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GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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SCN3A
sodium voltage-gated channel alpha subunit 3
Chromosome 2 · 2q24.3
NCBI Gene: 6328Ensembl: ENSG00000153253.20HGNC: HGNC:10590UniProt: A0A590UJH3
50PubMed Papers
22Diseases
75Drugs
37Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedIon ChannelTransporter
CLINICAL
FDA Approved TargetOMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
voltage-gated sodium channel activityvoltage-gated sodium channel complexplasma membranemembrane depolarization during action potentialfamilial focal epilepsy with variable focidevelopmental and epileptic encephalopathy, 62epilepsypartial epilepsy
✦AI Summary

SCN3A encodes Nav1.3, the pore-forming α subunit of a voltage-gated sodium channel that mediates action potential depolarization in excitable tissues 1. Nav1.3 selectively conducts Na+ ions across the plasma membrane in response to voltage changes, enabling electrical signal propagation in neurons and regulating cell excitability and secretory responses 2. SCN3A is transiently expressed during early fetal cortical development, particularly in neural progenitor cells and migrating neurons 3. Pathogenic SCN3A variants cause SCN3A-related neurodevelopmental disorder, characterized by treatment-resistant early-onset epilepsy (typically within the first year of life) and severe developmental delay 4. Notably, malformations of cortical development, including polymicrogyria, occur in >75% of affected individuals 4, suggesting a critical role in prenatal cortical folding and neuronal migration 3. Most pathogenic missense variants (91%) exhibit gain-of-function effects, with increased persistent current and altered voltage-dependent activation 4. Disease-associated variants cluster in transmembrane segments 4-6 of channel domains II-IV 4. Gain-of-function SCN3A variants produce aberrant neuronal firing patterns including paroxysmal bursting and action potential failures 5. Nav1.3-selective blockers normalize these abnormal firing patterns, offering potential therapeutic approaches for SCN3A-related encephalopathy 5. SCN3A variants are among the most frequently identified genetic causes in polymicrogyria cohorts 6.

Sources cited
1
SCN3A is one of four brain-expressed sodium channel genes associated with epilepsy; gain-of-function variants present with early-onset seizures responsive to sodium channel blockers
PMID: 32090326
2
SCN3A encodes Nav1.3, a voltage-gated sodium channel important for action potential initiation and propagation in the central nervous system
PMID: 37240836
3
SCN3A variants cause neurodevelopmental channelopathy with polymicrogyria; SCN3A is highly expressed in early fetal cortical development in progenitor cells and affects cortical folding and neuronal migration
PMID: 30146301
4
Pathogenic SCN3A variants cause treatment-resistant epilepsy with onset in the first year of life and severe developmental delay; 79% exhibit malformations of cortical development; most variants show gain-of-function with increased persistent current
PMID: 32515017
5
SCN3A variants produce increased persistent sodium current and abnormal neuronal firing patterns in stem cell-derived neurons; Nav1.3-selective blockers normalize these pathological effects
PMID: 37935051
6
SCN3A is among the most frequently identified genetic causes of polymicrogyria in a large exome sequencing cohort
PMID: 37486637
Disease Associationsⓘ22
familial focal epilepsy with variable fociOpen Targets
