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GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SCN9A
sodium voltage-gated channel alpha subunit 9
Chromosome 2 Β· 2q24.3
NCBI Gene: 6335Ensembl: ENSG00000169432.19HGNC: HGNC:10597UniProt: Q15858
203PubMed Papers
23Diseases
81Drugs
177Pathogenic Variants
FUNCTIONAL ROLE
Ion ChannelTransporter
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
FDA Approved TargetOMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
neuronal action potentialnode of Ranvieraxon terminusvoltage-gated sodium channel activityprimary erythermalgiaparoxysmal extreme pain disorderchannelopathy-associated congenital insensitivity to pain, autosomal recessivegeneralized epilepsy with febrile seizures plus, type 7
✦AI Summary

SCN9A encodes Nav1.7, the pore-forming alpha subunit of a voltage-gated sodium channel essential for action potential generation in excitable cells 1. The channel mediates sodium ion influx along the electrochemical gradient, enabling membrane depolarization and electrical signal propagation 2. Nav1.7 is strongly expressed in nociceptive neurons, where it plays a critical and non-redundant role in pain signal transmission 3. Loss-of-function SCN9A mutations cause congenital inability to experience pain, a rare condition where affected individuals completely lack nociception despite normal overall health 3. In contrast, gain-of-function mutations produce excessive nociceptor excitability, resulting in primary erythermalgia and paroxysmal extreme pain disorder (PEPD), characterized by severe, treatment-refractory burning pain in specific anatomical regions 4. Gain-of-function mutations correlating with greater hyperpolarizing shifts in Nav1.7 correlate with earlier symptom onset 5. SCN9A variants also contribute to small fiber neuropathy, affecting thinly myelinated and unmyelinated pain-sensing fibers 6. Despite historical inclusion in epilepsy gene panels, SCN9A is not associated with monogenic epilepsyβ€”high-frequency variants exist in asymptomatic populations, and pathogenic classifications lack supporting clinical evidence 7. These findings position Nav1.7 as a promising selective target for novel analgesic development.

Sources cited
1
Nav1.7 mediates depolarizing phase of action potentials in excitable membranes
PMID: 17145499
2
Sodium channel function in enabling Na+ ion passage and membrane depolarization
PMID: 15385606
3
SCN9A nonsense mutations cause congenital inability to experience pain; Nav1.7 is essential and non-redundant for nociception
PMID: 17167479
4
Gain-of-function SCN9A mutations cause primary erythermalgia and paroxysmal extreme pain disorder; loss-of-function causes insensitivity to pain
PMID: 18060017
5
SCN9A gain-of-function mutations correlating with hyperpolarizing shifts associate with earlier symptom onset in erythromelalgia
PMID: 30416015
6
SCN9A variants found in small fiber neuropathy patients affecting AΞ΄ and C-fibers
PMID: 39433284
7
SCN9A is not associated with monogenic epilepsy; high-frequency variants exist in asymptomatic populations
PMID: 40492992
Disease Associationsβ“˜23
primary erythermalgiaOpen Targets
0.82Strong
paroxysmal extreme pain disorderOpen Targets
0.80Strong
channelopathy-associated congenital insensitivity to pain, autosomal recessiveOpen Targets
0.69Moderate
generalized epilepsy with febrile seizures plus, type 7Open Targets
0.67Moderate
hereditary sensory and autonomic neuropathy type 2Open Targets
0.65Moderate
epilepsyOpen Targets
0.65Moderate
Channelopathy-associated congenital insensitivity to painOpen Targets
0.64Moderate
SeizureOpen Targets
0.64Moderate
hereditary sensory and autonomic neuropathyOpen Targets
0.62Moderate
PainOpen Targets
0.61Moderate
