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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.
SCN2A
sodium voltage-gated channel alpha subunit 2
Chromosome 2 ยท 2q24.3
NCBI Gene: 6326Ensembl: ENSG00000136531.19HGNC: HGNC:10588UniProt: Q99250
153PubMed Papers
23Diseases
75Drugs
694Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub GeneIon ChannelTransporter
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
FDA Approved TargetOMIM Disease Gene
DATA QUALITY
โœ“ Experimental GO Evidenceโœ“ Swiss-Prot Reviewed
voltage-gated sodium channel activityneuronal action potentialprotein bindingcalmodulin bindingdevelopmental and epileptic encephalopathy, 11seizures, benign familial infantile, 3Seizureepisodic ataxia, type 9
โœฆAI Summary

SCN2A encodes the neuronal sodium channel Nav1.2, a voltage-gated ion channel that mediates sodium ion permeability across excitable membranes 1. The channel forms a sodium-selective pore that opens and closes in response to membrane voltage changes, allowing Na+ ions to flow according to their electrochemical gradient 2. SCN2A is highly expressed in developing neurons and plays critical roles in neuronal excitability and action potential generation 2. SCN2A dysfunction causes a spectrum of neurodevelopmental disorders, with SCN2A haploinsufficiency being a leading monogenic cause of autism spectrum disorder, intellectual disability, and infantile seizures 3. Disease pathophysiology depends on mutation type: gain-of-function missense mutations typically cause early-infantile onset seizures responsive to sodium channel blockers, while loss-of-function truncating mutations cause later-onset epilepsies or non-seizure phenotypes with poor drug responsiveness 4. Beyond epilepsy, SCN2A variants are associated with episodic ataxia and developmental and epileptic encephalopathies 5. Recent evidence indicates microglial over-pruning of synapses contributes to autism-associated SCN2A deficiency 6. Emerging therapeutic approaches include CRISPR activation to upregulate the functional gene copy, which rescues electrophysiological deficits, synaptic transmission, and seizure susceptibility in preclinical models 3. Phenotype-genotype correlation enables precision medicine approaches guiding therapeutic selection 7.

Sources cited
1
SCN2A encodes Nav1.2 sodium channel and dysfunction is a leading cause of infantile seizures, autism, and intellectual disability
PMID: 29691040
2
SCN2A is a voltage-gated sodium channel ฮฑ-subunit gene responsible for significant neurological disease burden
PMID: 33531663
3
SCN2A haploinsufficiency causes neurodevelopmental disorder with autism, intellectual disability, and refractory epilepsy; CRISPR activation can rescue phenotypes
PMID: 40963013
4
Gain-of-function mutations cause early infantile seizures responsive to sodium channel blockers; loss-of-function mutations cause later-onset epilepsy or non-seizure phenotypes with poor drug response
PMID: 28379373
5
SCN2A variants present across spectrum including developmental and epileptic encephalopathies, benign neonatal-infantile seizures, episodic ataxia, and autism with or without seizures
PMID: 31924505
6
SCN2A deficiency causes microglial over-pruning of synapses during development, contributing to autism-associated phenotypes
PMID: 38499656
7
SCN2A pathogenic variants show phenotype-genotype correlation enabling precision medicine approaches for treatment selection
PMID: 31904126
Disease Associationsโ“˜23
developmental and epileptic encephalopathy, 11Open Targets
0.84Strong
seizures, benign familial infantile, 3Open Targets
0.81Strong
SeizureOpen Targets
0.77Strong
episodic ataxia, type 9Open Targets
0.75Strong
bipolar disorderOpen Targets