0.77Strong
developmental and epileptic encephalopathy, 62Open Targets
0.76Strong
epilepsyOpen Targets
0.75Strong
partial epilepsyOpen Targets
0.73Strong
SeizureOpen Targets
0.72Strong
genetic developmental and epileptic encephalopathyOpen Targets
0.63Moderate
PainOpen Targets
0.61Moderate
bipolar disorderOpen Targets
0.60Moderate
major depressive disorderOpen Targets
0.60Moderate
migraine disorderOpen Targets
0.60Moderate
PruritusOpen Targets
0.59Moderate
cardiac arrhythmiaOpen Targets
0.58Moderate
amyotrophic lateral sclerosisOpen Targets
0.58Moderate
hemorrhoidOpen Targets
0.58Moderate
trigeminal neuralgiaOpen Targets
0.58Moderate
Back painOpen Targets
0.58Moderate
atrial fibrillationOpen Targets
0.57Moderate
Ventricular arrhythmiaOpen Targets
0.57Moderate
Lennox-Gastaut syndromeOpen Targets
0.57Moderate
alcohol dependenceOpen Targets
0.57Moderate
Developmental and epileptic encephalopathy 62UniProt
Epilepsy, familial focal, with variable foci 4UniProt
Pathogenic Variants37
NM_006922.4(SCN3A):c.2624T>C (p.Ile875Thr)Pathogenic
Polymicrogyria;Developmental delay|not provided|Developmental and epileptic encephalopathy, 62|Epilepsy, familial focal, with variable foci 4|Developmental and epileptic encephalopathy|Epilepsy
★★★☆2024→ Residue 875
NM_006922.4(SCN3A):c.585_586del (p.Phe195fs)Pathogenic
not provided|Developmental and epileptic encephalopathy
★★★☆2024→ Residue 195
NM_006922.4(SCN3A):c.4457C>T (p.Thr1486Ile)Pathogenic
Developmental and epileptic encephalopathy, 62|not provided|Developmental and epileptic encephalopathy
★★☆☆2024→ Residue 1486
NM_006922.4(SCN3A):c.4862G>A (p.Arg1621Gln)Pathogenic
not provided|Developmental and epileptic encephalopathy, 62|Congenital bilateral perisylvian syndrome|Developmental and epileptic encephalopathy
★★☆☆2023→ Residue 1621
NM_006922.4(SCN3A):c.2653C>T (p.Leu885Phe)Likely pathogenic
Developmental and epileptic encephalopathy, 62
★★☆☆2022→ Residue 885
NM_006922.4(SCN3A):c.626T>C (p.Leu209Pro)Likely pathogenic
not provided|Developmental and epileptic encephalopathy, 62|atypical cerebral palsy
★★☆☆2022→ Residue 209
NM_006922.4(SCN3A):c.5295G>A (p.Met1765Ile)Pathogenic
Developmental and epileptic encephalopathy, 62|Epilepsy, familial focal, with variable foci 4
★★☆☆2022→ Residue 1765
NM_006922.4(SCN3A):c.4403T>G (p.Ile1468Arg)Likely pathogenic
not provided|Developmental and epileptic encephalopathy, 62|Developmental and epileptic encephalopathy
★★☆☆2021→ Residue 1468
NM_006922.4(SCN3A):c.3998C>T (p.Pro1333Leu)Pathogenic
not provided|Developmental and epileptic encephalopathy, 62|Developmental and epileptic encephalopathy
★★☆☆2021→ Residue 1333
NM_006922.4(SCN3A):c.5306T>C (p.Val1769Ala)Likely pathogenic
Inborn genetic diseases|Developmental and epileptic encephalopathy, 62|Developmental and epileptic encephalopathy
★★☆☆2021→ Residue 1769
NM_006922.4(SCN3A):c.2565+1G>CLikely pathogenic
Developmental and epileptic encephalopathy, 62
★☆☆☆2026
NM_006922.4(SCN3A):c.4456A>G (p.Thr1486Ala)Likely pathogenic
not provided
★☆☆☆2025→ Residue 1486
NM_006922.4(SCN3A):c.3393+2T>GPathogenic
Epilepsy, familial focal, with variable foci 4
★☆☆☆2025
NM_006922.4(SCN3A):c.4387T>C (p.Phe1463Leu)Likely pathogenic
not provided
★☆☆☆2025→ Residue 1463
NM_006922.4(SCN3A):c.1859G>A (p.Arg620Gln)Likely pathogenic
not provided
★☆☆☆2025→ Residue 620
NM_006922.4(SCN3A):c.4853C>T (p.Thr1618Ile)Likely pathogenic
Seizure
★☆☆☆2025→ Residue 1618
NM_006922.4(SCN3A):c.19del (p.Val7fs)Likely pathogenic
Epilepsy, familial focal, with variable foci 4
★☆☆☆2025→ Residue 7
NM_006922.4(SCN3A):c.5441_5442del (p.Leu1813_Ser1814insTer)Likely pathogenic
