CACNB3
protein-codingcalcium voltage-gated channel auxiliary subunit beta 3, the group of Membrane associated guanylate kinases|Calcium voltage-gated channel auxiliary beta subunits
Gene summary
This gene encodes a regulatory beta subunit of the voltage-dependent calcium channel. Beta subunits are composed of five domains, which contribute to the regulation of surface expression and gating of calcium channels and may also play a role in the regulation of transcription factors and calcium transport. [provided by RefSeq, Oct 2011]
- CACNLB3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CACNB3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000725.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 3 | ||||
| missense | 68 | 68 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 73 | 0 | 0 | 73 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000716.2 | 13 | MANE Select | |
| Ensembl | ENSP00000301050.2 | 13 | MANE Select | |
| RefSeq | NP_001193844.1 | 12 | Standard | |
| RefSeq | NP_001193845.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
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
Molecular Function
- voltage-gated calcium channel activity
- calcium channel regulator activity
- calcium channel activity
- protein binding
- high voltage-gated calcium channel activity
Cellular Component
- cytosol
- plasma membrane
- voltage-gated calcium channel complex
- membrane
- apical plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000301050
- Coding exons
- 13
- Length
- 15148
- Individuals with no LoFs
- 125727
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 21
- Defined
- 125748
- p
- 0.0000835
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.17 | 204 | 312 | 0.654 | 0.0000203 | 3144 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000090 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- LoFtool
- 0.332
- RVIS EVS
- -0.76
- RVIS percentile EVS
- 13.45
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.228
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |