CACNB3

calcium voltage-gated channel auxiliary subunit beta 3, the group of Membrane associated guanylate kinases|Calcium voltage-gated channel auxiliary beta subunits

Basic information

Region (hg38): 12:48813794-48828941

Previous symbols: [ "CACNLB3" ]

Links

ENSG00000167535NCBI:784OMIM:601958HGNC:1403Uniprot:P54284AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CACNB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CACNB3 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
0
missense
30
clinvar
30
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 30 0 0

Variants in CACNB3

This is a list of pathogenic ClinVar variants found in the CACNB3 region.

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

Position Type Phenotype Significance ClinVar
12-48818934-A-T not specified Uncertain significance (Jun 07, 2023)2559146
12-48818946-A-G not specified Uncertain significance (Apr 23, 2024)3262869
12-48818967-C-T not specified Uncertain significance (Nov 27, 2023)3136495
12-48823360-A-G not specified Uncertain significance (Feb 27, 2024)3136497
12-48823369-G-T not specified Uncertain significance (Jan 06, 2023)2474216
12-48823389-G-A not specified Uncertain significance (Feb 22, 2023)2469925
12-48823408-G-A not specified Uncertain significance (Jul 25, 2023)2590978
12-48823420-G-A not specified Uncertain significance (Dec 15, 2022)2335333
12-48823700-C-T not specified Uncertain significance (May 09, 2023)2519865
12-48823792-C-T not specified Uncertain significance (Apr 12, 2022)2283419
12-48824267-A-C not specified Uncertain significance (Mar 24, 2023)2529446
12-48824285-C-T not specified Uncertain significance (Sep 14, 2022)2311881
12-48824333-C-T not specified Uncertain significance (Aug 17, 2022)2307914
12-48824345-A-G not specified Uncertain significance (Feb 28, 2023)2491100
12-48824358-A-T not specified Uncertain significance (Jun 29, 2022)2372066
12-48824661-C-A Benign (Dec 31, 2019)788882
12-48824682-C-G not specified Uncertain significance (May 24, 2023)2524214
12-48824700-A-T not specified Uncertain significance (Mar 29, 2022)2262320
12-48824710-G-A not specified Uncertain significance (Oct 26, 2022)2350697
12-48824712-C-T not specified Uncertain significance (Aug 11, 2022)2383454
12-48825187-G-A not specified Uncertain significance (Oct 12, 2021)2379513
12-48825725-G-A not specified Uncertain significance (Mar 25, 2024)3262868
12-48825748-T-G not specified Uncertain significance (Sep 26, 2023)3136498
12-48826492-G-A not specified Uncertain significance (Apr 08, 2024)3262867
12-48826849-C-T not specified Uncertain significance (Dec 15, 2022)2335064

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CACNB3protein_codingprotein_codingENST00000301050 1315148
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0002890.9991257270211257480.0000835
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.172043120.6540.00002033144
Missense in Polyphen83150.140.552811539
Synonymous0.5981121200.9310.00000730956
Loss of Function3.011128.30.3890.00000146299

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001520.000152
Ashkenazi Jewish0.000.00
East Asian0.0001130.000109
Finnish0.000.00
European (Non-Finnish)0.0001150.000114
Middle Eastern0.0001130.000109
South Asian0.00006530.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Regulatory subunit of the voltage-gated calcium channel that gives rise to L-type calcium currents (PubMed:8119293). Increases CACNA1B peak calcium current and shifts the voltage dependencies of channel activation and inactivation (By similarity). Increases CACNA1C peak calcium current and shifts the voltage dependencies of channel activation and inactivation (By similarity). {ECO:0000250|UniProtKB:P54287, ECO:0000250|UniProtKB:Q9MZL3, ECO:0000269|PubMed:8119293}.;
Pathway
Oxytocin signaling pathway - Homo sapiens (human);Cardiac muscle contraction - Homo sapiens (human);Dilated cardiomyopathy (DCM) - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Arrhythmogenic Right Ventricular Cardiomyopathy;Myometrial Relaxation and Contraction Pathways;MAPK Signaling Pathway;Calcium Regulation in the Cardiac Cell;Developmental Biology;GPCR Dopamine D1like receptor;Metabolism;Regulation of insulin secretion;Neuronal System;Phase 0 - rapid depolarisation;Phase 2 - plateau phase;Cardiac conduction;Muscle contraction;Presynaptic depolarization and calcium channel opening;NCAM signaling for neurite out-growth;NCAM1 interactions;Transmission across Chemical Synapses;Axon guidance;Integration of energy metabolism (Consensus)

Recessive Scores

pRec
0.116

Intolerance Scores

loftool
0.332
rvis_EVS
-0.76
rvis_percentile_EVS
13.45

Haploinsufficiency Scores

pHI
0.333
hipred
Y
hipred_score
0.601
ghis
0.618

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.228

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cacnb3
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); immune system phenotype; homeostasis/metabolism phenotype; muscle phenotype;

Gene ontology

Biological process
calcium ion transport;chemical synaptic transmission;neuromuscular junction development;T cell receptor signaling pathway;detection of mechanical stimulus involved in sensory perception of pain;membrane depolarization;calcium ion transport into cytosol;calcium ion transmembrane transport via high voltage-gated calcium channel;protein localization to plasma membrane;positive regulation of protein targeting to membrane;cellular response to oxygen-glucose deprivation;regulation of membrane repolarization during action potential;regulation of voltage-gated calcium channel activity;negative regulation of voltage-gated calcium channel activity;positive regulation of high voltage-gated calcium channel activity;regulation of membrane hyperpolarization;negative regulation of detection of mechanical stimulus involved in sensory perception of touch;positive regulation of excitatory postsynaptic potential
Cellular component
cytosol;plasma membrane;voltage-gated calcium channel complex;membrane;apical plasma membrane;L-type voltage-gated calcium channel complex
Molecular function
voltage-gated calcium channel activity;calcium channel regulator activity;calcium channel activity;protein binding;high voltage-gated calcium channel activity;protein kinase binding