not provided
★☆☆☆2025→ Residue 1813
NM_006922.4(SCN3A):c.3723_3727dup (p.Ala1243fs)Likely pathogenic
Epilepsy
★☆☆☆2024→ Residue 1243
NM_006922.4(SCN3A):c.602C>A (p.Ala201Glu)Likely pathogenic
Seizure
★☆☆☆2024→ Residue 201
View on ClinVar ↗
Drug Targets75
ARTICAINEApproved
Sodium channel alpha subunit blocker
ARTICAINE HYDROCHLORIDEApproved
Sodium channel alpha subunit blocker
BENOXINATEApproved
Sodium channel alpha subunit blocker
Pruritus
BENOXINATE HYDROCHLORIDEPhase III
Sodium channel alpha subunit blocker
CARBAMAZEPINEApproved
Sodium channel alpha subunit blocker
epilepsy
CENOBAMATEApproved
Sodium channel alpha subunit inhibitor
Seizure
CHLOROPROCAINEApproved
Sodium channel alpha subunit blocker
CHLOROPROCAINE HYDROCHLORIDEPhase III
Sodium channel alpha subunit blocker
COCAINEApproved
Sodium channel alpha subunit blocker
COCAINE HYDROCHLORIDEApproved
Sodium channel alpha subunit blocker
DISOPYRAMIDEApproved
Sodium channel alpha subunit blocker
cardiac arrhythmia
DISOPYRAMIDE PHOSPHATEApproved
Sodium channel alpha subunit blocker
Ventricular arrhythmia
DRONEDARONEApproved
Sodium channel alpha subunit blocker
cardiac arrhythmia
DRONEDARONE HYDROCHLORIDEApproved
Sodium channel alpha subunit blocker
atrial fibrillation
DYCLONINEApproved
Sodium channel alpha subunit blocker
Pain
DYCLONINE HYDROCHLORIDEUNKNOWN
Sodium channel alpha subunit blocker
ELPETRIGINEPhase I
Sodium channel protein type II alpha subunit blocker
bipolar disorder
ENCAINIDEApproved
Sodium channel alpha subunit blocker
cardiac arrhythmia
ENCAINIDE HYDROCHLORIDEUNKNOWN
Sodium channel alpha subunit blocker
ESLICARBAZEPINEApproved
Sodium channel alpha subunit blocker
epilepsy
ESLICARBAZEPINE ACETATEApproved
Sodium channel alpha subunit blocker
Seizure
ETHOTOINApproved
Sodium channel alpha subunit blocker
Seizure
ETIDOCAINEApproved
Sodium channel alpha subunit blocker
Pain
EVENAMIDEPhase III
Sodium channel alpha subunit blocker
treatment refractory schizophrenia
FOSPHENYTOINApproved
Sodium channel alpha subunit blocker
epilepsy
FOSPHENYTOIN SODIUMApproved
Sodium channel alpha subunit blocker
HEXYLCAINEApproved
Sodium channel alpha subunit blocker
INDECAINIDEApproved
Sodium channel alpha subunit blocker
IRAMPANELPhase I
Glutamate receptor ionotropic AMPA antagonist
LACOSAMIDEApproved
Sodium channel alpha subunit blocker
epilepsy
LAMOTRIGINEApproved
Sodium channel alpha subunit blocker
epilepsy
LIDOCAINEApproved
Sodium channel alpha subunit blocker
premature ejaculation
LIDOCAINE HYDROCHLORIDEApproved
Sodium channel alpha subunit blocker
Pain
MEPHENYTOINApproved
Sodium channel alpha subunit blocker
epilepsy
MEPIVACAINEApproved
Sodium channel alpha subunit blocker
pain agnosia
MEPIVACAINE HYDROCHLORIDEPhase III
Sodium channel alpha subunit blocker
MEXILETINEApproved
Sodium channel alpha subunit blocker
cardiac arrhythmia
MEXILETINE HYDROCHLORIDEApproved
Sodium channel alpha subunit blocker
Ventricular arrhythmia
MORICIZINEApproved
Sodium channel alpha subunit blocker
cardiac arrhythmia
NERISPIRDINEPhase II
Voltage-gated potassium channel blocker
multiple sclerosis
NKTR-171IND
Sodium channel alpha subunit blocker
neuropathic pain
ORPHENADRINEApproved
Glutamate [NMDA] receptor antagonist
Parkinson disease
ORPHENADRINE CITRATEApproved
Glutamate [NMDA] receptor antagonist
Pain
ORPHENADRINE HYDROCHLORIDEApproved
Histamine H1 receptor antagonist
Parkinson disease
OXCARBAZEPINEApproved
Sodium channel alpha subunit blocker
epilepsy
PHENACEMIDEApproved
Sodium channel alpha subunit blocker
epilepsy
PHENAZOPYRIDINEApproved
Sodium channel alpha subunit blocker
