Affinage

SCN3B

Sodium channel regulatory subunit beta-3 · UniProt Q9NY72

Length
215 aa
Mass
24.7 kDa
Annotated
2026-06-10
19 papers in source corpus 14 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 4/5 claims corpus-supported (80%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SCN3B encodes the voltage-gated sodium channel β3-subunit (Navβ3), an auxiliary subunit that physically associates with the cardiac α-subunit Nav1.5 (SCN5A) to control the magnitude and kinetics of cardiac sodium current (PMID:11744748, PMID:20042427). Co-expression with Nav1.5 increases functional channel density at the plasma membrane and modulates gating by shifting steady-state inactivation and slowing recovery from inactivation (PMID:11744748). Genetic ablation in mice establishes that this subunit is required for normal ventricular and atrial electrophysiology: Scn3b-null myocytes show reduced peak Na+ current and altered inactivation, and intact hearts develop conduction abnormalities and arrhythmia susceptibility (PMID:19351516, PMID:19796257). Human loss-of-function missense and in-frame deletion variants cause Brugada syndrome, idiopathic ventricular fibrillation, and atrial fibrillation through two distinct mechanisms: impaired trafficking of Nav1.5 to the cell surface (PMID:20042427, PMID:23257389, PMID:38450374), and direct impairment of channel conduction or gating despite normal surface expression and Nav1.5 association, including dominant-negative effects on the wild-type subunit (PMID:20558140, PMID:39761910). Beyond its channel role, SCN3B is a direct p53 transcriptional target whose product localizes to the endoplasmic reticulum and drives p53-dependent apoptosis (PMID:15334053), and its transcription is further controlled by an IL-2/p53 input and by GATA4 acting at its promoter (PMID:26728597, PMID:36362949).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2001 High

    Established that SCN3B is a functional auxiliary subunit of the cardiac sodium channel rather than a silent partner, defining its core biophysical action on Nav1.5.

    Evidence Xenopus oocyte co-expression of Scn3b with SCN5a with macropatch electrophysiology, Northern and Western blot

    PMID:11744748

    Open questions at the time
    • Did not map the physical interaction interface with Nav1.5
    • Performed in oocytes, not native cardiomyocytes
  2. 2004 High

    Revealed a non-channel role for SCN3B as a direct p53 target gene and proapoptotic effector, separating its transcriptional regulation from its electrophysiological function.

    Evidence ChIP and reporter assays mapping two p53 response elements, plus adenoviral overexpression with apoptosis/colony-formation assays and ER immunolocalization

    PMID:15334053

    Open questions at the time
    • Mechanism linking ER-localized SCN3B to apoptosis not defined
    • Relationship between the proapoptotic role and the channel-modulatory role unresolved
  3. 2009 High

    Demonstrated in vivo that SCN3B is necessary for normal cardiac sodium current and conduction across both ventricular and atrial tissue, moving beyond heterologous systems.

    Evidence Scn3b knockout mice with whole-cell patch clamp, Langendorff perfusion, in vivo ECG and burst pacing

    PMID:19351516 PMID:19796257

    Open questions at the time
    • Did not resolve whether the deficit is trafficking versus gating in native myocytes
    • Sino-atrial node molecular mechanism not dissected
  4. 2009 High

    Linked a human SCN3B variant to arrhythmia and identified impaired Nav1.5 trafficking as a disease mechanism, while confirming the physical Navβ3–Nav1.5 association.

    Evidence V54G variant from an IVF patient studied by patch clamp, co-immunoprecipitation and trafficking immunocytochemistry in HEK-293/COS cells

    PMID:20042427

    Open questions at the time
    • Single patient variant
    • Did not test whether trafficking defect is direct or via misfolding
  5. 2010 Medium

    Expanded the disease spectrum to atrial fibrillation and showed that loss-of-function can occur with or without trafficking impairment, including a dominant-negative conduction defect.

    Evidence Patch clamp of AF-associated R6K/L10P/M161T mutants and surface biotinylation plus dominant-negative co-expression of A130V in HEK293/Nav1.5 cells

    PMID:20558140 PMID:21051419

    Open questions at the time
    • Molecular basis of the conduction-only A130V defect not structurally resolved
    • Single-lab functional characterization
  6. 2012 Medium

    Connected SCN3B to Brugada syndrome through a trafficking-dependent loss-of-function variant, reinforcing trafficking as a recurrent disease mechanism.

