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ยฉ 2026 GeneE
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GeneE
25 sources retrieved ยท Most recent: April 2026 ยท Index updated 14 days ago
โ“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SCN1A
sodium voltage-gated channel alpha subunit 1
Chromosome 2 ยท 2q24.3
NCBI Gene: 6323Ensembl: ENSG00000144285.24HGNC: HGNC:10585UniProt: A0A286YF26
399PubMed Papers
26Diseases
74Drugs
2,103Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedIon ChannelTransporter
RESEARCH IMPACT
Highly StudiedVariant-Rich
CLINICAL
FDA Approved TargetOMIM Disease Gene
DATA QUALITY
โœ“ Experimental GO Evidenceโœ“ Swiss-Prot Reviewed
plasma membranevoltage-gated sodium channel activitycardiac muscle cell action potential involved in contractionmembrane depolarization during action potentialDravet syndromegeneralized epilepsy with febrile seizures plus, type 2Generalized epilepsy with febrile seizures-plusepilepsy
โœฆAI Summary

SCN1A encodes the pore-forming alpha subunit of Nav1.1, a voltage-gated sodium channel essential for neuronal excitability and action potential propagation 1. Nav1.1 permits selective sodium ion influx across the neuronal membrane, enabling membrane depolarization and electrical signal propagation while maintaining balanced excitation and inhibition in neural circuits 2. The channel also contributes to mechanically-induced pain perception in somatosensory neurons. SCN1A mutations cause severe developmental epileptic encephalopathies, predominantly Dravet syndrome, accounting for approximately 70% of cases 3. Truncating mutations (frameshift, nonsense, splice-site) and missense mutations affecting conserved ion-pore regions correlate with earlier seizure onset and more severe phenotypes, particularly myoclonic and atypical absence seizures 45. Dravet syndrome presents as fever-triggered generalized seizures beginning in infancy, progressing to multiple seizure types and cognitive impairment by age two 6. Mechanistically, de novo SCN1A mutations cause loss-of-function, with haploinsufficiency as the primary mechanism; recent findings indicate specific interneuron dysfunction underlies disease pathogenesis 78. Interneuron-specific SCN1A gene replacement therapy shows promise in preclinical models, demonstrating potential therapeutic benefit while avoiding adverse effects from ubiquitous expression 8.

Sources cited
1
Nav1.1 pore structure and sodium ion conductance enabling membrane depolarization and action potential propagation
PMID: 14672992
2
SCN1A mutations as major genetic causes of neurodevelopmental disorders and sodium channelopathies
PMID: 33531663
3
Genotype-phenotype correlations showing truncating mutations associate with earlier seizure onset and myoclonic seizures
PMID: 21248271
4
De novo SCN1A mutations (frameshift, nonsense, splice-donor, missense) cause severe myoclonic epilepsy of infancy
PMID: 11359211
5
Approximately 70% of Dravet syndrome patients carry SCN1A mutations
PMID: 21504424
6
SCN1A mutations associated with expanded spectrum of infantile epileptic encephalopathies beyond Dravet syndrome
PMID: 17347258
7
SCN1A mutation spectrum including point mutations and whole gene deletions; haploinsufficiency mechanism in Dravet syndrome
PMID: 18930999
8
Interneuron-specific SCN1A gene replacement therapy rescues Dravet syndrome phenotypes in mouse models
PMID: 40106582
Disease Associationsโ“˜26
Dravet syndromeOpen Targets
0.87Strong
generalized epilepsy with febrile seizures plus, type 2Open Targets
0.85Strong
Generalized epilepsy with febrile seizures-plusOpen Targets
0.84Strong
epilepsyOpen Targets
0.81Strong
migraine, familial hemiplegic, 3Open Targets
0.79Strong
genetic developmental and epileptic encephalopathyOpen Targets
0.76Strong
