VEGFD

vascular endothelial growth factor D, the group of VEGF family

Basic information

Region (hg38): X:15345596-15384413

Previous symbols: [ "FIGF" ]

Links

ENSG00000165197 ∙ NCBI:2277 ∙ OMIM:300091 ∙ HGNC:3708 ∙ Uniprot:O43915 ∙ 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 VEGFD gene.

Variants pathogenicity by type

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

Variants in VEGFD

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

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

Position	Type	Phenotype	Significance	ClinVar
X-15355260-T-C			Benign (Feb 26, 2018)
X-15358015-G-A			Likely benign (Aug 01, 2022)
X-15358162-G-A			Likely benign (Jan 01, 2023)
X-15383862-C-T			Uncertain significance (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VEGFD	protein_coding	protein_coding	ENST00000297904	7	38786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000250	0.768	125715	8	22	125745	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.499	121	137	0.880	0.0000104	2348
Missense in Polyphen		32	42.436	0.75408		697
Synonymous	-0.662	55	49.1	1.12	0.00000378	643
Loss of Function	1.16	9	13.6	0.662	0.00000114	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000460	0.000417
Ashkenazi Jewish	0.00	0.00
East Asian	0.000443	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000111	0.0000791
Middle Eastern	0.000443	0.000326
South Asian	0.000220	0.000131
Other	0.000222	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Growth factor active in angiogenesis, lymphangiogenesis and endothelial cell growth, stimulating their proliferation and migration and also has effects on the permeability of blood vessels. May function in the formation of the venous and lymphatic vascular systems during embryogenesis, and also in the maintenance of differentiated lymphatic endothelium in adults. Binds and activates VEGFR-2 (KDR/FLK1) and VEGFR-3 (FLT4) receptors. {ECO:0000269|PubMed:21148085}.
• 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);Focal Adhesion;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;VEGFR3 signaling in lymphatic endothelium;VEGF binds to VEGFR leading to receptor dimerization;Signaling by VEGF;GPCR signaling-G alpha i;Signaling by Receptor Tyrosine Kinases;VEGF;Alpha9 beta1 integrin signaling events;VEGF and VEGFR signaling network (Consensus)

Recessive Scores

• pRec: 0.182

Intolerance Scores

• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.460
• ghis: 0.513

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Vegfd
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; normal 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); immune system phenotype

Zebrafish Information Network

• Gene name: vegfd
• Affected structure: medial facial lymph vessel
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: angiogenesis;response to hypoxia;positive regulation of protein phosphorylation;positive regulation of endothelial cell proliferation;sprouting angiogenesis;platelet degranulation;cell population proliferation;positive regulation of cell population proliferation;response to bacterium;regulation of signaling receptor activity;vascular endothelial growth factor signaling pathway;positive regulation of angiogenesis;vascular endothelial growth factor receptor signaling pathway;positive chemotaxis;induction of positive chemotaxis;positive regulation of cell division;positive regulation of mast cell chemotaxis;dopaminergic neuron differentiation
• Cellular component: extracellular region;extracellular space;membrane;platelet alpha granule lumen
• Molecular function: platelet-derived growth factor receptor binding;vascular endothelial growth factor receptor binding;protein binding;growth factor activity;chemoattractant activity;protein homodimerization activity;vascular endothelial growth factor receptor 3 binding