CAVIN1

caveolae associated protein 1, the group of Cavins

Basic information

Region (hg38): 17:42402449-42423256

Previous symbols: [ "PTRF" ]

Links

ENSG00000177469 ∙ NCBI:284119 ∙ OMIM:603198 ∙ HGNC:9688 ∙ Uniprot:Q6NZI2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Berardinelli-Seip congenital lipodystrophy (Supportive), mode of inheritance: AR
• congenital generalized lipodystrophy type 4 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lipodystrophy, congenital generalized, type 4	AR	Cardiovascular	Among other manifestations, individuals may demonstrate cardiac arrhythmias, and appropriate surveillance and management may be beneficial	Cardiovascular; Endocrine; Gastrointestinal; Musculoskeletal	12116229; 18698612; 19726876; 20300641; 20684003

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CAVIN1 gene.

• Congenital generalized lipodystrophy type 4 (1 variants)
• Congenital generalized lipodystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAVIN1 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			5	9	1	15
missense			38	1		39
nonsense		3				3
start loss						0
frameshift	2	1				3
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			22	17	19	58
Total	2	4	66	27	20

Variants in CAVIN1

This is a list of pathogenic ClinVar variants found in the CAVIN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42402476-C-T		Congenital generalized lipodystrophy type 4	Likely benign (Jan 13, 2018)
17-42402572-C-A		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 12, 2018)
17-42402639-A-G		Congenital generalized lipodystrophy type 4	Likely benign (Jan 13, 2018)
17-42402697-T-G		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 13, 2018)
17-42402732-A-G		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 12, 2018)
17-42402775-G-A		Congenital generalized lipodystrophy type 4	Likely benign (Jan 13, 2018)
17-42402792-G-C		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 13, 2018)
17-42402831-G-A		Congenital generalized lipodystrophy type 4	Likely benign (Apr 27, 2017)
17-42402899-G-C		Congenital generalized lipodystrophy type 4	Likely benign (Apr 27, 2017)
17-42402938-A-G		Congenital generalized lipodystrophy type 4	Benign (Apr 27, 2017)
17-42402983-G-C		Congenital generalized lipodystrophy type 4	Benign (Apr 27, 2017)
17-42403096-A-C		Congenital generalized lipodystrophy type 4	Benign (Apr 27, 2017)
17-42403138-G-A		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 13, 2018)
17-42403179-C-T		Congenital generalized lipodystrophy type 4	Likely benign (Jan 12, 2018)
17-42403208-C-T		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 13, 2018)
17-42403241-C-G		Congenital generalized lipodystrophy type 4	Likely benign (Apr 27, 2017)
17-42403374-C-A		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 13, 2018)
17-42403455-C-T		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 12, 2018)
17-42403473-C-T		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 12, 2018)
17-42403486-A-C		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 12, 2018)
17-42403502-A-G		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 13, 2018)
17-42403577-G-A		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 13, 2018)
17-42403688-G-A		Congenital generalized lipodystrophy type 4	Uncertain significance (Jan 12, 2018)
17-42403689-C-T		Congenital generalized lipodystrophy type 4	Benign (Apr 27, 2017)
17-42403781-C-T		Congenital generalized lipodystrophy type 4	Benign (Apr 27, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAVIN1	protein_coding	protein_coding	ENST00000357037	2	21066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00497	0.895	125730	0	17	125747	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.38	195	257	0.759	0.0000196	2482
Missense in Polyphen		116	153.97	0.75337		1540
Synonymous	1.08	108	123	0.876	0.00000997	806
Loss of Function	1.40	5	9.71	0.515	4.26e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000545	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in caveolae formation and organization. Essential for the formation of caveolae in all tissues (PubMed:18056712, PubMed:18191225, PubMed:19726876). Core component of the CAVIN complex which is essential for recruitment of the complex to the caveolae in presence of calveolin-1 (CAV1). Essential for normal oligomerization of CAV1. Promotes ribosomal transcriptional activity in response to metabolic challenges in the adipocytes and plays an important role in the formation of the ribosomal transcriptional loop. Dissociates transcription complexes paused by DNA-bound TTF1, thereby releasing both RNA polymerase I and pre-RNA from the template (By similarity). {ECO:0000250|UniProtKB:O54724, ECO:0000269|PubMed:18056712, ECO:0000269|PubMed:18191225, ECO:0000269|PubMed:19726876}.
• Disease: DISEASE: Congenital generalized lipodystrophy 4 (CGL4) [MIM:613327]: A disorder characterized by the association of congenital generalized lipodystrophy with muscular dystrophy and cardiac anomalies. Congenital generalized lipodystrophy is characterized by a near complete absence of adipose tissue, extreme insulin resistance, hypertriglyceridemia, hepatic steatosis and early onset of diabetes. {ECO:0000269|PubMed:19726876, ECO:0000269|PubMed:20684003}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Gene expression (Transcription);RNA Polymerase I Transcription Termination;RNA Polymerase I Transcription;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.265

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.593
• hipred: Y
• hipred_score: 0.672
• ghis: 0.622

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Cavin1
• Phenotype: muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; 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); 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); growth/size/body region phenotype; renal/urinary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: cavin1a
• Affected structure: skeletal muscle cell
• Phenotype tag: abnormal
• Phenotype quality: convolute

Gene ontology

• Biological process: transcription initiation from RNA polymerase I promoter;termination of RNA polymerase I transcription;rRNA transcription;positive regulation of cell motility
• Cellular component: nucleus;nucleoplasm;cytoplasm;mitochondrion;endoplasmic reticulum;cytosol;plasma membrane;caveola;protein-containing complex;intracellular membrane-bounded organelle;membrane raft
• Molecular function: RNA binding;protein binding;rRNA primary transcript binding;identical protein binding