Pain
PHENAZOPYRIDINE HYDROCHLORIDEPhase III
Sodium channel alpha subunit blocker
urinary tract infection
PHENYTOINApproved
Sodium channel alpha subunit blocker
epilepsy
PHENYTOIN SODIUMApproved
Sodium channel alpha subunit blocker
epilepsy
PRILOCAINEApproved
Sodium channel alpha subunit blocker
Pain
PRILOCAINE HYDROCHLORIDEUNKNOWN
Sodium channel alpha subunit blocker
PRIMIDONEApproved
GABA-A receptor; anion channel positive allosteric modulator
epilepsy
PROCAINAMIDEApproved
Sodium channel alpha subunit blocker
cardiac arrhythmia
PROCAINAMIDE HYDROCHLORIDEApproved
Sodium channel alpha subunit blocker
PROCAINEApproved
Sodium channel alpha subunit blocker
hemorrhoid
PROCAINE HYDROCHLORIDEPhase II
Sodium channel alpha subunit blocker
HIV infection
PROPAFENONEApproved
Beta-1 adrenergic receptor antagonist
cardiac arrhythmia
PROPAFENONE HYDROCHLORIDEApproved
Beta-1 adrenergic receptor antagonist
PROPARACAINEApproved
Sodium channel alpha subunit blocker
PROPARACAINE HYDROCHLORIDEUNKNOWN
Sodium channel alpha subunit blocker
PROPOXYCAINEApproved
Sodium channel alpha subunit blocker
Pain
QUINIDINEApproved
Sodium channel alpha subunit blocker
cardiac arrhythmia
QUINIDINE GLUCONATEApproved
Sodium channel alpha subunit blocker
QUINIDINE SULFATEApproved
Sodium channel alpha subunit blocker
RALFINAMIDEPhase III
Glutamate [NMDA] receptor antagonist
neuropathic pain
RILUZOLEApproved
Sodium channel alpha subunit blocker
amyotrophic lateral sclerosis
ROPIVACAINEApproved
Sodium channel alpha subunit blocker
ROPIVACAINE HYDROCHLORIDEApproved
Sodium channel alpha subunit blocker
Pain
RUFINAMIDEApproved
Sodium channel alpha subunit blocker
TETRACAINEApproved
Sodium channel alpha subunit blocker
Pain
TETRACAINE HYDROCHLORIDEPhase III
Sodium channel alpha subunit blocker
TOCAINIDEApproved
Sodium channel alpha subunit blocker
cardiac arrhythmia
TOPIRAMATEApproved
Glutamate receptor ionotropic AMPA antagonist
epilepsy
ZONISAMIDEApproved
Sodium channel alpha subunit blocker
epilepsy
Related Genes
KCNQ2Protein interaction100%CALHM1Protein interaction93%SCN1AProtein interaction87%FGF13Protein interaction81%NAV1Protein interaction77%TRPM4Protein interaction73%
Tissue Expression6 tissues
Brain
100%
Heart
21%
Bone Marrow
17%
Ovary
6%
Lung
1%
Liver
1%
Gene Interaction Network
Click a node to explore
SCN3AKCNQ2CALHM1SCN1AFGF13NAV1TRPM4
PROTEIN STRUCTURE
Preparing viewer…
PDB7W77 · 3.30 Å · EM
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.35Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.27 [0.21–0.35]
RankingsWhere SCN3A stands among ~20K protein-coding genes
  • #8,873of 20,598
    Most Researched50
  • #23of 1,025
    FDA-Approved Drug Targets59 · top 5%
  • #1,624of 5,498
    Most Pathogenic Variants37
  • #1,530of 17,882
    Most Constrained (LOEUF)0.35 · top 10%
Genes detectedSCN3A
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Biological concepts in human sodium channel epilepsies and their relevance in clinical practice.
PMID: 32090326
Epilepsia · 2020
1.00
2
Exome Sequencing and the Identification of New Genes and Shared Mechanisms in Polymicrogyria.
PMID: 37486637
JAMA Neurol · 2023
0.90
3
Clinical exome sequencing: results from 2819 samples reflecting 1000 families.
PMID: 27848944
Eur J Hum Genet · 2017
0.80
4
SCN1A, SCN2A and SCN3A gene polymorphisms and responsiveness to antiepileptic drugs: a multicenter cohort study and meta-analysis.
PMID: 23859570
Pharmacogenomics · 2013
0.70
5
SCN3A-Related Neurodevelopmental Disorder: A Spectrum of Epilepsy and Brain Malformation.
PMID: 32515017
Ann Neurol · 2020
0.60