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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
KCNA3
potassium voltage-gated channel subfamily A member 3
Chromosome 1 Β· 1p13.3
NCBI Gene: 3738Ensembl: ENSG00000177272.10HGNC: HGNC:6221UniProt: P22001
140PubMed Papers
20Diseases
7Drugs
16Pathogenic Variants
FUNCTIONAL ROLE
Ion ChannelTransporter
CLINICAL
FDA Approved Target
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
voltage-gated potassium channel activityprotein bindingvoltage-gated potassium channel complexaction potentialmultiple sclerosisMyasthenia gravisLambert-Eaton myasthenic syndromeNeurodevelopmental disorder
✦AI Summary

KCNA3 encodes Kv1.3, a voltage-gated potassium channel critical for immune cell function and neuronal signaling. Despite UniProt annotation suggesting absent channel activity, functional studies demonstrate KCNA3 mediates potassium ion transport and delayed rectifier potassium channel activity 1. JAK2 signaling upregulates KCNA3 channel activity and membrane abundance, linking it to interferon-Ξ³-regulated lymphocyte function 2. De novo heterozygous missense variants in KCNA3 cause developmental and epileptic encephalopathies (DEE), with 86% of carriers presenting severe neurological phenotypes including intellectual disability, epilepsy, and autism spectrum disorder 1. Functional analysis reveals heterogeneous effects ranging from loss-of-function (altered inactivation kinetics, depolarized activation threshold) to mixed loss- and gain-of-function properties 13. The antidepressant fluoxetine shows potential therapeutic benefit for gain-of-function variants 1. Beyond neurology, KCNA3 hypermethylation serves as a biomarker for esophageal cancer detection. A dual-marker blood test targeting methylated KCNA3 and OTOP2 achieves 87.4% sensitivity and 93.3% specificity for esophageal cancer detection with excellent stage-stratified performance 45. KCNA3 also associates with autoimmune pancreatitis susceptibility in genome-wide studies 6.

Sources cited
1
De novo KCNA3 missense variants cause DEE; functional studies reveal loss-of-function and mixed gain/loss-of-function effects; fluoxetine shows potential therapeutic benefit for gain-of-function variants
PMID: 37964487
2
De novo KCNA3-V478M variant in selectivity filter causes loss-of-function properties and early-onset epilepsy; demonstrates KCNA3 role in human epilepsy
PMID: 40472070
3
JAK2 signaling upregulates KCNA3 channel activity and membrane protein abundance; interferon-Ξ³ upregulates voltage-gated K+ current in T cells through JAK2-dependent mechanism
PMID: 25644777
4
KCNA3 hypermethylation in circulating cell-free DNA serves as biomarker for esophageal cancer; IEsohunter test targeting KCNA3 and OTOP2 achieves 87.4% sensitivity and 93.3% specificity
PMID: 38890756
5
KCNA3 methylation in cell-free DNA is ESCC-specific marker; dual-marker panel with KCNA3 and OTOP2 achieves 84.91% sensitivity and 94.32% specificity for esophageal cancer detection
PMID: 37650127
6
KCNA3 identified as susceptibility gene for autoimmune pancreatitis through genome-wide association studies
PMID: 27832379
Disease Associationsβ“˜20
multiple sclerosisOpen Targets
0.60Moderate
Myasthenia gravisOpen Targets
0.56Moderate
Lambert-Eaton myasthenic syndromeOpen Targets
0.56Moderate
Neurodevelopmental disorderOpen Targets
0.53Moderate
Muscle weaknessOpen Targets
0.46Moderate
congenital myasthenic syndromeOpen Targets
0.43Moderate
Congenital myasthenic syndromesOpen Targets
0.43Moderate
neoplasmOpen Targets
0.39Weak
cancerOpen Targets
0.39Weak
epilepsyOpen Targets
0.39Weak
autoimmune diseaseOpen Targets
0.38Weak
cardiac arrhythmiaOpen Targets
0.37Weak
nervous system diseaseOpen Targets
0.37Weak
immune system diseaseOpen Targets
0.37Weak
Intellectual disabilityOpen Targets
0.37Weak
neurodegenerative diseaseOpen Targets
0.37Weak
autoimmune disorder of the nervous systemOpen Targets
0.37Weak
nervous system neoplasmOpen Targets
0.37Weak
neuromuscular diseaseOpen Targets
0.37Weak
paraneoplastic neurologic syndromeOpen Targets
0.37Weak
Pathogenic Variants16
NM_002232.5(KCNA3):c.1430C>A (p.Pro477His)Likely pathogenic
KCNA3-associated disorder|KCNA3-associated developmental and epileptic encephalopathy|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 477
