CAVIN3

caveolae associated protein 3, the group of Cavins

Basic information

Region (hg38): 11:6318945-6320532

Previous symbols: [ "PRKCDBP" ]

Links

ENSG00000170955 ∙ NCBI:112464 ∙ OMIM:618303 ∙ HGNC:9400 ∙ Uniprot:Q969G5 ∙ 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 CAVIN3 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAVIN3 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in CAVIN3

This is a list of pathogenic ClinVar variants found in the CAVIN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6319175-C-G		not specified	Uncertain significance (Mar 07, 2023)
11-6319195-C-T		not specified	Uncertain significance (Mar 07, 2023)
11-6319204-C-A		not specified	Uncertain significance (Mar 06, 2023)
11-6319287-T-C		not specified	Uncertain significance (Dec 15, 2022)
11-6319318-G-T		not specified	Uncertain significance (Jun 02, 2023)
11-6319323-G-A		not specified	Uncertain significance (Mar 11, 2024)
11-6319353-G-A		not specified	Uncertain significance (Nov 07, 2022)
11-6319380-C-T		not specified	Uncertain significance (Feb 16, 2023)
11-6319479-T-G		not specified	Uncertain significance (Sep 22, 2023)
11-6319501-G-T		not specified	Uncertain significance (May 01, 2022)
11-6319509-G-T		not specified	Uncertain significance (May 17, 2023)
11-6320140-G-T		not specified	Uncertain significance (Aug 02, 2022)
11-6320193-G-A		not specified	Uncertain significance (Jan 08, 2024)
11-6320197-C-T		not specified	Uncertain significance (Sep 22, 2023)
11-6320290-C-G		not specified	Uncertain significance (Dec 19, 2023)
11-6320293-T-C		not specified	Uncertain significance (Jan 30, 2024)
11-6320301-C-A		not specified	Uncertain significance (Feb 05, 2024)
11-6320427-C-T		not specified	Uncertain significance (Aug 10, 2023)
11-6320452-C-A		not specified	Uncertain significance (Dec 19, 2023)
11-6320460-A-G		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAVIN3	protein_coding	protein_coding	ENST00000303927	2	1702

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000800	0.330	124303	1	122	124426	0.000494

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.329	148	137	1.08	0.00000640	1586
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000589	0.0000589
Ashkenazi Jewish	0.0115	0.0101
East Asian	0.0000610	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.000153	0.000143
Middle Eastern	0.0000610	0.0000545
South Asian	0.0000722	0.0000655
Other	0.000356	0.000328

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: Beta-agonist/Beta-blocker Pathway, Pharmacodynamics (Consensus)

Recessive Scores

• pRec: 0.230

Haploinsufficiency Scores

• pHI: 0.102
• hipred: Y
• hipred_score: 0.506
• ghis: 0.426

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cavin3
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; cellular 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; respiratory system phenotype

Gene ontology

• 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
• Cellular component: cytoplasm;cytosol;caveola;protein-containing complex
• Molecular function: protein kinase C binding;protein binding