunit alpha isoform X6

  7. XM_054343326.1 → XP_054199301.1  sodium channel protein type 9 subunit alpha isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15858.3 GenPept UniProtKB/Swiss-Prot:Q15858

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