Seroatlas · Human Serome Atlas

SCN9A

Sodium channel protein type 9 subunit alpha

Also known as: ETHA, Nav1.7, NE-NA, NENA, PN1, SCN9A_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q15858
Gene: SCN9A
Ensembl: ENSG00000169432
Chromosome: 2
Canonical length: 1988 aa
Protein class: Disease related genes, FDA approved drug targets, Human disease related genes, Predicted membrane proteins, Transporters, Voltage-gated ion channels
Subcellular location: Plasma membrane,Actin filaments,Focal adhesion sites

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

1988 residues, UniProt reviewed canonical sequence.

>Q15858|SCN9A
     1  MAMLPPPGPQ SFVHFTKQSL ALIEQRIAER KSKEPKEEKK DDDEEAPKPS SDLEAGKQLP
    61  FIYGDIPPGM VSEPLEDLDP YYADKKTFIV LNKGKTIFRF NATPALYMLS PFSPLRRISI
   121  KILVHSLFSM LIMCTILTNC IFMTMNNPPD WTKNVEYTFT GIYTFESLVK ILARGFCVGE
   181  FTFLRDPWNW LDFVVIVFAY LTEFVNLGNV SALRTFRVLR ALKTISVIPG LKTIVGALIQ
   241  SVKKLSDVMI LTVFCLSVFA LIGLQLFMGN LKHKCFRNSL ENNETLESIM NTLESEEDFR
   301  KYFYYLEGSK DALLCGFSTD SGQCPEGYTC VKIGRNPDYG YTSFDTFSWA FLALFRLMTQ
   361  DYWENLYQQT LRAAGKTYMI FFVVVIFLGS FYLINLILAV VAMAYEEQNQ ANIEEAKQKE
   421  LEFQQMLDRL KKEQEEAEAI AAAAAEYTSI RRSRIMGLSE SSSETSKLSS KSAKERRNRR
   481  KKKNQKKLSS GEEKGDAEKL SKSESEDSIR RKSFHLGVEG HRRAHEKRLS TPNQSPLSIR
   541  GSLFSARRSS RTSLFSFKGR GRDIGSETEF ADDEHSIFGD NESRRGSLFV PHRPQERRSS
   601  NISQASRSPP MLPVNGKMHS AVDCNGVVSL VDGRSALMLP NGQLLPEVII DKATSDDSGT
   661  TNQIHKKRRC SSYLLSEDML NDPNLRQRAM SRASILTNTV EELEESRQKC PPWWYRFAHK
   721  FLIWNCSPYW IKFKKCIYFI VMDPFVDLAI TICIVLNTLF MAMEHHPMTE EFKNVLAIGN
   781  LVFTGIFAAE MVLKLIAMDP YEYFQVGWNI FDSLIVTLSL VELFLADVEG LSVLRSFRLL
   841  RVFKLAKSWP TLNMLIKIIG NSVGALGNLT LVLAIIVFIF AVVGMQLFGK SYKECVCKIN
   901  DDCTLPRWHM NDFFHSFLIV FRVLCGEWIE TMWDCMEVAG QAMCLIVYMM VMVIGNLVVL
   961  NLFLALLLSS FSSDNLTAIE EDPDANNLQI AVTRIKKGIN YVKQTLREFI LKAFSKKPKI
  1021  SREIRQAEDL NTKKENYISN HTLAEMSKGH NFLKEKDKIS GFGSSVDKHL MEDSDGQSFI
  1081  HNPSLTVTVP IAPGESDLEN MNAEELSSDS DSEYSKVRLN RSSSSECSTV DNPLPGEGEE
  1141  AEAEPMNSDE PEACFTDGCV WRFSCCQVNI ESGKGKIWWN IRKTCYKIVE HSWFESFIVL
  1201  MILLSSGALA FEDIYIERKK TIKIILEYAD KIFTYIFILE MLLKWIAYGY KTYFTNAWCW
  1261  LDFLIVDVSL VTLVANTLGY SDLGPIKSLR TLRALRPLRA LSRFEGMRVV VNALIGAIPS
  1321  IMNVLLVCLI FWLIFSIMGV NLFAGKFYEC INTTDGSRFP ASQVPNRSEC FALMNVSQNV
  1381  RWKNLKVNFD NVGLGYLSLL QVATFKGWTI IMYAAVDSVN VDKQPKYEYS LYMYIYFVVF
  1441  IIFGSFFTLN LFIGVIIDNF NQQKKKLGGQ DIFMTEEQKK YYNAMKKLGS KKPQKPIPRP
  1501  GNKIQGCIFD LVTNQAFDIS IMVLICLNMV TMMVEKEGQS QHMTEVLYWI NVVFIILFTG
  1561  ECVLKLISLR HYYFTVGWNI FDFVVVIISI VGMFLADLIE TYFVSPTLFR VIRLARIGRI
  1621  LRLVKGAKGI RTLLFALMMS LPALFNIGLL LFLVMFIYAI FGMSNFAYVK KEDGINDMFN
  1681  FETFGNSMIC LFQITTSAGW DGLLAPILNS KPPDCDPKKV HPGSSVEGDC GNPSVGIFYF
  1741  VSYIIISFLV VVNMYIAVIL ENFSVATEES TEPLSEDDFE MFYEVWEKFD PDATQFIEFS
  1801  KLSDFAAALD PPLLIAKPNK VQLIAMDLPM VSGDRIHCLD ILFAFTKRVL GESGEMDSLR
  1861  SQMEERFMSA NPSKVSYEPI TTTLKRKQED VSATVIQRAY RRYRLRQNVK NISSIYIKDG
  1921  DRDDDLLNKK DMAFDNVNEN SSPEKTDATS STTSPPSYDS VTKPDKEKYE QDRTEKEDKG
  1981  KDSKESKK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SCN9A can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Cell surface
Secreted: No
Transmembrane segments: 24
Mean surface accessibility (rSASA): 0.37
Highest tissue expression: 5.7 nTPM

