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SCN2B

sodium voltage-gated channel beta subunit 2, the group of Sodium voltage-gated channel beta subunits|V-set domain containing

Basic information

Region (hg38): 11:118162805-118176639

Links

ENSG00000149575NCBI:6327OMIM:601327HGNC:10589Uniprot:O60939AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Brugada syndrome (Limited), mode of inheritance: AD
  • Brugada syndrome (Supportive), mode of inheritance: AD
  • familial atrial fibrillation (Supportive), mode of inheritance: AD
  • atrial fibrillation, familial, 14 (Moderate), mode of inheritance: AD
  • Brugada syndrome 1 (Disputed Evidence), mode of inheritance: AD
  • atrial fibrillation, familial, 14 (Limited), mode of inheritance: Unknown
  • atrial fibrillation, familial, 14 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Atrial fibrillation, familial 14ADCardiovascularIn Atrial fibrillation, surveillance (eg, with echocardiogram and electrocardiogram) may allow early management, which may be beneficialCardiovascular19808477

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCN2B gene.

  • Atrial fibrillation, familial, 14 (110 variants)
  • Cardiovascular phenotype (85 variants)
  • not provided (29 variants)
  • not specified (12 variants)
  • Inborn genetic diseases (4 variants)
  • Primary dilated cardiomyopathy (1 variants)
  • SCN2B-related condition (1 variants)
  • Variant of unknown significance (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCN2B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
48
clinvar
48
missense
82
clinvar
6
clinvar
88
nonsense
0
start loss
0
frameshift
3
clinvar
3
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
1
2
non coding
1
clinvar
12
clinvar
11
clinvar
24
Total 0 0 87 66 11

Variants in SCN2B

This is a list of pathogenic ClinVar variants found in the SCN2B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
11-118166849-G-A Benign (Jun 13, 2018)1296386
11-118166882-A-C Atrial fibrillation, familial, 14 Uncertain significance (Mar 18, 2020)2435691
11-118166891-T-A Cardiovascular phenotype Uncertain significance (Aug 07, 2021)1753587
11-118166895-C-T Atrial fibrillation, familial, 14 • Cardiovascular phenotype Conflicting classifications of pathogenicity (Dec 06, 2023)947137
11-118166896-G-A Atrial fibrillation, familial, 14 Likely benign (Oct 23, 2023)1096955
11-118166901-C-G Cardiovascular phenotype Uncertain significance (Dec 16, 2022)2496754
11-118166903-T-C Variant of unknown significance • Atrial fibrillation, familial, 14 • Cardiovascular phenotype Uncertain significance (Aug 04, 2023)60776
11-118166905-C-T Atrial fibrillation, familial, 14 Likely benign (Jul 17, 2019)1141620
11-118166906-G-A Atrial fibrillation, familial, 14 • Cardiovascular phenotype Uncertain significance (Jan 08, 2024)191493
11-118166909-TT-GG Cardiovascular phenotype • Atrial fibrillation, familial, 14 Conflicting classifications of pathogenicity (Nov 27, 2023)422854
11-118166913-C-T Atrial fibrillation, familial, 14 Uncertain significance (Jun 03, 2023)1378025
11-118166919-C-T Atrial fibrillation, familial, 14 Uncertain significance (Jul 19, 2022)1520112
11-118166920-G-A Atrial fibrillation, familial, 14 • Cardiovascular phenotype Likely benign (Oct 07, 2021)415258
11-118166923-C-T Atrial fibrillation, familial, 14 • Cardiovascular phenotype Benign/Likely benign (Sep 04, 2023)1165438
11-118166924-G-A Atrial fibrillation, familial, 14 • Cardiovascular phenotype Likely benign (Sep 28, 2022)655020
11-118166937-C-T Cardiovascular phenotype Uncertain significance (Aug 31, 2021)1750888
11-118166938-C-T Cardiovascular phenotype Likely benign (Jun 06, 2019)1750826
11-118166941-G-A Atrial fibrillation, familial, 14 Likely benign (Aug 25, 2020)1086808
11-118166942-G-C Cardiovascular phenotype Uncertain significance (Dec 04, 2022)2447543
11-118166947-C-T Cardiovascular phenotype Likely benign (Nov 07, 2022)2447542
11-118166950-G-A Atrial fibrillation, familial, 14 Likely benign (Jan 14, 2023)2782512
11-118166957-G-A Cardiovascular phenotype • Atrial fibrillation, familial, 14 Uncertain significance (Oct 04, 2023)1749641
11-118166957-G-C Atrial fibrillation, familial, 14 • Cardiovascular phenotype Conflicting classifications of pathogenicity (Jan 04, 2024)408874
11-118166959-G-A Cardiovascular phenotype Likely benign (Sep 13, 2020)1749524
11-118166959-G-T Cardiovascular phenotype Uncertain significance (Mar 19, 2023)2562613

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SCN2Bprotein_codingprotein_codingENST00000278947 414723
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.001710.7231257301171257480.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3171201300.9220.000008751419
Missense in Polyphen4051.5370.77615545
Synonymous-0.7656355.71.130.00000400425
Loss of Function0.82757.430.6733.25e-793

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008700.0000870
Ashkenazi Jewish0.000.00
East Asian0.0005980.000598
Finnish0.00004620.0000462
European (Non-Finnish)0.00003530.0000264
Middle Eastern0.0005980.000598
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Crucial in the assembly, expression, and functional modulation of the heterotrimeric complex of the sodium channel. The subunit beta-2 causes an increase in the plasma membrane surface area and in its folding into microvilli. Interacts with TNR may play a crucial role in clustering and regulation of activity of sodium channels at nodes of Ranvier (By similarity). {ECO:0000250}.;
Disease
DISEASE: Note=Genetic variations in SCN2B may be involved in Brugada syndrome (PubMed:23559163). This tachyarrhythmia is characterized by right bundle branch block and ST segment elevation on an electrocardiogram (ECG). It can cause the ventricles to beat so fast that the blood is prevented from circulating efficiently in the body. When this situation occurs, the individual will faint and may die in a few minutes if the heart is not reset. {ECO:0000269|PubMed:23559163}.;
Pathway
Antiarrhythmic Pathway, Pharmacodynamics;Developmental Biology;Phase 0 - rapid depolarisation;Cardiac conduction;Muscle contraction;Interaction between L1 and Ankyrins;L1CAM interactions;Axon guidance (Consensus)

Recessive Scores

pRec
0.133

Intolerance Scores

loftool
0.268
rvis_EVS
-0.45
rvis_percentile_EVS
24

Haploinsufficiency Scores

pHI
0.214
hipred
N
hipred_score
0.345
ghis
0.707

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.248

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Scn2b
Phenotype
homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process
chemical synaptic transmission;nervous system development;sodium ion transmembrane transport;response to pyrethroid;cardiac muscle contraction;regulation of atrial cardiac muscle cell membrane depolarization;cardiac muscle cell action potential involved in contraction;membrane depolarization during cardiac muscle cell action potential;regulation of heart rate by cardiac conduction;regulation of sodium ion transmembrane transporter activity
Cellular component
voltage-gated sodium channel complex
Molecular function
voltage-gated ion channel activity;sodium channel regulator activity;voltage-gated sodium channel activity involved in cardiac muscle cell action potential