The protein encoded by this gene is a member of the platelet-derived growth factor/vascular endothelial growth factor (PDGF/VEGF) family and is active in angiogenesis, lymphangiogenesis, and endothelial cell growth. This secreted protein undergoes a complex proteolytic maturation, generating multiple processed forms which bind and activate VEGFR-2 and VEGFR-3 receptors. This pr... See more...

Aliases for VEGFD Gene

Aliases for VEGFD Gene

  • Vascular Endothelial Growth Factor D 2 3 4 5
  • VEGF-D 2 3 4
  • C-Fos Induced Growth Factor (Vascular Endothelial Growth Factor D) 2 3
  • FIGF 3 4
  • C-Fos-Induced Growth Factor 4
  • VEGFD 5

External Ids for VEGFD Gene

Previous HGNC Symbols for VEGFD Gene

  • FIGF

Summaries for VEGFD Gene

Entrez Gene Summary for VEGFD Gene

  • The protein encoded by this gene is a member of the platelet-derived growth factor/vascular endothelial growth factor (PDGF/VEGF) family and is active in angiogenesis, lymphangiogenesis, and endothelial cell growth. This secreted protein undergoes a complex proteolytic maturation, generating multiple processed forms which bind and activate VEGFR-2 and VEGFR-3 receptors. This protein is structurally and functionally similar to vascular endothelial growth factor C. Read-through transcription has been observed between this locus and the upstream PIR (GeneID 8544) locus. [provided by RefSeq, Feb 2011]

GeneCards Summary for VEGFD Gene

VEGFD (Vascular Endothelial Growth Factor D) is a Protein Coding gene. Diseases associated with VEGFD include Anal Canal Squamous Cell Carcinoma and Kidney Angiomyolipoma. Among its related pathways are HIF1Alpha Pathway and Signaling by GPCR. An important paralog of this gene is VEGFC.

UniProtKB/Swiss-Prot Summary for VEGFD Gene

  • 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.

Gene Wiki entry for VEGFD Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VEGFD Gene

Genomics for VEGFD Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for VEGFD Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ015384 Promoter/Enhancer 1 EPDnew Ensembl 605.2 -0.2 -188 0.8 SP1 CEBPA CEBPB YY1 NR2F2 NR2F1 RAD21 ZFP91 NR2F6 HNF4A VEGFD BMX PIR RF01045-154 PIR-FIGF
GH0XJ015386 Enhancer 0.2 Ensembl 600.7 -1.1 -1088 0.2 VEGFD BMX PIR RF01045-154 PIR-FIGF
GH0XJ015492 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 5.4 -108.7 -108709 2.2 CTCF PRDM10 IKZF1 ZNF692 BACH1 JUND ZIC2 RBFOX2 PKNOX1 ZNF24 PIR PIR-FIGF VEGFD BMX
GH0XJ015789 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 5.2 -406.5 -406479 2.6 CREB1 PRDM10 ZNF629 RFX1 POLR2A BACH1 LARP7 ZNF143 RBFOX2 PKNOX1 ZRSR2 NONHSAG054084.2 CA5B CA5BP1 VEGFD RF00017-8175 AP1S2
GH0XJ015737 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 5.2 -354.1 -354076 2.6 SP1 CREB1 TEAD4 PRDM10 IKZF1 ZNF692 PRDM1 ZNF143 PATZ1 POLR2A CA5B CLTRN CA5BP1 ENSG00000200620 VEGFD piR-32214-707 lnc-CLTRN-2 ZRSR2 CA5BP1-CA5B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VEGFD on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VEGFD

Genomic Locations for VEGFD Gene

Genomic Locations for VEGFD Gene
chrX:15,345,596-15,384,413
(GRCh38/hg38)
Size:
38,818 bases
Orientation:
Minus strand
chrX:15,363,713-15,402,535
(GRCh37/hg19)
Size:
38,823 bases
Orientation:
Minus strand

Genomic View for VEGFD Gene

Genes around VEGFD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VEGFD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VEGFD Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for VEGFD Gene

Proteins for VEGFD Gene

  • Protein details for VEGFD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43915-VEGFD_HUMAN
    Recommended name:
    Vascular endothelial growth factor D
    Protein Accession:
    O43915
    Secondary Accessions:
    • B2R7Z3

    Protein attributes for VEGFD Gene

    Size:
    354 amino acids
    Molecular mass:
    40444 Da
    Quaternary structure:
    • Homodimer; non-covalent and antiparallel.