Expression across tissuesHPA

Tissue

hypothalamus: 5.7 nTPM
testis: 4.6 nTPM
placenta: 4 nTPM
liver: 3.6 nTPM
colon: 2.9 nTPM
rectum: 2.9 nTPM

Single-cell type

sertoli cells: 810 nCPM
hofbauer cells: 347 nCPM
oligodendrocyte progenitor cells: 300 nCPM
other brain neurons: 286 nCPM
respiratory ionocytes: 244 nCPM
corticotrophs: 203 nCPM

Immune cell

plasmacytoid DC: 24 nTPM
myeloid DC: 1.4 nTPM
neutrophil: 0.9 nTPM
NK-cell: 0.5 nTPM
basophil: 0.2 nTPM
classical monocyte: 0.1 nTPM

Brain region

hypothalamus: 49 nTPM
midbrain: 45 nTPM
pons: 29 nTPM
medulla oblongata: 22 nTPM
basal ganglia: 15 nTPM
thalamus: 14 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SCN9A.

Disease | AllUniProt

Conditions SCN9A is implicated in, by any mechanism.

Primary erythermalgia (PERYTHM) MIM:133020
Indifference to pain, congenital, autosomal recessive (CIP) MIM:243000
Paroxysmal extreme pain disorder (PEXPD) MIM:167400

Disease | GeneticClinVar

180 pathogenic / likely-pathogenic of 3,017 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Neuropathy, hereditary sensory and autonomic, type 2A
Generalized epilepsy with febrile seizures plus, type 7
Channelopathy-associated congenital insensitivity to pain, autosomal recessive
Primary erythromelalgia
Paroxysmal extreme pain disorder

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.71
gnomAD pLI: 0
gnomAD missense Z: 1.06
DepMap mean gene effect: 0
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

voltage-gated sodium channel activity

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of SCN9A in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads SCN9A as an antibody target. Whether an autoantibody or antibody against SCN9A could matter depends on whether native SCN9A is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SCN9A is annotated at the cell surface, where native SCN9A is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label SCN9A as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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