VEGFB

vascular endothelial growth factor B, the group of VEGF family

Basic information

Region (hg38): 11:64234583-64239264

Previous symbols: [ "VRF" ]

Links

ENSG00000173511 ∙ NCBI:7423 ∙ OMIM:601398 ∙ HGNC:12681 ∙ Uniprot:P49765 ∙ 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 VEGFB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VEGFB 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					1	1
missense			22	3	2	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	22	3	3

Variants in VEGFB

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

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

Position	Type	Phenotype	Significance	ClinVar
11-64234841-C-T		not specified	Uncertain significance (Oct 27, 2021)
11-64234861-C-G		not specified	Uncertain significance (Jan 07, 2022)
11-64234864-G-A		not specified	Uncertain significance (Jun 29, 2023)
11-64234886-C-G		not specified	Uncertain significance (Apr 06, 2024)
11-64235465-T-C		not specified	Uncertain significance (Sep 14, 2023)
11-64235483-C-G		not specified	Uncertain significance (Apr 19, 2023)
11-64235840-G-A		not specified	Uncertain significance (Aug 19, 2023)
11-64235842-G-A		not specified	Uncertain significance (Aug 02, 2023)
11-64235856-C-T			Benign (Aug 01, 2018)
11-64235858-G-A		not specified	Uncertain significance (Aug 16, 2021)
11-64235862-G-C		not specified	Uncertain significance (Sep 20, 2023)
11-64235930-C-G		not specified	Uncertain significance (Dec 18, 2023)
11-64235995-C-G			Likely benign (Nov 01, 2023)
11-64236001-C-T		not specified	Uncertain significance (Dec 13, 2023)
11-64236002-G-A		not specified	Uncertain significance (May 31, 2022)
11-64236266-C-T		not specified	Uncertain significance (Oct 10, 2023)
11-64236302-G-A		not specified	Uncertain significance (Oct 26, 2021)
11-64236318-G-A		not specified	Uncertain significance (Feb 08, 2023)
11-64237214-G-T		not specified	Uncertain significance (Feb 05, 2024)
11-64237220-C-T			Benign (Dec 31, 2019)
11-64237452-G-A			Benign (May 31, 2018)
11-64237461-C-T		not specified	Uncertain significance (Dec 08, 2023)
11-64237506-C-A		not specified	Uncertain significance (Oct 06, 2021)
11-64237511-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-64237529-C-T		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VEGFB	protein_coding	protein_coding	ENST00000309422	6	4250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-9	0.0297	125679	0	63	125742	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.708	152	129	1.18	0.00000806	1303
Missense in Polyphen		38	38.992	0.97457		375
Synonymous	-1.30	68	55.7	1.22	0.00000388	457
Loss of Function	-0.862	12	9.18	1.31	3.91e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000709	0.000699
Ashkenazi Jewish	0.000110	0.0000992
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000275	0.000273
Middle Eastern	0.000435	0.000435
South Asian	0.000295	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Growth factor for endothelial cells. VEGF-B167 binds heparin and neuropilin-1 whereas the binding to neuropilin-1 of VEGF-B186 is regulated by proteolysis.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Focal adhesion - Homo sapiens (human);Relaxin signaling pathway - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);VEGF Signaling Pathway;Heart Development;Focal Adhesion;miR-148a-miR-31-FIH1-HIF1α-Notch signaling in glioblastoma;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Signal Transduction;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;GPCR signaling-G alpha s Epac and ERK;VEGF ligand-receptor interactions;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;GPCR signaling-G alpha s PKA and ERK;Hemostasis;VEGF binds to VEGFR leading to receptor dimerization;Signaling by VEGF;GPCR signaling-G alpha i;Signaling by Receptor Tyrosine Kinases;VEGF;VEGF and VEGFR signaling network;VEGFR1 specific signals (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.245
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.15

Haploinsufficiency Scores

• pHI: 0.308
• hipred: N
• hipred_score: 0.396
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.519

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vegfb
• 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); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism 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

Zebrafish Information Network

• Gene name: vegfba
• Affected structure: hyaloid vessel
• Phenotype tag: abnormal
• Phenotype quality: hypoplastic

Gene ontology

• Biological process: angiogenesis;response to hypoxia;positive regulation of protein phosphorylation;positive regulation of endothelial cell proliferation;sprouting angiogenesis;platelet degranulation;protein O-linked glycosylation;regulation of signaling receptor activity;vascular endothelial growth factor signaling pathway;response to drug;positive regulation of angiogenesis;vascular endothelial growth factor receptor signaling pathway;positive chemotaxis;induction of positive chemotaxis;positive regulation of cell division;cardiac muscle contraction;positive regulation of mast cell chemotaxis;coronary vasculature development
• Cellular component: extracellular region;extracellular space;membrane;platelet alpha granule lumen
• Molecular function: vascular endothelial growth factor receptor binding;protein binding;growth factor activity;heparin binding;chemoattractant activity;protein homodimerization activity;vascular endothelial growth factor receptor 1 binding;protein heterodimerization activity