    Evidence Val110Ile variant studied by patch clamp and surface-expression assays in transfected cells

    PMID:23257389

    Open questions at the time
    • Single-lab study
    • No native cardiomyocyte validation
  7. 2016 High

    Showed transcriptional control of SCN3B by an IL-2/p53 input and demonstrated a developmentally regulated compensatory role for SCN3B in masking SCN5A mutant phenotypes.

    Evidence qRT-PCR/Western/patch clamp in HL-1 and HEK293 cells for IL-2 regulation, and SCN3B knockdown plus heterologous rescue in LQTS3/BrS iPSC-derived cardiomyocytes

    PMID:26728597 PMID:27677334

    Open questions at the time
    • IL-2 effect on sodium current shown to be partly SCN3B-independent, leaving the direct contribution unclear
    • Developmental switch governing embryonic SCN3B expression undefined
  8. 2022 Medium

    Defined upstream transcriptional and post-transcriptional regulators of SCN3B, placing it within GATA4-driven promoter regulation and a miR-190a-5p/IL-2 axis.

    Evidence Luciferase reporter and GATA4 interaction assays for 5′UTR variants, and luciferase/patch clamp/ELISA/FISH for the miR-190a-5p/IL-2 axis

    PMID:35083300 PMID:36362949

    Open questions at the time
    • GATA4 occupancy not confirmed in cardiomyocytes in vivo
    • Single-lab reporter-based evidence
  9. 2025 High

    Resolved that some Brugada-associated SCN3B loss-of-function arises from localized structural perturbation impairing gating and channel availability rather than trafficking or Nav1.5 binding.

    Evidence ΔT138 in-frame deletion analyzed by circular dichroism, biotinylation, co-IP, surface cross-linking, patch clamp and computational modelling

    PMID:39761910

    Open questions at the time
    • No high-resolution structure of the Navβ3–Nav1.5 complex
    • Mechanism by which the β3 perturbation alters α-subunit gating not defined at atomic level

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the dual identity of SCN3B — as a membrane sodium-channel β-subunit and as an ER-localized p53-dependent proapoptotic effector — is integrated within a single cell remains unresolved.
  • No study connects the channel-modulatory and apoptotic functions mechanistically
  • No structural model of the Navβ3–Nav1.5 interaction in the corpus

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 4 GO:0140110 transcription regulator activity 2
Localization
GO:0005886 plasma membrane 4 GO:0005783 endoplasmic reticulum 1
Pathway
R-HSA-112316 Neuronal System 3 R-HSA-5357801 Programmed Cell Death 1
Partners
Complex memberships
voltage-gated sodium channel (Nav1.5/SCN5A complex)

