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): 12:48813793-48828941

Previous symbols: [ "CACNLB3" ]

Links

ENSG00000167535 ∙ NCBI:784 ∙ OMIM:601958 ∙ HGNC:1403 ∙ Uniprot:P54284 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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			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)
12-48818946-A-G		not specified	Uncertain significance (Apr 23, 2024)
12-48818967-C-T		not specified	Uncertain significance (Nov 27, 2023)
12-48823360-A-G		not specified	Uncertain significance (Feb 27, 2024)
12-48823369-G-T		not specified	Uncertain significance (Jan 06, 2023)
12-48823389-G-A		not specified	Uncertain significance (Feb 22, 2023)
12-48823408-G-A		not specified	Uncertain significance (Jul 25, 2023)
12-48823420-G-A		not specified	Uncertain significance (Dec 15, 2022)
12-48823700-C-T		not specified	Uncertain significance (May 09, 2023)
12-48823792-C-T		not specified	Uncertain significance (Apr 12, 2022)
12-48824267-A-C		not specified	Uncertain significance (Mar 24, 2023)
12-48824285-C-T		not specified	Uncertain significance (Sep 14, 2022)
12-48824333-C-T		not specified	Uncertain significance (Aug 17, 2022)
12-48824345-A-G		not specified	Uncertain significance (Feb 28, 2023)
12-48824358-A-T		not specified	Uncertain significance (Jun 29, 2022)
12-48824661-C-A			Benign (Dec 31, 2019)
12-48824682-C-G		not specified	Uncertain significance (May 24, 2023)
12-48824700-A-T		not specified	Uncertain significance (Mar 29, 2022)
12-48824710-G-A		not specified	Uncertain significance (Oct 26, 2022)
12-48824712-C-T		not specified	Uncertain significance (Aug 11, 2022)
12-48825187-G-A		not specified	Uncertain significance (Oct 12, 2021)
12-48825725-G-A		not specified	Uncertain significance (Mar 25, 2024)
12-48825748-T-G		not specified	Uncertain significance (Sep 26, 2023)
12-48826492-G-A		not specified	Uncertain significance (Apr 08, 2024)
12-48826849-C-T		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CACNB3	protein_coding	protein_coding	ENST00000301050	13	15148

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000289	0.999	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.17	204	312	0.654	0.0000203	3144
Missense in Polyphen		83	150.14	0.55281		1539
Synonymous	0.598	112	120	0.931	0.00000730	956
Loss of Function	3.01	11	28.3	0.389	0.00000146	299

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000113	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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