    Three dimensional structures from OCA and Proteopedia for VEGFD Gene

neXtProt entry for VEGFD Gene

Post-translational modifications for VEGFD Gene

  • Undergoes a complex proteolytic maturation which generates a variety of processed secreted forms with increased activity toward VEGFR-3 and VEGFR-2. VEGF-D first form an antiparallel homodimer linked by disulfide bonds before secretion. The fully processed VEGF-D is composed mostly of two VEGF homology domains (VHDs) bound by non-covalent interactions.
  • Glycosylation at Asn155, Asn185, and Asn287
  • Modification sites at PhosphoSitePlus

Other Protein References for VEGFD Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VEGFD Gene

Domains & Families for VEGFD Gene

Gene Families for VEGFD Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted secreted proteins

Protein Domains for VEGFD Gene

InterPro:
Blocks:
  • Platelet-derived growth factor (PDGF)
  • CXCXC repeat
ProtoNet:

Suggested Antigen Peptide Sequences for VEGFD Gene

GenScript: Design optimal peptide antigens:
  • c-Fos-induced growth factor (VEGFD_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O43915

UniProtKB/Swiss-Prot:

VEGFD_HUMAN :
  • Belongs to the PDGF/VEGF growth factor family.
Family:
  • Belongs to the PDGF/VEGF growth factor family.
genes like me logo Genes that share domains with VEGFD: view

Function for VEGFD Gene

Molecular function for VEGFD Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for VEGFD Gene

Gene Ontology (GO) - Molecular Function for VEGFD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005161 platelet-derived growth factor receptor binding TAS 9479493
GO:0005172 vascular endothelial growth factor receptor binding IPI 9435229
GO:0005515 protein binding IPI 27107012
GO:0008083 growth factor activity IBA 21873635
GO:0042056 chemoattractant activity IDA 19275959
genes like me logo Genes that share ontologies with VEGFD: view
genes like me logo Genes that share phenotypes with VEGFD: view

Animal Models for VEGFD Gene

MGI Knock Outs for VEGFD:

Animal Model Products

  • Taconic Biosciences Mouse Models for VEGFD

CRISPR Products

miRNA for VEGFD Gene

miRTarBase miRNAs that target VEGFD

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VEGFD

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VEGFD Gene

Localization for VEGFD Gene

Subcellular locations from UniProtKB/Swiss-Prot for VEGFD Gene

Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VEGFD gene
Compartment Confidence
extracellular 5
plasma membrane 2
cytoskeleton 2
mitochondrion 2
nucleus 2
cytosol 2
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for VEGFD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IEA,IBA 21873635
GO:0016020 membrane IEA --
GO:0031093 platelet alpha granule lumen TAS --
genes like me logo Genes that share ontologies with VEGFD: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for VEGFD Gene

Pathways & Interactions for VEGFD Gene

PathCards logo

SuperPathways for VEGFD Gene

SuperPathway Contained pathways
1 Apoptotic Pathways in Synovial Fibroblasts
.85
.85
.84
.84
.74
.72
.66
.65
.64
.62
.61
.60
.57
.57
2 GPCR Pathway
.73
.73
.62
.59
.58
.58
.55
.38
3 TGF-Beta Pathway
.60
.60
.57
.51
.43
.41
4 ERK Signaling
.61
.61
.58
.51
.49
5 Nanog in Mammalian ESC Pluripotency
.62
.62
.59
.48
genes like me logo Genes that share pathways with VEGFD: view

Pathways by source for VEGFD Gene

1 GeneGo (Thomson Reuters) pathway for VEGFD Gene
  • Development VEGF-family signaling
62 Qiagen pathways for VEGFD Gene
  • 14-3-3 Induced Intracellular Signaling
  • Actin-Based Motility by Rho Family GTPases
  • Activation of cAMP-Dependent PKA
  • Activation of PKA through GPCR
  • Activation of PKC through GPCR

SIGNOR curated interactions for VEGFD Gene

Activates:

Gene Ontology (GO) - Biological Process for VEGFD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IBA 21873635
GO:0001666 response to hypoxia IBA 21873635
GO:0001934 positive regulation of protein phosphorylation IBA 21873635
GO:0001938 positive regulation of endothelial cell proliferation IBA 21873635
GO:0002040 sprouting angiogenesis IBA 21873635
genes like me logo Genes that share ontologies with VEGFD: view

Drugs & Compounds for VEGFD Gene

(6) Drugs for VEGFD Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for VEGFD Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with VEGFD: view

Transcripts for VEGFD Gene

mRNA/cDNA for VEGFD Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VEGFD

Alternative Splicing Database (ASD) splice patterns (SP) for VEGFD Gene

No ASD Table

Relevant External Links for VEGFD Gene

GeneLoc Exon Structure for
VEGFD

Expression for VEGFD Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VEGFD

mRNA Expression by UniProt/SwissProt for VEGFD Gene:

O43915-VEGFD_HUMAN
Tissue specificity: Highly expressed in lung, heart, small intestine and fetal lung, and at lower levels in skeletal muscle, colon, and pancreas.