bipolar disorderOpen Targets
0.61Moderate
major depressive disorderOpen Targets
0.60Moderate
migraine disorderOpen Targets
0.60Moderate
partial epilepsyOpen Targets
0.60Moderate
PruritusOpen Targets
0.59Moderate
trigeminal neuralgiaOpen Targets
0.59Moderate
cardiac arrhythmiaOpen Targets
0.58Moderate
amyotrophic lateral sclerosisOpen Targets
0.58Moderate
hemorrhoidOpen Targets
0.58Moderate
Back painOpen Targets
0.58Moderate
Indifference to pain, congenital, autosomal recessiveUniProt
Paroxysmal extreme pain disorderUniProt
Primary erythermalgiaUniProt
Pathogenic Variants177
NM_001365536.1(SCN9A):c.2521C>T (p.Arg841Ter)Pathogenic
not specified|Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A|Channelopathy-associated congenital insensitivity to pain, autosomal recessive
β˜…β˜…β˜†β˜†2026β†’ Residue 841
NM_001365536.1(SCN9A):c.1567C>T (p.Arg523Ter)Pathogenic
Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A|not provided|Channelopathy-associated congenital insensitivity to pain, autosomal recessive
β˜…β˜…β˜†β˜†2026β†’ Residue 523
NM_001365536.1(SCN9A):c.611_612dup (p.Val205fs)Pathogenic
not provided|Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7
β˜…β˜…β˜†β˜†2025β†’ Residue 205
NM_001365536.1(SCN9A):c.4928C>A (p.Ala1643Glu)Pathogenic
not provided|Paroxysmal extreme pain disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 1643
NM_001365536.1(SCN9A):c.2723G>A (p.Trp908Ter)Pathogenic
Channelopathy-associated congenital insensitivity to pain, autosomal recessive|Generalized epilepsy with febrile seizures plus, type 7|Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A
β˜…β˜…β˜†β˜†2025β†’ Residue 908
NM_001365536.1(SCN9A):c.5008A>T (p.Lys1670Ter)Pathogenic
Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 1670
NM_001365536.1(SCN9A):c.829C>T (p.Arg277Ter)Pathogenic
Channelopathy-associated congenital insensitivity to pain, autosomal recessive|Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 277
NM_001365536.1(SCN9A):c.4495C>T (p.Arg1499Ter)Pathogenic
not provided|Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7|Channelopathy-associated congenital insensitivity to pain, autosomal recessive
β˜…β˜…β˜†β˜†2025β†’ Residue 1499
NM_001365536.1(SCN9A):c.2424G>A (p.Trp808Ter)Pathogenic
Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7|Inborn genetic diseases|Channelopathy-associated congenital insensitivity to pain, autosomal recessive
β˜…β˜…β˜†β˜†2025β†’ Residue 808
NM_001365536.1(SCN9A):c.5351del (p.Glu1784fs)Pathogenic
Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7|Inborn genetic diseases|not provided|Channelopathy-associated congenital insensitivity to pain, autosomal recessive|Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus;Channelopathy-associated congenital insensitivity to pain, autosomal recessive;Paroxysmal extreme pain disorder;Primary erythromelalgia
β˜…β˜…β˜†β˜†2025β†’ Residue 1784
NM_001365536.1(SCN9A):c.4399-1C>TLikely pathogenic
Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7|not provided
β˜…β˜…β˜†β˜†2025
NM_001365536.1(SCN9A):c.4415T>C (p.Ile1472Thr)Pathogenic
Paroxysmal extreme pain disorder|Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1472
NM_001365536.1(SCN9A):c.2109dup (p.Glu704Ter)Pathogenic
Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 704
NM_001365536.1(SCN9A):c.3928G>T (p.Val1310Phe)Pathogenic
Paroxysmal extreme pain disorder|Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1310
NM_001365536.1(SCN9A):c.2576T>C (p.Ile859Thr)Pathogenic
Primary erythromelalgia|Abnormality of pain sensation;Acute episodes of neuropathic symptoms|Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A|SCN9A-related peripheral neuropathies associated with increased pain|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 859
