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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
    mouse all
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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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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