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2001 SCN3B (Scn3b) co-expression with the cardiac alpha-subunit SCN5a in Xenopus oocytes produced a ~3-fold increase in functional sodium channel expression, suggesting SCN3B improves efficiency of channel trafficking to the plasma membrane. SCN3B also caused a significant depolarising shift in the half-voltage of steady-state inactivation compared to SCN5a alone, and recovery from inactivation was significantly slower for SCN5a+SCN3b than for SCN5a+SCN1b. Xenopus oocyte co-expression, cell-attached macropatch electrophysiology, Northern blot, Western blot The Journal of physiology High 11744748
2004 SCN3B is a p53-inducible gene: p53 directly binds two functional response elements (RE1 upstream of exon 1, RE2 in intron 3) as shown by chromatin immunoprecipitation and reporter assays. SCN3B protein localises to the endoplasmic reticulum, and overexpression of SCN3B induces apoptosis and suppresses colony formation, identifying it as a proapoptotic effector downstream of p53. Chromatin immunoprecipitation, reporter gene assay, cDNA representational difference analysis, adenovirus-mediated overexpression, immunofluorescence localisation Oncogene High 15334053
2009 In Scn3b knockout mice, ventricular myocytes showed reduced peak Na+ current densities and a negatively shifted inactivation curve. Intact Langendorff-perfused Scn3b−/− hearts displayed shorter ventricular effective refractory periods and inducible ventricular tachycardias, establishing that Scn3b is required for normal ventricular sodium channel function and electrophysiology. Scn3b knockout mice (homologous recombination), whole-cell patch clamp on isolated myocytes, Langendorff perfusion electrophysiology, RT-PCR Progress in biophysics and molecular biology High 19351516
2009 Scn3b knockout mice exhibit atrial electrophysiological abnormalities including slower heart rate, prolonged PR interval, longer sinus node recovery times, and susceptibility to atrial tachycardia/fibrillation upon burst pacing, demonstrating a role for Scn3b in sino-atrial node function and intracardiac conduction. Scn3b knockout mice, in vivo ECG recordings, Langendorff-perfused atrial electrograms, burst pacing protocols, immunofluorescence, RT-PCR Acta physiologica High 19796257
2009 A novel SCN3B missense mutation V54G (Navbeta3-V54G), identified in an idiopathic ventricular fibrillation patient, significantly decreased peak sodium current and caused a positive shift of inactivation when co-expressed with Nav1.5. Co-immunoprecipitation demonstrated physical association of Navbeta3 with Nav1.5, and immunocytochemistry showed the V54G mutation dramatically reduced trafficking of Nav1.5 to the plasma membrane. Whole-cell patch clamp (HEK-293 and COS cells), co-immunoprecipitation, immunocytochemistry Cardiovascular research High 20042427
2010 Three SCN3B missense mutations (R6K, L10P, M161T) identified in lone atrial fibrillation patients all caused loss-of-function reduction in cardiac sodium current when expressed electrophysiologically, supporting a mechanistic link between SCN3B loss of function and AF susceptibility. Direct sequencing, electrophysiological studies (heterologous expression patch clamp) Cardiovascular research Medium 21051419
2010 SCN3B mutation A130V dramatically decreased cardiac sodium current density in HEK293/Nav1.5 stable cells without affecting activation/inactivation kinetics or cell surface expression of Nav1.5 or SCN3B. When co-expressed with wild-type SCN3B, A130V negated wild-type function, demonstrating a dominant-negative mechanism that does not involve impaired trafficking but likely impairs ion conduction. Whole-cell patch clamp, biotinylation-based surface protein isolation, Western blot, co-expression dominant-negative assay Biochemical and biophysical research communications High 20558140
2012 SCN3B mutation Val110Ile, found in Brugada syndrome patients, impaired cytoplasmic trafficking of Nav1.5, decreased Nav1.5 cell surface expression in transfected cells, and significantly reduced whole-cell sodium currents, establishing a trafficking-dependent loss-of-function mechanism for this BrS-associated variant. Direct sequencing, transfection, whole-cell patch clamp, surface expression assay (immunofluorescence/Western blot) Circulation journal Medium 23257389
2016 IL-2 upregulates SCN3B transcript and protein expression (via p53) in HL-1 cardiomyocytes and increases sodium current density. The effect of IL-2 on sodium currents was shown to be independent of SCN3B itself (IL-2 increased sodium current even when SCN3B was separately manipulated), placing IL-2-p53-SCN3B in a regulatory pathway modulating cardiac sodium channel activity. qRT-PCR, Western blot, whole-cell patch clamp, HEK293 and HL-1 cells BMC cardiovascular disorders Medium 26728597
2016 SCN3B is highly expressed in embryonic hearts and iPSC-derived cardiomyocytes. In a heterologous expression system, SCN3B augmented INa of mutated SCN5A (E1784K). Knockdown of SCN3B in LQTS3/BrS iPSC-derived cardiomyocytes unmasked the Brugada syndrome electrophysiological phenotype, demonstrating that embryonic SCN3B expression compensates for the loss-of-function effect of this SCN5A mutation. iPSC-derived cardiomyocytes, heterologous expression electrophysiology, SCN3B knockdown, patch clamp Scientific reports High 27677334
2022 Two rare variants in the 5′UTR of SCN3B (c.-324C>A and c.-303C>T) were identified in lone AF patients. Functional reporter assays showed that the c.-324C>A (A allele) increases SCN3B transcriptional activity, and this effect is enhanced by interaction with transcription factor GATA4, identifying GATA4 as a transcriptional regulator of SCN3B. Luciferase reporter assay, transcription factor binding assay (GATA4 interaction) Life (Basel, Switzerland) Medium 36362949
2022 miR-190a-5p directly downregulates IL-2, and this reduces the IL-2-driven increase in SCN3B sodium current; inhibition of miR-190a-5p reversed this suppression, establishing a miR-190a-5p/IL-2/SCN3B axis in cardiac arrhythmias. Luciferase reporter assay, qRT-PCR, whole-cell patch clamp, ELISA, FISH Frontiers in cardiovascular medicine Medium 35083300
2025 A novel SCN3B in-frame deletion (ΔT138) associated with Brugada syndrome caused highly localised structural perturbations (confirmed by circular dichroism spectroscopy) without grossly disrupting protein architecture. Biotinylation and co-immunoprecipitation showed normal surface expression and interaction with Nav1.5, yet patch clamp revealed reduced peak current, decreased channel availability, and accelerated fast inactivation (especially when WT and ΔT138 β3 were co-expressed), consistent with a loss-of-function affecting gating rather than trafficking. Site-directed mutagenesis, circular dichroism spectroscopy, biotinylation, co-immunoprecipitation, surface cross-linking, whole-cell patch clamp, computational modelling Journal of molecular and cellular cardiology High 39761910
2024 A Scn3b P87I mutation in a Brugada syndrome patient reduced peak INa by ~60% without altering activation/inactivation half-maximal voltages or late sodium current. Confocal imaging and Western blot demonstrated decreased plasma membrane localisation of both SCN3B and Nav1.5 (SCN5A), indicating loss of function via impaired trafficking. Whole-cell patch clamp, confocal immunofluorescence, Western blot, computational action potential simulation Frontiers in cardiovascular medicine Medium 38450374

