HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
SCN3B
sodium voltage-gated channel beta subunit 3
Chromosome 11 · 11q24.1
NCBI Gene: 55800Ensembl: ENSG00000166257.11HGNC: HGNC:20665UniProt: Q9NY72
47PubMed Papers
22Diseases
0Drugs
2Pathogenic Variants
FUNCTIONAL ROLE
Ion ChannelTransporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingsodium channel regulator activityregulation of ventricular cardiac muscle cell membrane depolarizationprotein localization to plasma membraneatrial fibrillationfamilial atrial fibrillationcardiac arrhythmiaBrugada syndrome
✦AI Summary

SCN3B encodes the β3 auxiliary subunit of voltage-gated sodium (Nav) channels, serving as a crucial regulatory component that modulates channel trafficking, localization, and functional properties in excitable tissues 1. The protein primarily functions to modulate cardiac sodium channel activity, particularly affecting SCN5A/Nav1.5 channels by causing loss-of-function effects that reduce sodium current density 1. Mechanistically, SCN3B can be regulated by inflammatory mediators like IL-2, which upregulates its transcription through p53-dependent pathways and increases sodium current density in cardiac cells 2. The gene shows tissue-specific regulation, with GATA4 serving as a transcriptional regulator in cardiac tissue 3. Disease associations include cardiac arrhythmias, where loss-of-function mutations in SCN3B contribute to early-onset lone atrial fibrillation by reducing sodium current 1, and gain-of-function promoter variants can also cause atrial fibrillation 3. Recently, biallelic truncating variants have been linked to neurodevelopmental disorders with intellectual disability, autism, and seizures 4. Interestingly, SCN3B also functions independently of ion channel activity in cancer contexts, where it acts as a tumor suppressor by inhibiting cell migration through modulation of actin cytoskeleton organization 56. Clinical significance extends beyond cardiac disorders to potential therapeutic targets in colorectal cancer 7 and epilepsy 8.

Sources cited
1
SCN3B serves as regulatory subunit of cardiac sodium channels and loss-of-function mutations cause early-onset lone atrial fibrillation
PMID: 21051419
2
IL-2 upregulates SCN3B transcription through p53-dependent pathways and increases sodium current density
PMID: 26728597
3
GATA4 serves as transcriptional regulator of SCN3B and gain-of-function promoter variants cause atrial fibrillation
PMID: 36362949
4
Biallelic truncating variants in SCN3B cause neurodevelopmental disorders with intellectual disability and seizures
PMID: 40879121
5
SCN3B inhibits glioma cell migration independently of ion channel activity through actin cytoskeleton modulation
PMID: 40245999
6
SCN3B acts as tumor suppressor in breast cancer by inhibiting cell migration and invasion
PMID: 40072811
7
SCN3B identified as potential therapeutic target in colorectal cancer
PMID: 38769694
8
SCN3B identified as potential therapeutic target for epilepsy treatment
PMID: 26742644
Disease Associationsⓘ22
atrial fibrillationOpen Targets
0.69Moderate
familial atrial fibrillationOpen Targets
0.39Weak
cardiac arrhythmiaOpen Targets
0.36Weak
Brugada syndromeOpen Targets
0.28Weak
polyarteritis nodosaOpen Targets
0.24Weak
Abnormality of the cardiovascular systemOpen Targets
0.19Weak
response to antihypertensive drugOpen Targets
0.19Weak
sudden cardiac arrestOpen Targets
0.14Weak
genetic disorderOpen Targets
0.12Weak
Prolonged QT intervalOpen Targets
0.12Weak
Romano-Ward syndromeOpen Targets
0.10Suggestive
Familial progressive cardiac conduction defectOpen Targets
0.10Suggestive
Familial short QT syndromeOpen Targets
0.09Suggestive
hypertrophic cardiomyopathyOpen Targets
0.08Suggestive
Arrhythmogenic right ventricular dysplasiaOpen Targets
0.08Suggestive
Rare familial disorder with hypertrophic cardiomyopathyOpen Targets
0.08Suggestive
catecholaminergic polymorphic ventricular tachycardiaOpen Targets
0.07Suggestive
dilated cardiomyopathyOpen Targets
0.07Suggestive
cardiac conduction defectOpen Targets
0.07Suggestive
Idiopathic ventricular fibrillation, not Brugada typeOpen Targets
0.07Suggestive
Atrial fibrillation, familial, 16UniProt
Brugada syndrome 7UniProt
Pathogenic Variants2
NM_001040151.2(SCN3B):c.482T>C (p.Met161Thr)Pathogenic
Atrial fibrillation, familial, 16
☆☆☆☆2011→ Residue 161
NM_001040151.2(SCN3B):c.17G>A (p.Arg6Lys)Pathogenic
Atrial fibrillation, familial, 16
☆☆☆☆2011→ Residue 6
View on ClinVar ↗
Related Genes
SCN11AProtein interaction100%CACNA1HProtein interaction92%KCNJ8Protein interaction89%SCN2AProtein interaction88%SCN4AProtein interaction88%SCN9AProtein interaction88%
Tissue Expression6 tissues
Brain
100%
Heart
10%
Ovary
5%
Lung
3%
Bone Marrow
2%
Liver
1%
Gene Interaction Network
Click a node to explore
SCN3BSCN11ACACNA1HKCNJ8SCN2ASCN4ASCN9A
PROTEIN STRUCTURE
Preparing viewer…
PDB4L1D · 2.50 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.68LoF Tolerant
pLIⓘ
0.32Tolerant
Observed/Expected LoF0.41 [0.26–0.68]
RankingsWhere SCN3B stands among ~20K protein-coding genes
  • #9,272of 20,598
    Most Researched47
  • #4,451of 5,498
    Most Pathogenic Variants2
  • #5,024of 17,882
    Most Constrained (LOEUF)0.68
Genes detectedSCN3B
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Enterotoxin-related genes PPFIA4 and SCN3B promote colorectal cancer development and progression.
PMID: 38769694
J Biochem Mol Toxicol · 2024
1.00
2
Identification of novel gene and pathway targets for human epilepsy treatment.
PMID: 26742644
Biol Res · 2016
0.90
3
Two Novel Functional Mutations in Promoter Region of
PMID: 36362949
Life (Basel) · 2022
0.80
4
Biallelic Truncating Variants in SCN3B Encoding Nav Channel Subunit β3 Lead to Neurodevelopmental Phenotype with and without Epilepsy and Ataxia.
PMID: 40879121
Ann Neurol · 2025
0.70
5
Regulation of SCN3B/scn3b by Interleukin 2 (IL-2): IL-2 modulates SCN3B/scn3b transcript expression and increases sodium current in myocardial cells.
PMID: 26728597
BMC Cardiovasc Disord · 2016
0.60