Evidence on tissue expression from TISSUES for VEGFD Gene

  • Lung(4.6)
  • Heart(3.3)
  • Nervous system(3)
  • Muscle(2.9)
  • Lymph node(2.7)
  • Blood(2.6)
  • Intestine(2.5)
  • Bone marrow(2.4)
  • Kidney(2.3)
  • Eye(2.3)
  • Skin(2.2)
  • Stomach(2.2)
  • Liver(2.1)
  • Spleen(2.1)
  • Pancreas(2.1)
genes like me logo Genes that share expression patterns with VEGFD: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for VEGFD Gene

Orthologs for VEGFD Gene

This gene was present in the common ancestor of chordates.

Orthologs for VEGFD Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia FIGF 30 31
  • 99.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia FIGF 30 31
  • 87.66 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia FIGF 30 31
  • 87.38 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Figf 30 31
  • 86.21 (n)
OneToOne
Vegfd 17
Rat
(Rattus norvegicus)
Mammalia Figf 30
  • 85.47 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia FIGF 31
  • 79 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia FIGF 31
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves FIGF 30 31
  • 73.06 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia FIGF 31
  • 60 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia figf 30
  • 63.41 (n)
Zebrafish
(Danio rerio)
Actinopterygii figf 30 31
  • 56.28 (n)
OneToOne
Species where no ortholog for VEGFD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for VEGFD Gene

ENSEMBL:
Gene Tree for VEGFD (if available)
TreeFam:
Gene Tree for VEGFD (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VEGFD: view image

Paralogs for VEGFD Gene

Paralogs for VEGFD Gene

genes like me logo Genes that share paralogs with VEGFD: view

Variants for VEGFD Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VEGFD Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
740215 Likely Benign: not provided 15,358,015(-) G/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
778978 Benign: not provided 15,355,260(-) T/C NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for VEGFD Gene

Structural Variations from Database of Genomic Variants (DGV) for VEGFD Gene

Variant ID Type Subtype PubMed ID
esv3558643 CNV deletion 23714750
nsv528343 CNV gain 19592680
nsv6813 CNV deletion 18451855

Variation tolerance for VEGFD Gene

Residual Variation Intolerance Score: 56.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.35; 41.83% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VEGFD Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VEGFD

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VEGFD Gene

Disorders for VEGFD Gene

MalaCards: The human disease database

(33) MalaCards diseases for VEGFD Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
anal canal squamous cell carcinoma
  • squamous cell carcinoma of the anal canal
kidney angiomyolipoma
  • angiomyolipoma of kidney
primary lymphedema
  • lymphedema primary
breast ductal carcinoma
  • duct carcinoma
lymphangioleiomyomatosis
  • lam
- elite association - COSMIC cancer census association via MalaCards
Search VEGFD in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with VEGFD: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VEGFD Gene

Publications for VEGFD Gene

  1. Human FIGF: cloning, gene structure, and mapping to chromosome Xp22.1 between the PIGA and the GRPR genes. (PMID: 9479493) Rocchigiani M … Oliviero S (Genomics 1998) 2 3 4 23
  2. Biosynthesis of vascular endothelial growth factor-D involves proteolytic processing which generates non-covalent homodimers. (PMID: 10542248) Stacker SA … Achen MG (The Journal of biological chemistry 1999) 3 4 23
  3. Vascular endothelial growth factor D (VEGF-D) is a ligand for the tyrosine kinases VEGF receptor 2 (Flk1) and VEGF receptor 3 (Flt4). (PMID: 9435229) Achen MG … Stacker SA (Proceedings of the National Academy of Sciences of the United States of America 1998) 3 4 23
  4. Molecular cloning of a novel vascular endothelial growth factor, VEGF-D. (PMID: 9205122) Yamada Y … Hirata Y (Genomics 1997) 3 4 23
  5. [Expressions of VEGF-C and VEGF-D and their correlation with lymphangiogenesis and angiogenesis in gallbladder carcinoma]. (PMID: 20450586) Jiang L … Wang XX (Zhonghua zhong liu za zhi [Chinese journal of oncology] 2010) 3 23

Products for VEGFD Gene

  • Addgene plasmids for VEGFD

Sources for VEGFD Gene