SeizureOpen Targets
0.75Strong
febrile seizures, familial, 3aOpen Targets
0.70Moderate
Lennox-Gastaut syndromeOpen Targets
0.67Moderate
migraine disorderOpen Targets
0.67Moderate
partial epilepsyOpen Targets
0.66Moderate
major depressive disorderOpen Targets
0.61Moderate
PainOpen Targets
0.61Moderate
bipolar disorderOpen Targets
0.60Moderate
amyotrophic lateral sclerosisOpen Targets
0.59Moderate
atrial fibrillationOpen Targets
0.59Moderate
PruritusOpen Targets
0.59Moderate
cardiac arrhythmiaOpen Targets
0.59Moderate
developmental and epileptic encephalopathyOpen Targets
0.58Moderate
hemorrhoidOpen Targets
0.58Moderate
Developmental and epileptic encephalopathy 6BUniProt
Dravet syndromeUniProt
Febrile seizures, familial, 3AUniProt
Generalized epilepsy with febrile seizures plus 2UniProt
Intractable childhood epilepsy with generalized tonic-clonic seizuresUniProt
Migraine, familial hemiplegic, 3UniProt
Pathogenic Variants2,103
NM_001165963.4(SCN1A):c.1709G>A (p.Ser570Asn)Likely pathogenic
Severe myoclonic epilepsy in infancy;Generalized epilepsy with febrile seizures plus, type 2|not provided|Inborn genetic diseases|Early-infantile DEE|Generalized epilepsy with febrile seizures plus
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 570
NM_001165963.4(SCN1A):c.1259C>T (p.Ala420Val)Likely pathogenic
Severe myoclonic epilepsy in infancy|Generalized epilepsy with febrile seizures plus|Early-infantile DEE
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 420
NM_001165963.4(SCN1A):c.2792G>A (p.Arg931His)Pathogenic
Severe myoclonic epilepsy in infancy|not provided|Generalized epilepsy with febrile seizures plus, type 2;Severe myoclonic epilepsy in infancy;Migraine, familial hemiplegic, 3|Migraine, familial hemiplegic, 3|Early-infantile DEE
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 931
NM_001165963.4(SCN1A):c.4916G>C (p.Arg1639Pro)Pathogenic
not provided|Severe myoclonic epilepsy in infancy|Early-infantile DEE
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 1639
NM_001165963.4(SCN1A):c.5511del (p.Pro1838fs)Likely pathogenic
Severe myoclonic epilepsy in infancy
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 1838
NM_001165963.4(SCN1A):c.2303C>T (p.Pro768Leu)Likely pathogenic
Severe myoclonic epilepsy in infancy|not provided|Early-infantile DEE
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 768
NM_001165963.4(SCN1A):c.3629C>T (p.Thr1210Met)Likely pathogenic
Inborn genetic diseases|Generalized epilepsy with febrile seizures plus|Early-infantile DEE
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 1210
NM_001165963.4(SCN1A):c.4219C>T (p.Arg1407Ter)Pathogenic
not provided|Severe myoclonic epilepsy in infancy|Inborn genetic diseases|SCN1A-related disorder|Early-infantile DEE|Seizure
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 1407
NM_001165963.4(SCN1A):c.4931G>A (p.Gly1644Asp)Pathogenic
not provided|Severe myoclonic epilepsy in infancy
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 1644
NM_001165963.4(SCN1A):c.1278C>A (p.Tyr426Ter)Pathogenic
Generalized epilepsy with febrile seizures plus, type 2|Early-infantile DEE
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 426
NM_001165963.4(SCN1A):c.301C>T (p.Arg101Trp)Pathogenic
Severe myoclonic epilepsy in infancy|not provided|Migraine, familial hemiplegic, 3|Early-infantile DEE
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 101
NM_001165963.4(SCN1A):c.602+1G>APathogenic
Severe myoclonic epilepsy in infancy|not provided|Generalized epilepsy with febrile seizures plus, type 2;Migraine, familial hemiplegic, 3;Severe myoclonic epilepsy in infancy|Generalized epilepsy with febrile seizures plus, type 2|Autism;Global developmental delay;Seizure|Focal impaired awareness seizure|Migraine, familial hemiplegic, 3|Generalized epilepsy with febrile seizures plus, type 2;Migraine, familial hemiplegic, 3;Severe myoclonic epilepsy in infancy;Developmental and epileptic encephalopathy 6B|Developmental and epileptic encephalopathy, 76|Seizure|See cases|Early-infantile DEE