0.72Strong
epilepsyOpen Targets
0.70Moderate
complex neurodevelopmental disorderOpen Targets
0.67Moderate
partial epilepsyOpen Targets
0.66Moderate
infantile spasmsOpen Targets
0.64Moderate
Benign familial neonatal-infantile seizuresOpen Targets
0.63Moderate
PainOpen Targets
0.61Moderate
benign familial infantile epilepsyOpen Targets
0.61Moderate
major depressive disorderOpen Targets
0.60Moderate
migraine disorderOpen Targets
0.60Moderate
Lennox-Gastaut syndromeOpen 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
Developmental and epileptic encephalopathy 11UniProt
Episodic ataxia 9UniProt
Seizures, benign familial infantile, 3UniProt
Pathogenic Variants694
NM_001040142.2(SCN2A):c.2657T>C (p.Leu886Ser)Likely pathogenic
not provided|Seizures, benign familial infantile, 3;Developmental and epileptic encephalopathy, 11|Developmental and epileptic encephalopathy|Complex neurodevelopmental disorder
โ˜…โ˜…โ˜…โ˜†2025โ†’ Residue 886
NM_001040142.2(SCN2A):c.1094C>T (p.Thr365Met)Likely pathogenic
not provided|Inborn genetic diseases|Complex neurodevelopmental disorder
โ˜…โ˜…โ˜…โ˜†2025โ†’ Residue 365
NM_001040142.2(SCN2A):c.4782G>T (p.Trp1594Cys)Likely pathogenic
Complex neurodevelopmental disorder
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 1594
NM_001040142.2(SCN2A):c.4782G>C (p.Trp1594Cys)Likely pathogenic
not provided|Inborn genetic diseases|Complex neurodevelopmental disorder
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 1594
NM_001040142.2(SCN2A):c.4780T>A (p.Trp1594Arg)Likely pathogenic
Complex neurodevelopmental disorder
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 1594
NM_001040142.2(SCN2A):c.3778A>G (p.Lys1260Glu)Likely pathogenic
Complex neurodevelopmental disorder|Developmental and epileptic encephalopathy, 11;Seizures, benign familial infantile, 3
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 1260
NM_001040142.2(SCN2A):c.3778A>C (p.Lys1260Gln)Likely pathogenic
Complex neurodevelopmental disorder
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 1260
NM_001040142.2(SCN2A):c.5636T>C (p.Met1879Thr)Likely pathogenic
Seizures, benign familial infantile, 3;Developmental and epileptic encephalopathy, 11|Developmental and epileptic encephalopathy, 11|not provided|Complex neurodevelopmental disorder
โ˜…โ˜…โ˜…โ˜†2024โ†’ Residue 1879
NM_001040142.2(SCN2A):c.5317G>A (p.Ala1773Thr)Pathogenic
not provided|Seizures, benign familial infantile, 3;Developmental and epileptic encephalopathy, 11|Inborn genetic diseases|Developmental and epileptic encephalopathy, 11|Complex neurodevelopmental disorder|West syndrome|SCN2A-related disorder
โ˜…โ˜…โ˜…โ˜†2023โ†’ Residue 1773
NM_001040142.2(SCN2A):c.2558G>A (p.Arg853Gln)Pathogenic
not provided|Developmental and epileptic encephalopathy, 11|Developmental and epileptic encephalopathy, 11;Seizures, benign familial infantile, 3|Complex neurodevelopmental disorder|West syndrome
โ˜…โ˜…โ˜…โ˜†2023โ†’ Residue 853
NM_001040142.2(SCN2A):c.3331G>T (p.Glu1111Ter)Pathogenic
Intellectual disability|Developmental and epileptic encephalopathy, 11
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 1111
NM_001040142.2(SCN2A):c.5318C>T (p.Ala1773Val)Pathogenic
Inborn genetic diseases|Developmental and epileptic encephalopathy, 11;Seizures, benign familial infantile, 3|Complex neurodevelopmental disorder|not provided
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 1773
NM_001040142.2(SCN2A):c.3703C>T (p.Arg1235Ter)Pathogenic
not provided|Developmental and epileptic encephalopathy, 11|Inborn genetic diseases|Seizures, benign familial infantile, 3;Developmental and epileptic encephalopathy, 11
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 1235
