CAVIN2

caveolae associated protein 2, the group of Cavins

Basic information

Region (hg38): 2:191834310-191847088

Previous symbols: [ "SDPR" ]

Links

ENSG00000168497 ∙ NCBI:8436 ∙ OMIM:606728 ∙ HGNC:10690 ∙ Uniprot:O95810 ∙ 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 CAVIN2 gene.

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	2	4
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	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)
2-191835954-G-A		not specified	Uncertain significance (Apr 13, 2023)
2-191835963-G-A		not specified	Uncertain significance (Jun 19, 2024)
2-191836010-A-G			Likely benign (Jun 04, 2018)
2-191836074-A-T		not specified	Uncertain significance (Jun 13, 2023)
2-191836115-C-G		not specified	Uncertain significance (Jan 30, 2024)
2-191836213-C-T		not specified	Uncertain significance (Sep 14, 2022)
2-191836276-C-T		not specified	Uncertain significance (May 20, 2024)
2-191836369-T-G		not specified	Uncertain significance (May 24, 2024)
2-191836374-G-A		not specified	Uncertain significance (Sep 29, 2023)
2-191836396-C-T		not specified	Uncertain significance (Nov 07, 2022)
2-191836433-G-T		not specified	Uncertain significance (Mar 01, 2024)
2-191836458-C-T		not specified	Uncertain significance (Jan 17, 2024)
2-191836535-C-A		not specified	Uncertain significance (Nov 17, 2023)
2-191836543-C-T		not specified	Uncertain significance (Jun 23, 2021)
2-191836588-C-T		not specified	Uncertain significance (Dec 17, 2023)
2-191836603-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-191836615-T-C		not specified	Uncertain significance (Aug 17, 2021)
2-191836632-T-C		not specified	Uncertain significance (Jun 27, 2023)
2-191836659-T-C		not specified	Uncertain significance (Apr 20, 2023)
2-191836677-G-A		not specified	Uncertain significance (Dec 17, 2023)
2-191836682-T-C			Benign (Jun 21, 2018)
2-191836684-T-C		not specified	Uncertain significance (Aug 30, 2022)
2-191836693-C-T		not specified	Uncertain significance (Aug 09, 2021)
2-191836701-G-A		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAVIN2	protein_coding	protein_coding	ENST00000304141	2	12954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.24e-9	0.0796	125680	0	68	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.246	251	262	0.957	0.0000173	2816
Missense in Polyphen		88	89.654	0.98155		985
Synonymous	0.674	107	116	0.921	0.00000866	828
Loss of Function	-0.246	12	11.1	1.08	7.36e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000325	0.000325
Ashkenazi Jewish	0.00	0.00
East Asian	0.00185	0.00185
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.00185	0.00185
South Asian	0.000229	0.000229
Other	0.000163	0.000163

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

• 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_gene_trap: N

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