NM_002232.5(KCNA3):c.1328C>T (p.Thr443Ile)Likely pathogenic
Neurodevelopmental disorder|KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜…β˜†β˜†2024β†’ Residue 443
NM_002232.5(KCNA3):c.1424C>G (p.Pro475Arg)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 475
NM_002232.5(KCNA3):c.1460A>G (p.Tyr487Cys)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 487
NM_002232.5(KCNA3):c.1366G>A (p.Gly456Arg)Likely pathogenic
KCNA3-associated disorder
β˜…β˜†β˜†β˜†2024β†’ Residue 456
NM_002232.5(KCNA3):c.1574G>A (p.Ser525Asn)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜†β˜†β˜†2023β†’ Residue 525
NM_002232.5(KCNA3):c.1402G>C (p.Gly468Arg)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜†β˜†β˜†2023β†’ Residue 468
NM_002232.5(KCNA3):c.1403G>T (p.Gly468Val)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜†β˜†β˜†2023β†’ Residue 468
NM_002232.5(KCNA3):c.1402_1403delinsTT (p.Gly468Phe)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜†β˜†β˜†2023β†’ Residue 468
NM_002232.5(KCNA3):c.1378G>A (p.Val460Met)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜†β˜†β˜†2023β†’ Residue 460
NM_002232.5(KCNA3):c.1432G>A (p.Val478Met)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜†β˜†β˜†2023β†’ Residue 478
NM_002232.5(KCNA3):c.1363A>G (p.Ile455Val)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy|not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 455
NM_002232.5(KCNA3):c.32C>G (p.Pro11Arg)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜†β˜†β˜†2023β†’ Residue 11
NM_002232.5(KCNA3):c.1070C>T (p.Ala357Val)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜†β˜†β˜†2023β†’ Residue 357
NM_002232.5(KCNA3):c.1081G>A (p.Ala361Thr)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜†β˜†β˜†2023β†’ Residue 361
NM_002232.5(KCNA3):c.1292T>A (p.Ile431Asn)Likely pathogenic
KCNA3-associated developmental and epileptic encephalopathy
β˜…β˜†β˜†β˜†2023β†’ Residue 431
View on ClinVar β†—
Drug Targets7
AMIFAMPRIDINEApproved
Voltage-gated potassium channel blocker
Myasthenia gravis
AMIFAMPRIDINE PHOSPHATEApproved
Voltage-gated potassium channel blocker
Lambert-Eaton myasthenic syndrome
DALFAMPRIDINEApproved
Voltage-gated potassium channel blocker
multiple sclerosis
GUANIDINEPhase III
Voltage-gated potassium channel blocker
neuroendocrine neoplasm
GUANIDINE HYDROCHLORIDEApproved
Voltage-gated potassium channel blocker
Myasthenia gravis
NERISPIRDINEPhase II
Voltage-gated potassium channel blocker
multiple sclerosis
TEDISAMILApproved
Voltage-gated potassium channel blocker
cardiac arrhythmia
Related Genes
KCNV2Shared pathway100%KCNV1Shared pathway100%KCND1Shared pathway100%KCNA10Shared pathway100%KCNA7Shared pathway100%KCNAB1Protein interaction99%
Tissue Expression6 tissues
Bone Marrow
100%
Brain
28%
Lung
21%
Heart
9%
Liver
3%
Ovary
3%
Gene Interaction Network
Click a node to explore
KCNA3KCNV2KCNV1KCND1KCNA10KCNA7KCNAB1
PROTEIN STRUCTURE
Preparing viewer…
PDB4BGC Β· 1.20 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.78LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.52 [0.36–0.78]
RankingsWhere KCNA3 stands among ~20K protein-coding genes
  • #3,278of 20,598
    Most Researched140 Β· top quartile
  • #295of 1,025
    FDA-Approved Drug Targets5
  • #2,389of 5,498
    Most Pathogenic Variants16
  • #6,359of 17,882
    Most Constrained (LOEUF)0.78
Genes detectedKCNA3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
De novo variants in KCNA3 cause developmental and epileptic encephalopathy.
PMID: 37964487
Ann Neurol Β· 2024
1.00
2
Consistent Safety and Efficacy of Sotatercept for Pulmonary Arterial Hypertension in
PMID: 40035659
Am J Respir Crit Care Med Β· 2025
0.90
3
Non-invasive diagnosis of esophageal cancer by a simplified circulating cell-free DNA methylation assay targeting OTOP2 and KCNA3: a double-blinded, multicenter, prospective study.
PMID: 38890756
J Hematol Oncol Β· 2024
0.80
4
Genome-wide methylation profiling identified methylated KCNA3 and OTOP2 as promising diagnostic markers for esophageal squamous cell carcinoma.
PMID: 37650127
Chin Med J (Engl) Β· 2024
0.70
5
Immunogenetics of IgG4-Related AIP.
PMID: 27832379
Curr Top Microbiol Immunol Β· 2017
0.60