NM_001365536.1(SCN9A):c.258+1G>APathogenic
not provided|Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7
β˜…β˜…β˜†β˜†2024
NM_001365536.1(SCN9A):c.4733G>A (p.Trp1578Ter)Pathogenic
Channelopathy-associated congenital insensitivity to pain, autosomal recessive|Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 1578
NM_001365536.1(SCN9A):c.1642C>T (p.Arg548Ter)Pathogenic
Pain insensitivity|Generalized epilepsy with febrile seizures plus, type 7;Neuropathy, hereditary sensory and autonomic, type 2A|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 548
NM_001365536.1(SCN9A):c.2719C>T (p.Arg907Trp)Pathogenic
not provided|Neuropathy, hereditary sensory and autonomic, type 2A;Generalized epilepsy with febrile seizures plus, type 7|Generalized epilepsy with febrile seizures plus;Primary erythromelalgia;Neuropathy, hereditary sensory and autonomic, type 2A;Paroxysmal extreme pain disorder;Channelopathy-associated congenital insensitivity to pain, autosomal recessive|Inborn genetic diseases
β˜…β˜…β˜†β˜†2024β†’ Residue 907
NM_001365536.1(SCN9A):c.1185C>G (p.Asn395Lys)Pathogenic
not provided|SCN9A-related disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 395
View on ClinVar β†—
Drug Targets81
ARTICAINEApproved
Sodium channel alpha subunit blocker
ARTICAINE HYDROCHLORIDEApproved
Sodium channel alpha subunit blocker
AZD3161Phase I
Sodium channel protein type IX alpha subunit blocker
peripheral neuropathy
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
DSP-2230Phase I
Sodium channel protein type X alpha subunit blocker
neuropathic pain
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
PF-05089771Phase II
Sodium channel protein type IX alpha subunit blocker
Chronic pain
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
RG6029Phase I
Sodium channel protein type IX alpha subunit blocker
Chronic pain
RG7893Phase I
Sodium channel protein type IX alpha subunit blocker
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
VIXOTRIGINEPhase III
Sodium channel protein type IX alpha subunit blocker
trigeminal neuralgia
XEN403Phase I
Sodium channel protein type IX alpha subunit blocker
Pain
ZONISAMIDEApproved
Sodium channel alpha subunit blocker
epilepsy
Related Genes
KCNQ2Protein interaction100%FGF13Protein interaction94%CALHM1Protein interaction93%SCN3BProtein interaction88%AGLProtein interaction81%MPV17Protein interaction81%
Tissue Expression6 tissues
Bone Marrow
100%
Liver
63%
Lung
11%
Heart
11%
Brain
6%
Ovary
5%
Gene Interaction Network
Click a node to explore
SCN9AKCNQ2FGF13CALHM1SCN3BAGLMPV17
PROTEIN STRUCTURE
Preparing viewer…
PDB8YHZ Β· 1.62 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.85LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.72 [0.61–0.85]
RankingsWhere SCN9A stands among ~20K protein-coding genes
  • #2,074of 20,598
    Most Researched203 Β· top quartile
  • #16of 1,025
    FDA-Approved Drug Targets59 Β· top 5%
  • #407of 5,498
    Most Pathogenic Variants177 Β· top 10%
  • #7,448of 17,882
    Most Constrained (LOEUF)0.85
Genes detectedSCN9A
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
An SCN9A channelopathy causes congenital inability to experience pain.
PMID: 17167479
Nature Β· 2006
1.00
2
The Evolving Landscape of Small Fiber Neuropathy.
PMID: 39433284
Semin Neurol Β· 2025
0.90
3
Pediatric Erythromelalgia and SCN9A Mutations: Systematic Review and Single-Center Case Series.
PMID: 30416015
J Pediatr Β· 2019
0.80
4
No association between SCN9A and monogenic human epilepsy disorders.
PMID: 33216760
PLoS Genet Β· 2020
0.70
5
Analysis of SCN9A Gene Variants for Acute and Chronic Postoperative Pain and Morphine Consumption After Total Hysterectomy.
PMID: 32403129
Pain Med Β· 2020
0.68