CAVIN3
protein-codingcaveolae associated protein 3, the group of Cavins
Gene summary
The protein encoded by this gene was identified as a binding protein of the protein kinase C, delta (PRKCD). The expression of this gene in cultured cell lines is strongly induced by serum starvation. The expression of this protein was found to be down-regulated in various cancer cell lines, suggesting the possible tumor suppressor function of this protein. [provided by RefSeq, Jul 2008]
- PRKCDBP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~1.6 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 CAVIN3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_145040.3. 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 | 0 | |||||
| missense | 61 | 1 | 62 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 61 | 1 | 0 | 62 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_659477.2 | 2 | MANE Select | |
| Ensembl | ENSP00000307292.3 | 2 | MANE Select | |
| Ensembl | ENSP00000432047.1 | 3 | Standard | |
| Ensembl | ENSP00000432047.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Beta-agonist/Beta-blocker Pathway, Pharmacodynamics
Biological Process
- cortical actin cytoskeleton organization
- circadian regulation of gene expression
- negative regulation of protein kinase B signaling
- positive regulation of ERK1 and ERK2 cascade
- negative regulation of fermentation
Molecular Function
- protein kinase C binding
- protein binding
Cellular Component
- cytoplasm
- cytosol
- caveola
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000303927
- Coding exons
- 2
- Length
- 1702
- Individuals with no LoFs
- 124303
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 122
- Defined
- 124426
- p
- 0.000494
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.329 | 148 | 137 | 1.08 | 0.00000640 | 1586 |
| Missense (PolyPhen) | 57 | 57.328 | 0.99428 | 660 | ||
| Synonymous | -0.400 | 69 | 64.9 | 1.06 | 0.00000309 | 594 |
| Loss of Function | -0.0969 | 6 | 5.75 | 1.04 | 2.53e-7 | 67 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000059 | 0.000029 | rare |
| Ashkenazi Jewish | 0.011 | 0.010 | notable |
| East Asian | 0.000061 | 0.000055 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00015 | 0.00014 | rare |
| South Asian | 0.000072 | 0.000065 | rare |
| Other | 0.00036 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulates the traffic and/or budding of caveolae (PubMed:19262564). Plays a role in caveola formation in a tissue- specific manner. Required for the formation of caveolae in smooth muscle but not in the lung and heart endothelial cells. Regulates the equilibrium between cell surface-associated and cell surface- dissociated caveolae by promoting the rapid release of caveolae from the cell surface. Plays a role in the regulation of the circadian clock. Modulates the period length and phase of circadian gene expression and also regulates expression and interaction of the core clock components PER1/2 and CRY1/2 (By similarity). {ECO:0000250|UniProtKB:Q91VJ2, ECO:0000250|UniProtKB:Q9Z1H9, ECO:0000269|PubMed:19262564}.;
Recessive Scores
- pRec
- 0.230
Essentials
- Essential (gene trap)
- N