Seroatlas · Human Serome Atlas

SCN3A

Sodium channel protein type 3 subunit alpha

Also known as: Nav1.3, SCN3A_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
Q9NY46
Gene
SCN3A
Ensembl
ENSG00000153253
Chromosome
2
Canonical length
2000 aa
Protein class
Disease related genes, FDA approved drug targets, Human disease related genes, Plasma proteins, Predicted membrane proteins, Voltage-gated ion channels

OverviewNCBI Gene

Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family, and is found in a cluster of five alpha subunit genes on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

2000 residues, UniProt reviewed canonical sequence.

>Q9NY46|SCN3A
     1  MAQALLVPPG PESFRLFTRE SLAAIEKRAA EEKAKKPKKE QDNDDENKPK PNSDLEAGKN
    61  LPFIYGDIPP EMVSEPLEDL DPYYINKKTF IVMNKGKAIF RFSATSALYI LTPLNPVRKI
   121  AIKILVHSLF SMLIMCTILT NCVFMTLSNP PDWTKNVEYT FTGIYTFESL IKILARGFCL
   181  EDFTFLRDPW NWLDFSVIVM AYVTEFVSLG NVSALRTFRV LRALKTISVI PGLKTIVGAL
   241  IQSVKKLSDV MILTVFCLSV FALIGLQLFM GNLRNKCLQW PPSDSAFETN TTSYFNGTMD
   301  SNGTFVNVTM STFNWKDYIG DDSHFYVLDG QKDPLLCGNG SDAGQCPEGY ICVKAGRNPN
   361  YGYTSFDTFS WAFLSLFRLM TQDYWENLYQ LTLRAAGKTY MIFFVLVIFL GSFYLVNLIL
   421  AVVAMAYEEQ NQATLEEAEQ KEAEFQQMLE QLKKQQEEAQ AVAAASAASR DFSGIGGLGE
   481  LLESSSEASK LSSKSAKEWR NRRKKRRQRE HLEGNNKGER DSFPKSESED SVKRSSFLFS
   541  MDGNRLTSDK KFCSPHQSLL SIRGSLFSPR RNSKTSIFSF RGRAKDVGSE NDFADDEHST
   601  FEDSESRRDS LFVPHRHGER RNSNVSQASM SSRMVPGLPA NGKMHSTVDC NGVVSLVGGP
   661  SALTSPTGQL PPEGTTTETE VRKRRLSSYQ ISMEMLEDSS GRQRAVSIAS ILTNTMEELE
   721  ESRQKCPPCW YRFANVFLIW DCCDAWLKVK HLVNLIVMDP FVDLAITICI VLNTLFMAME
   781  HYPMTEQFSS VLTVGNLVFT GIFTAEMVLK IIAMDPYYYF QEGWNIFDGI IVSLSLMELG
   841  LSNVEGLSVL RSFRLLRVFK LAKSWPTLNM LIKIIGNSVG ALGNLTLVLA IIVFIFAVVG
   901  MQLFGKSYKE CVCKINDDCT LPRWHMNDFF HSFLIVFRVL CGEWIETMWD CMEVAGQTMC
   961  LIVFMLVMVI GNLVVLNLFL ALLLSSFSSD NLAATDDDNE MNNLQIAVGR MQKGIDYVKN
  1021  KMRECFQKAF FRKPKVIEIH EGNKIDSCMS NNTGIEISKE LNYLRDGNGT TSGVGTGSSV
  1081  EKYVIDENDY MSFINNPSLT VTVPIAVGES DFENLNTEEF SSESELEESK EKLNATSSSE
  1141  GSTVDVVLPR EGEQAETEPE EDLKPEACFT EGCIKKFPFC QVSTEEGKGK IWWNLRKTCY
  1201  SIVEHNWFET FIVFMILLSS GALAFEDIYI EQRKTIKTML EYADKVFTYI FILEMLLKWV
  1261  AYGFQTYFTN AWCWLDFLIV DVSLVSLVAN ALGYSELGAI KSLRTLRALR PLRALSRFEG
  1321  MRVVVNALVG AIPSIMNVLL VCLIFWLIFS IMGVNLFAGK FYHCVNMTTG NMFDISDVNN
  1381  LSDCQALGKQ ARWKNVKVNF DNVGAGYLAL LQVATFKGWM DIMYAAVDSR DVKLQPVYEE
  1441  NLYMYLYFVI FIIFGSFFTL NLFIGVIIDN FNQQKKKFGG QDIFMTEEQK KYYNAMKKLG
  1501  SKKPQKPIPR PANKFQGMVF DFVTRQVFDI SIMILICLNM VTMMVETDDQ GKYMTLVLSR
  1561  INLVFIVLFT GEFVLKLVSL RHYYFTIGWN IFDFVVVILS IVGMFLAEMI EKYFVSPTLF
  1621  RVIRLARIGR ILRLIKGAKG IRTLLFALMM SLPALFNIGL LLFLVMFIYA IFGMSNFAYV
  1681  KKEAGIDDMF NFETFGNSMI CLFQITTSAG WDGLLAPILN SAPPDCDPDT IHPGSSVKGD
  1741  CGNPSVGIFF FVSYIIISFL VVVNMYIAVI LENFSVATEE SAEPLSEDDF EMFYEVWEKF
  1801  DPDATQFIEF SKLSDFAAAL DPPLLIAKPN KVQLIAMDLP MVSGDRIHCL DILFAFTKRV
  1861  LGESGEMDAL RIQMEDRFMA SNPSKVSYEP ITTTLKRKQE EVSAAIIQRN FRCYLLKQRL
  1921  KNISSNYNKE AIKGRIDLPI KQDMIIDKLN GNSTPEKTDG SSSTTSPPSY DSVTKPDKEK
  1981  FEKDKPEKES KGKEVRENQK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SCN3A 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)
0.38
Highest tissue expression
8.6 nTPM

Expression across tissuesHPA

Tissue

  • cerebral cortex: 8.6 nTPM
  • thymus: 3.7 nTPM
  • basal ganglia: 2.6 nTPM
  • hypothalamus: 2.3 nTPM
  • amygdala: 1.9 nTPM
  • cerebellum: 1.9 nTPM

Single-cell type

  • thymocytes: 506 nCPM
  • oligodendrocyte progenitor cells: 385 nCPM
  • brain inhibitory neurons: 346 nCPM
  • cone photoreceptor cells: 304 nCPM
  • other brain neurons: 263 nCPM
  • brain excitatory neurons: 255 nCPM

Immune cell

  • naive B-cell: 15 nTPM
  • memory B-cell: 13 nTPM
  • plasmacytoid DC: 0.4 nTPM
  • NK-cell: 0.2 nTPM
  • naive CD4 T-cell: 0.1 nTPM
  • T-reg: 0.1 nTPM

Brain region

  • hypothalamus: 52 nTPM
  • basal ganglia: 39 nTPM
  • cerebral cortex: 37 nTPM
  • midbrain: 36 nTPM
  • pons: 36 nTPM
  • cerebellum: 31 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SCN3A.

Disease | AllUniProt

Conditions SCN3A is implicated in, by any mechanism.

  • Epilepsy, familial focal, with variable foci 4 (FFEVF4) MIM:617935
  • Developmental and epileptic encephalopathy 62 (DEE62) MIM:617938

Disease | GeneticClinVar

38 pathogenic / likely-pathogenic of 2,112 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

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)
0.17
gnomAD pLI
1
gnomAD missense Z
4.62
DepMap mean gene effect
0.05
DepMap dependency class
none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of SCN3A 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 SCN3A as an antibody target. Whether an autoantibody or antibody against SCN3A could matter depends on whether native SCN3A is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SCN3A is annotated at the cell surface, where native SCN3A 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 SCN3A as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/SCN3A. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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