NM_001040142.2(SCN2A):c.4766A>G (p.Tyr1589Cys)Pathogenic
Developmental and epileptic encephalopathy, 11;Seizures, benign familial infantile, 3|Seizures, benign familial infantile, 3|Complex neurodevelopmental disorder|Seizures, benign familial infantile, 5
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 1589
NM_001040142.2(SCN2A):c.4454G>A (p.Gly1485Asp)Likely pathogenic
Developmental and epileptic encephalopathy|See cases|Developmental and epileptic encephalopathy, 11
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 1485
NM_001040142.2(SCN2A):c.3631G>A (p.Glu1211Lys)Pathogenic
Developmental and epileptic encephalopathy, 11|Seizures, benign familial infantile, 3|not provided|Developmental and epileptic encephalopathy, 11;Seizures, benign familial infantile, 3|West syndrome|Complex neurodevelopmental disorder|Developmental and epileptic encephalopathy, 11;Seizures, benign familial infantile, 3;Episodic ataxia, type 9
โ˜…โ˜…โ˜†โ˜†2026โ†’ Residue 1211
NM_001040142.2(SCN2A):c.2567G>A (p.Arg856Gln)Pathogenic
Seizure|not provided|Complex neurodevelopmental disorder|Seizures, benign familial infantile, 3;Developmental and epileptic encephalopathy, 11|SCN2A-related disorder
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 856
NM_001040142.2(SCN2A):c.2674G>A (p.Val892Ile)Pathogenic
Seizures, benign familial infantile, 3|not provided|Developmental and epileptic encephalopathy, 11;Seizures, benign familial infantile, 3|Developmental and epileptic encephalopathy, 11;Episodic ataxia, type 9;Seizures, benign familial infantile, 3|Developmental and epileptic encephalopathy, 11
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 892
NM_001040142.2(SCN2A):c.3956G>A (p.Arg1319Gln)Pathogenic
Seizures, benign familial infantile, 3|not provided|Developmental and epileptic encephalopathy, 11;Seizures, benign familial infantile, 3|Developmental and epileptic encephalopathy, 11|Complex neurodevelopmental disorder|Benign familial infantile epilepsy|Developmental and epileptic encephalopathy|benign sporadic infantile epilepsy
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 1319
NM_001040142.2(SCN2A):c.4908C>G (p.Ile1636Met)Pathogenic
not provided|Seizures, benign familial infantile, 3;Developmental and epileptic encephalopathy, 11
โ˜…โ˜…โ˜†โ˜†2025โ†’ Residue 1636
View on ClinVar โ†—
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
SPTBN4Protein interaction100%NFASCProtein interaction100%CALM1Protein interaction99%CALM2Protein interaction99%CALM3Protein interaction99%ANK2Protein interaction97%
Tissue Expression6 tissues
Brain
100%
Ovary
2%
Liver
1%
Heart
1%
Lung
0%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
SCN2ASPTBN4NFASCCALM1CALM2CALM3ANK2
PROTEIN STRUCTURE
Preparing viewerโ€ฆ
PDB4RLY ยท 2.50 ร… ยท X-ray
View on RCSB โ†—
Constraintโ“˜
LOEUFโ“˜
0.16Highly Constrained
pLIโ“˜
1.00Intolerant
Observed/Expected LoF0.11 [0.07โ€“0.16]
RankingsWhere SCN2A stands among ~20K protein-coding genes
  • #2,959of 20,598
    Most Researched153 ยท top quartile
  • #18of 1,025
    FDA-Approved Drug Targets59 ยท top 5%
  • #68of 5,498
    Most Pathogenic Variants694 ยท top 5%
  • #259of 17,882
    Most Constrained (LOEUF)0.16 ยท top 5%
Genes detectedSCN2A
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
Neurodevelopmental disorders-the history and future of a diagnostic conceptโ€ฉ.
PMID: 32699506
Dialogues Clin Neurosci ยท 2020
0.90
3
Progress in Understanding and Treating SCN2A-Mediated Disorders.
PMID: 29691040
Trends Neurosci ยท 2018
0.80
4
CRISPR activation for SCN2A-related neurodevelopmental disorders.
PMID: 40963013
Nature ยท 2025
0.70
5
Impaired cerebellar plasticity hypersensitizes sensory reflexes in SCN2A-associated ASD.
PMID: 38412857
Neuron ยท 2024
0.60