โ˜…โ˜…โ˜†โ˜†2026
NM_001165963.4(SCN1A):c.2729A>G (p.Gln910Arg)Pathogenic
not provided|Early-infantile DEE
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 910
NM_001165963.4(SCN1A):c.4934G>A (p.Arg1645Gln)Pathogenic
Severe myoclonic epilepsy in infancy|not provided|Generalized epilepsy with febrile seizures plus, type 2;Migraine, familial hemiplegic, 3;Severe myoclonic epilepsy in infancy|Migraine, familial hemiplegic, 3|Inborn genetic diseases|Early-infantile DEE
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 1645
NM_001165963.4(SCN1A):c.5180A>G (p.Asp1727Gly)Pathogenic
Severe myoclonic epilepsy in infancy
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 1727
NM_001165963.4(SCN1A):c.841C>T (p.Pro281Ser)Pathogenic
Generalized epilepsy with febrile seizures plus, type 2|Early-infantile DEE
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 281
NM_001165963.4(SCN1A):c.3734G>A (p.Arg1245Gln)Pathogenic
Severe myoclonic epilepsy in infancy|not provided|Generalized epilepsy with febrile seizures plus, type 2|Generalized epilepsy with febrile seizures plus, type 2;Migraine, familial hemiplegic, 3;Severe myoclonic epilepsy in infancy;Developmental and epileptic encephalopathy 6B|Early-infantile DEE
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 1245
NM_001165963.4(SCN1A):c.2904C>A (p.Cys968Ter)Pathogenic
not provided|Early-infantile DEE
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 968
NM_001165963.4(SCN1A):c.2576G>A (p.Arg859His)Pathogenic
not provided|Autosomal dominant epilepsy|Generalized epilepsy with febrile seizures plus, type 2|Seizure|Severe myoclonic epilepsy in infancy|SCN1A-related disorder|Early-infantile DEE
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 859
NM_001165963.4(SCN1A):c.2593C>T (p.Arg865Ter)Pathogenic
Severe myoclonic epilepsy in infancy|not provided|Seizure|SCN1A-related disorder|Early-infantile DEE
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 865
View on ClinVar โ†—
Drug Targets74
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
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
SPTBN4Protein interaction100%NFASCProtein interaction100%SCN5AProtein interaction97%PCDH19Protein interaction94%ATP1A2Protein interaction93%PRKACAProtein interaction92%
Tissue Expression6 tissues
Brain
100%
Lung
14%
Heart
1%
Liver
0%
Bone Marrow
0%
Ovary
0%
Gene Interaction Network
Click a node to explore
SCN1ASPTBN4NFASCSCN5APCDH19ATP1A2PRKACA
PROTEIN STRUCTURE
Preparing viewerโ€ฆ
PDB7DTD ยท 3.30 ร… ยท EM
View on RCSB โ†—
Constraintโ“˜
LOEUFโ“˜
0.10Highly Constrained
pLIโ“˜
1.00Intolerant
Observed/Expected LoF0.06 [0.03โ€“0.10]
RankingsWhere SCN1A stands among ~20K protein-coding genes
  • #735of 20,598
    Most Researched399 ยท top 5%
  • #14of 1,025
    FDA-Approved Drug Targets59 ยท top 5%
  • #13of 5,498
    Most Pathogenic Variants2,103 ยท top 1%
  • #50of 17,882
    Most Constrained (LOEUF)0.10 ยท top 1%
Genes detectedSCN1A
Sources retrieved25 papers
Response timeโ€”
๐Ÿ“„ Sources
25โ–ผ
1
Sodium channelopathies in neurodevelopmental disorders.
PMID: 33531663
Nat Rev Neurosci ยท 2021
1.00
2
Genotype-phenotype associations in SCN1A-related epilepsies.
PMID: 21248271
Neurology ยท 2011
0.90
3
The spectrum of SCN1A-related infantile epileptic encephalopathies.
PMID: 17347258
Brain ยท 2007
0.80
4
Interneuron-specific dual-AAV
PMID: 40106582
Sci Transl Med ยท 2025
0.70
5
Association between two SCN1A polymorphisms and resistance to sodium channel blocking AEDs: a meta-analysis.
PMID: 29582177
Neurol Sci ยท 2018
0.60