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FLASH GENE
Symbol SCN9A contributors: mct/npt - updated : 27-10-2017
HGNC name sodium channel, voltage-gated, type IX, alpha subunit
HGNC id 10597
Corresponding disease
CIEP congenital inability to experience pain/anosmia
ETHA erythermalgia, primary
GEFSP2 generalized epilepsy with febrile seizures plus, 2
PEXPD paroxysmal extreme pain disorder
Location 2q24.3      Physical location : 167.051.703 - 167.232.497
Synonym name
  • voltage-gated sodium channel alpha subunit Nav1.7
  • sodium channel, voltage-gated, type IX, alpha polypeptide
  • neuroendocrine sodium channel
  • peripheral sodium channel 1
  • Synonym symbol(s) PN1, NE-NA, NENA, Nav1.7
    DNA
    TYPE functioning gene
    STRUCTURE 116.62 kb     30 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    regulatory sequence Promoter
    text structure
  • a putative SCN9A 5' prime non-coding exon approximately 64,000 nucleotides from the translation start site (Diss 2008)
  • ; possesses numerous core elements of a TATA-less promoter within a well-defined CpG island (Diss 2008)
    MAPPING cloned Y linked N status provisional
    Physical map
    FIGN 2q24.2 fidgetin GRB14 2q22-q24 growth factor receptor-bound protein 14 KIAA0977 2q24.3 growth factor receptor-bound protein 14 FLJ39822 2q24.3 hypothetical protein FLJ39822 SCN3A 2q24.3 sodium channel, voltage-gated, type III, alpha SCN2A2 2q23-q24.3 sodium channel, voltage-gated, type II, alpha 2 TAIP-2 2q24.3 TGF-beta induced apotosis protein 2 GALNT3 2q24-q31 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3) FLJ11457 2q31.1 hypothetical protein FLJ11457 SCN1A 2q24 sodium channel, voltage-gated, type I, alpha SCN9A 2q24 sodium channel, voltage-gated, type IX, alpha SCN7A 2q21-q23 sodium channel, voltage-gated, type VII, alpha CMYA3 2q31.1 cardiomyopathy associated 3 LOC90643 2q31.1 similar to Meningioma-expressed antigen 6/11 (MEA6) (MEA11) B3GALT1 2q24.3 UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1 STK39 2q24.3 serine threonine kinase 39 (STE20/SPS1 homolog, yeast) LOC253782 2q31.1 hypothetical protein LOC253782 NOSTRIN 2q31.1 nitric oxide synthase trafficker AD024 IGRP 2q24-q31 nitric oxide synthase trafficker ABCB11 2q24.1 ATP-binding cassette, sub-family B (MDR/TAP), member 11 DHRS9 2q31.1 dehydrogenase/reductase (SDR family) member 9 LRP2 2q31-q32.1 low density lipoprotein-related protein 2 DKFZp762I194 2q31.1 hypothetical protein DKFZp762I194 SARCOSIN 2q31.1 hypothetical protein DKFZp762I194 FLJ21901 2q31 hypothetical protein FLJ21901 PPIG 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) LOC129881 2q31.1 hypothetical LOC129881
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    30 - 9771 - 1977 - Han, Singh (2009)
    - - 9400 - - carcinoma cell line Klugbauer, Chatelier (2008)
    - - 6371 - - carcinoma cell line Klugbauer, Chatelier (2008)
    - - 1585 - - in dorsal root ganglia Raymond, Chatelier (2008)
    - - 1618 - 539 in dorsal root ganglia Raymond, Chatelier (2008)
    EXPRESSION
    Type restricted
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Digestivemouth    
    Nervousgangliasensory gangliadorsal root  
    Respiratoryrespiratory tractlarynx   
    Urinarybladder    
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Epithelialsecretoryglandularendocrine 
    Epithelialsensory   
    cells
    SystemCellPubmedSpeciesStageRna symbol
    nervousbrain
    Nervousneuron
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • 4 internal repeats, each with 5 hydrophobic segments (S1, S2, S3, S5, S6)and one positively charged segment (S4)
  • a IQ domain
  • HOMOLOGY
    interspecies homolog to murine Scn9a
    ortholog to rattus Pn1 sodium channel
    Homologene
    FAMILY
  • sodium channel family
  • CATEGORY transport channel
    SUBCELLULAR LOCALIZATION     plasma membrane
    basic FUNCTION
  • mediating the voltage-dependent sodium ion permeability of excitable membranes
  • playing a role in pain mechanisms, especially in the development of inflammatory pain
  • with SCN2A, and SCN3A, likely account for the tetrodotoxin-sensitive sodium currents in taste receptor cells (Gao 2009)
  • essential and non-redundant requirement for nociception
  • acting as a critical element of peripheral nociception
  • plays an important role in cell migration, endocytosis, and secretion and have a potential role in the aortic progression of intimal hyperplasia after balloon injury (Meguro 2009)
  • play a crucial role in pain sensation and in nociception (Chatelier 2008)
  • is not only necessary for pain sensation but is also an essential requirement for odour perception
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism
    signaling neurotransmission
    a component
  • beyond the thermosensors, the FGF13c/SCN9A omplex is essential for sustaining the transmission of noxious heat signals
  • INTERACTION
    DNA
    RNA
    small molecule
    protein
  • interacts with NEDD4 and NEDD4L
  • DPYSL2 protein SUMOylation modulates SCN9A channel trafficking
  • diverse modifications of DPYSL2 cross-talk to control SCN9A activity
  • FGF13 interacted with the sodium channel SCN9A in a heat-facilitated manner (FGF13 increased SCN9A sodium currents and maintained the membrane localization of SCN9A during noxious heat stimulation, enabling the sustained firing of action potentials)
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) ETHA , CIEP , PEXPD , GEFSP2
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    tumoral     --over  
    in prostate cancer (Diss 2008)
    constitutional germinal mutation     loss of function
    loss-of-function mutations in a single gene, SCN9A, cause a general loss of two major senses—nociception and smell
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target extremely promising target for selective pharmaceutical intervention in the analgesia
    ANIMAL & CELL MODELS