BVES

blood vessel epicardial substance

Basic information

Region (hg38): 6:105096822-105137157

Links

ENSG00000112276 ∙ NCBI:11149 ∙ OMIM:604577 ∙ HGNC:1152 ∙ Uniprot:Q8NE79 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive limb-girdle muscular dystrophy type 2X (Moderate), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2X (Supportive), mode of inheritance: AR
• tetralogy of fallot (Limited), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy type 2X (Strong), mode of inheritance: AR
• autosomal recessive limb-girdle muscular dystrophy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, limb-girdle, autosomal recessive, 25	AR	Cardiovascular	Individuals have been described as developing cardiac arrhythmias in early adulthood, and awareness may allow prompt diagnosis, surveillance, and management	Cardiovascular; Musculoskeletal	26642364

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BVES 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				3		3
missense		2	35	2	3	42
nonsense		3				3
start loss						0
frameshift		2	1			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1	1	3
non coding				11	18	29
Total	0	7	36	16	21

Variants in BVES

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

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

Position	Type	Phenotype	Significance	ClinVar
6-105100845-A-T			Likely benign (Sep 18, 2018)
6-105100975-C-T		Autosomal recessive limb-girdle muscular dystrophy type 2X	Benign (Jul 14, 2021)
6-105101099-T-C		Autosomal recessive limb-girdle muscular dystrophy type 2X	Uncertain significance (Oct 10, 2019)
6-105101109-T-C		Inborn genetic diseases	Uncertain significance (Sep 24, 2024)
6-105101139-C-T		Autosomal recessive limb-girdle muscular dystrophy type 2X	Uncertain significance (Jul 08, 2019)
6-105101158-T-C			Likely benign (Aug 01, 2024)
6-105101171-G-T		Inborn genetic diseases	Uncertain significance (Jul 11, 2023)
6-105101178-T-A		Inborn genetic diseases	Uncertain significance (Oct 16, 2024)
6-105101198-T-C		Inborn genetic diseases	Uncertain significance (Aug 01, 2024)
6-105115676-G-A			Benign (Dec 31, 2019)
6-105115705-G-GA		Autosomal recessive limb-girdle muscular dystrophy type 2X	Uncertain significance (Mar 01, 2019)
6-105115706-G-A		Autosomal recessive limb-girdle muscular dystrophy type 2X	Uncertain significance (Mar 16, 2020)
6-105115707-T-C		Autosomal recessive limb-girdle muscular dystrophy type 2X	Uncertain significance (Jun 27, 2023)
6-105115712-C-T		Autosomal recessive limb-girdle muscular dystrophy type 2X • Inborn genetic diseases	Uncertain significance (Nov 27, 2024)
6-105115713-G-A		Autosomal recessive limb-girdle muscular dystrophy type 2X	Uncertain significance (Oct 22, 2019)
6-105115734-C-T		Inborn genetic diseases • Autosomal recessive limb-girdle muscular dystrophy type 2X	Uncertain significance (Jan 21, 2025)
6-105115749-A-T		Inborn genetic diseases	Uncertain significance (May 16, 2024)
6-105115768-C-T		Autosomal recessive limb-girdle muscular dystrophy type 2X	Uncertain significance (Jun 06, 2019)
6-105115799-C-T		BVES-related disorder	Uncertain significance (Oct 10, 2023)
6-105115802-A-G		BVES-related disorder	Benign/Likely benign (May 01, 2024)
6-105115803-G-C		Autosomal recessive limb-girdle muscular dystrophy type 2X	Uncertain significance (Dec 24, 2019)
6-105115808-T-C		Inborn genetic diseases • Autosomal recessive limb-girdle muscular dystrophy type 2X	Uncertain significance (Sep 01, 2021)
6-105116009-A-G			Likely benign (Sep 22, 2018)
6-105116015-C-A			Benign (Jul 06, 2018)
6-105116431-CCT-C			Likely benign (Sep 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BVES	protein_coding	protein_coding	ENST00000314641	7	40353

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000934	0.937	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.716	168	196	0.856	0.00000982	2370
Missense in Polyphen		48	65.845	0.72899		834
Synonymous	-0.0702	70	69.3	1.01	0.00000359	665
Loss of Function	1.74	11	19.3	0.571	0.00000122	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000663	0.000663
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000164	0.000163
South Asian	0.0000750	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell adhesion molecule involved in the establishment and/or maintenance of cell integrity. Involved in the formation and regulation of the tight junction (TJ) paracellular permeability barrier in epithelial cells (PubMed:16188940). Plays a role in VAMP3-mediated vesicular transport and recycling of different receptor molecules through its interaction with VAMP3. Plays a role in the regulation of cell shape and movement by modulating the Rho-family GTPase activity through its interaction with ARHGEF25/GEFT. Induces primordial adhesive contact and aggregation of epithelial cells in a Ca(2+)-independent manner. Also involved in striated muscle regeneration and repair and in the regulation of cell spreading (By similarity). Important for the maintenance of cardiac function. Plays a regulatory function in heart rate dynamics mediated, at least in part, through cAMP- binding and, probably, by increasing cell surface expression of the potassium channel KCNK2 and enhancing current density (PubMed:26642364). Is also a caveolae-associated protein important for the preservation of caveolae structural and functional integrity as well as for heart protection against ischemia injury. {ECO:0000250|UniProtKB:Q5PQZ7, ECO:0000250|UniProtKB:Q9ES83, ECO:0000269|PubMed:16188940, ECO:0000269|PubMed:26642364}.
• Pathway: Tight junction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.955
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.304
• hipred: N
• hipred_score: 0.415
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bves
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); muscle phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: bves
• Affected structure: red sensitive photoreceptor cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: positive regulation of receptor recycling;regulation of heart rate;hematopoietic progenitor cell differentiation;response to ischemia;heart development;muscle organ development;skeletal muscle tissue development;regulation of cell shape;vesicle-mediated transport;substrate adhesion-dependent cell spreading;positive regulation of locomotion;regulation of membrane potential;regulation of GTPase activity;vesicle docking;striated muscle cell differentiation;sinoatrial node cell development;cell migration involved in heart development;epithelial cell-cell adhesion;regulation of endocytic recycling
• Cellular component: plasma membrane;caveola;bicellular tight junction;membrane;integral component of membrane;lateral plasma membrane;cell junction;cell projection membrane;sarcolemma
• Molecular function: structural molecule activity;protein binding;cAMP binding