Source papers

Stage 0 corpus · 19 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2010 Mutations in sodium channel β-subunit SCN3B are associated with early-onset lone atrial fibrillation. Cardiovascular research 99 21051419
2001 The sodium channel beta-subunit SCN3b modulates the kinetics of SCN5a and is expressed heterogeneously in sheep heart. The Journal of physiology 92 11744748
2024 Is the voltage-gated sodium channel β3 subunit (SCN3B) a biomarker for glioma? Functional & integrative genomics 65 39289188
2010 Functional dominant-negative mutation of sodium channel subunit gene SCN3B associated with atrial fibrillation in a Chinese GeneID population. Biochemical and biophysical research communications 65 20558140
2009 Loss-of-function mutation of the SCN3B-encoded sodium channel {beta}3 subunit associated with a case of idiopathic ventricular fibrillation. Cardiovascular research 63 20042427
2012 Novel SCN3B mutation associated with brugada syndrome affects intracellular trafficking and function of Nav1.5. Circulation journal : official journal of the Japanese Circulation Society 60 23257389
2004 Identification of SCN3B as a novel p53-inducible proapoptotic gene. Oncogene 60 15334053
2009 Scn3b knockout mice exhibit abnormal ventricular electrophysiological properties. Progress in biophysics and molecular biology 53 19351516
2016 Regulation of SCN3B/scn3b by Interleukin 2 (IL-2): IL-2 modulates SCN3B/scn3b transcript expression and increases sodium current in myocardial cells. BMC cardiovascular disorders 45 26728597
2009 Scn3b knockout mice exhibit abnormal sino-atrial and cardiac conduction properties. Acta physiologica (Oxford, England) 44 19796257
2016 Embryonic type Na+ channel β-subunit, SCN3B masks the disease phenotype of Brugada syndrome. Scientific reports 37 27677334
2019 Effects of GRM4, SCN2A and SCN3B polymorphisms on antiepileptic drugs responsiveness and epilepsy susceptibility. Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society 17 31297029
2022 Two Novel Functional Mutations in Promoter Region of SCN3B Gene Associated with Atrial Fibrillation. Life (Basel, Switzerland) 6 36362949
2022 miR-190a-5p Partially Represses the Abnormal Electrical Activity of SCN3B in Cardiac Arrhythmias by Downregulation of IL-2. Frontiers in cardiovascular medicine 5 35083300
2025 A novel SCN3B in-frame codon deletion in a Brugada syndrome patient: Implications for disrupted NaV1.5 function. Journal of molecular and cellular cardiology 3 39761910
2024 Enterotoxin-related genes PPFIA4 and SCN3B promote colorectal cancer development and progression. Journal of biochemical and molecular toxicology 3 38769694
2010 Mutational analysis of SCN2B, SCN3B and SCN4B in a large Chinese Han family with generalized tonic-clonic seizure. Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology 3 20730464
2024 Identification of a novel Scn3b mutation in a Chinese Brugada syndrome pedigree: implications for Nav1.5 electrophysiological properties and intracellular distribution of Nav1.5 and Navβ3. Frontiers in cardiovascular medicine 1 38450374
2025 SCN3B is an Anti-breast Cancer Molecule with Migration Inhibition Effect. Biochemical genetics 0 40072811

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