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CAVIN2

caveolae associated protein 2, the group of Cavins

Basic information

Region (hg38): 2:191834309-191847088

Previous symbols: [ "SDPR" ]

Links

ENSG00000168497NCBI:8436OMIM:606728HGNC:10690Uniprot:O95810AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAVIN2 gene.

  • Inborn genetic diseases (5 variants)
  • not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAVIN2 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
2
clinvar
2
clinvar
4
missense
5
clinvar
5
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 2 2

Variants in CAVIN2

This is a list of pathogenic ClinVar variants found in the CAVIN2 region.

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

Position Type Phenotype Significance ClinVar
2-191835949-C-T not specified Uncertain significance (Jan 09, 2024)3137873
2-191835954-G-A not specified Uncertain significance (Apr 13, 2023)2536775
2-191836010-A-G Likely benign (Jun 04, 2018)717193
2-191836074-A-T not specified Uncertain significance (Jun 13, 2023)2560094
2-191836115-C-G not specified Uncertain significance (Jan 30, 2024)3137872
2-191836213-C-T not specified Uncertain significance (Sep 14, 2022)3137897
2-191836374-G-A not specified Uncertain significance (Sep 29, 2023)3137896
2-191836396-C-T not specified Uncertain significance (Nov 07, 2022)3137895
2-191836433-G-T not specified Uncertain significance (Mar 01, 2024)3137894
2-191836458-C-T not specified Uncertain significance (Jan 17, 2024)3137893
2-191836535-C-A not specified Uncertain significance (Nov 17, 2023)3137891
2-191836543-C-T not specified Uncertain significance (Jun 23, 2021)3137890
2-191836588-C-T not specified Uncertain significance (Dec 17, 2023)3137889
2-191836603-C-T not specified Uncertain significance (Dec 19, 2022)3137888
2-191836615-T-C not specified Uncertain significance (Aug 17, 2021)3137887
2-191836632-T-C not specified Uncertain significance (Jun 27, 2023)2597411
2-191836659-T-C not specified Uncertain significance (Apr 20, 2023)2539286
2-191836677-G-A not specified Uncertain significance (Dec 17, 2023)3137885
2-191836682-T-C Benign (Jun 21, 2018)782418
2-191836684-T-C not specified Uncertain significance (Aug 30, 2022)3137884
2-191836693-C-T not specified Uncertain significance (Aug 09, 2021)3137883
2-191836701-G-A not specified Uncertain significance (Jan 09, 2024)3137882
2-191836704-A-T not specified Uncertain significance (Jan 17, 2024)3137881
2-191836713-T-G not specified Uncertain significance (Aug 12, 2021)3137880
2-191836716-T-A not specified Uncertain significance (Jan 24, 2023)2478450

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CAVIN2protein_codingprotein_codingENST00000304141 212954
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
7.24e-90.07961256800681257480.000270
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2462512620.9570.00001732816
Missense in Polyphen8889.6540.98155985
Synonymous0.6741071160.9210.00000866828
Loss of Function-0.2461211.11.087.36e-7123

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003250.000325
Ashkenazi Jewish0.000.00
East Asian0.001850.00185
Finnish0.0001390.000139
European (Non-Finnish)0.0001240.000123
Middle Eastern0.001850.00185
South Asian0.0002290.000229
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays an important role in caveolar biogenesis and morphology. Regulates caveolae morphology by inducing membrane curvature within caveolae (PubMed:19525939). Plays a role in caveola formation in a tissue-specific manner. Required for the formation of caveolae in the lung and fat endothelia but not in the heart endothelia. Negatively regulates the size or stability of CAVIN complexes in the lung endothelial cells. May play a role in targeting PRKCA to caveolae (By similarity). {ECO:0000250|UniProtKB:Q66H98, ECO:0000269|PubMed:19525939}.;
Pathway
Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;EGFR1 (Consensus)

Recessive Scores

pRec
0.272

Intolerance Scores

loftool
rvis_EVS
0.22
rvis_percentile_EVS
68.38

Haploinsufficiency Scores

pHI
0.252
hipred
Y
hipred_score
0.506
ghis
0.479

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Cavin2
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); respiratory system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype;

Zebrafish Information Network

Gene name
cavin2a
Affected structure
dorsal longitudinal anastomotic vessel
Phenotype tag
abnormal
Phenotype quality
aplastic/hypoplastic

Gene ontology

Biological process
plasma membrane tubulation
Cellular component
nucleoplasm;cytoplasm;cytosol;plasma membrane;caveola;actin cytoskeleton;membrane raft
Molecular function
phosphatidylserine binding;protein kinase C binding;protein binding;phospholipid binding