mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for VEGFA
Gene summary
Basic gene Info.Gene symbolVEGFA
Gene namevascular endothelial growth factor A
SynonymsMVCD1|VEGF|VPF
CytomapUCSC genome browser: 6p12
Type of geneprotein-coding
RefGenesNM_001025366.2,
NM_001025367.2,NM_001025368.2,NM_001025369.2,NM_001025370.2,
NM_001033756.2,NM_001171622.1,NM_001171623.1,NM_001171624.1,
NM_001171625.1,NM_001171626.1,NM_001171627.1,NM_001171628.1,
NM_001171629.1,NM_001171630.1,NM_001204384.1,NM_001204385.1,
NM_001287044.1,NM_003376.5,
Descriptionvascular permeability factor
Modification date20141222
dbXrefs MIM : 192240
HGNC : HGNC
Ensembl : ENSG00000112715
HPRD : 01889
Vega : OTTHUMG00000014745
ProteinUniProt: P15692
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_VEGFA
BioGPS: 7422
PathwayNCI Pathway Interaction Database: VEGFA
KEGG: VEGFA
REACTOME: VEGFA
Pathway Commons: VEGFA
ContextiHOP: VEGFA
ligand binding site mutation search in PubMed: VEGFA
UCL Cancer Institute: VEGFA
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0000122negative regulation of transcription from RNA polymerase II promoter18093989
GO:0001525angiogenesis11427521
GO:0001666response to hypoxia16490744
GO:0001934positive regulation of protein phosphorylation18386220
GO:0001938positive regulation of endothelial cell proliferation10022831
GO:0002042cell migration involved in sprouting angiogenesis18059339
GO:0002092positive regulation of receptor internalization20660291
GO:0002575basophil chemotaxis17082651
GO:0008284positive regulation of cell proliferation7929439
GO:0008360regulation of cell shape10527820
GO:0010595positive regulation of endothelial cell migration10022831
GO:0010628positive regulation of gene expression18386220
GO:0030224monocyte differentiation21149635
GO:0030225macrophage differentiation21149635
GO:0030335positive regulation of cell migration17470632
GO:0030823regulation of cGMP metabolic process16150726
GO:0030949positive regulation of vascular endothelial growth factor receptor signaling pathway1312256
GO:0031334positive regulation of protein complex assembly16489009
GO:0031954positive regulation of protein autophosphorylation17470632
GO:0032147activation of protein kinase activity18059339
GO:0032793positive regulation of CREB transcription factor activity20497126
GO:0033138positive regulation of peptidyl-serine phosphorylation18440775
GO:0035148tube formation19033661
GO:0035767endothelial cell chemotaxis18440775
GO:0035924cellular response to vascular endothelial growth factor stimulus18440775
GO:0038033positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway18440775
GO:0038084vascular endothelial growth factor signaling pathway23639442
GO:0038091positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway17470632
GO:0043117positive regulation of vascular permeability16109918
GO:0043154negative regulation of cysteine-type endopeptidase activity involved in apoptotic process18386220
GO:0043406positive regulation of MAP kinase activity18440775
GO:0043536positive regulation of blood vessel endothelial cell migration18440775
GO:0045766positive regulation of angiogenesis18440775
GO:0045785positive regulation of cell adhesion19674970
GO:0045944positive regulation of transcription from RNA polymerase II promoter18059339
GO:0048010vascular endothelial growth factor receptor signaling pathway21245381
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation10022831
GO:0050918positive chemotaxis19275959
GO:0050927positive regulation of positive chemotaxis12744932
GO:0050930induction of positive chemotaxis19275959
GO:0051272positive regulation of cellular component movement10527820
GO:0051894positive regulation of focal adhesion assembly16489009
GO:0060754positive regulation of mast cell chemotaxis19275959
GO:0070374positive regulation of ERK1 and ERK2 cascade23639442
GO:0071456cellular response to hypoxia10575000
GO:0090037positive regulation of protein kinase C signaling18059339
GO:0090050positive regulation of cell migration involved in sprouting angiogenesis20551324
GO:1900086positive regulation of peptidyl-tyrosine autophosphorylation20660291
GO:1900745positive regulation of p38MAPK cascade18386220
GO:1901727positive regulation of histone deacetylase activity20497126
GO:1902966positive regulation of protein localization to early endosome23639442
GO:1903572positive regulation of protein kinase D signaling20497126


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Ligand binding site mutations for VEGFA
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
 : non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
Q113H112RCOAD1
R108R108LLUAD1
Q113H112YOV1
Y65,D67P66LSKCM1
Q113,I109P111LSKCM1
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.


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Protein structure related information for VEGFA
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
Y65P66L-0.96755392
D67P66L-0.96755392
R108R108L-0.8447906
Q113P111L-0.50924953
I109P111L-0.50924953
Q113H112Y-0.33234322
Q113H112R-0.2941577
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for VEGFA from PDB

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Differential gene expression and gene-gene network for VEGFA
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of VEGFA and the right PPI network was created from samples without mutations in the LBS of VEGFA. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for VEGFA
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0027627Neoplasm Metastasis312AlteredExpression, Biomarker
umls:C0017636Glioblastoma92AlteredExpression, Biomarker
umls:C0007131Carcinoma, Non-Small-Cell Lung85Biomarker, GeneticVariation
umls:C0011884Diabetic Retinopathy77AlteredExpression, Biomarker, GeneticVariation
umls:C0242383Macular Degeneration76Biomarker, GeneticVariation
umls:C0007137Carcinoma, Squamous Cell65AlteredExpression, Biomarker, GeneticVariation
umls:C0027651Neoplasms61AlteredExpression, Biomarker, GeneticVariation
umls:C1956346Coronary Artery Disease44Biomarker, GeneticVariation, Therapeutic
umls:C0003873Arthritis, Rheumatoid44Biomarker, GeneticVariation
umls:C0011860Diabetes Mellitus, Type 242Biomarker, GeneticVariation
umls:C0035309Retinal Diseases41Biomarker, GeneticVariation
umls:C0151744Myocardial Ischemia34Biomarker, GeneticVariation, Therapeutic
umls:C0004096Asthma32AlteredExpression, Biomarker, GeneticVariation
umls:C0033578Prostatic Neoplasms30AlteredExpression, Biomarker, GeneticVariation
umls:C0011881Diabetic Nephropathies30Biomarker, GeneticVariation
umls:C0004153Atherosclerosis28AlteredExpression, Biomarker, GeneticVariation
umls:C0009375Colonic Neoplasms20AlteredExpression, Biomarker, GeneticVariation
umls:C0033860Psoriasis20AlteredExpression, Biomarker, GeneticVariation
umls:C0006118Brain Neoplasms18AlteredExpression, Biomarker
umls:C0085109Corneal Neovascularization16Biomarker
umls:C0023890Liver Cirrhosis14Biomarker, GeneticVariation
umls:C0002395Alzheimer Disease10Biomarker, GeneticVariation
umls:C0021368Inflammation10AlteredExpression, Biomarker, GeneticVariation
umls:C0027686Neovascularization, Pathologic10AlteredExpression, Biomarker, GeneticVariation
umls:C0271051Macular Edema10Biomarker, GeneticVariation
umls:C0018801Heart Failure9Biomarker, GeneticVariation
umls:C0038358Stomach Ulcer7Biomarker, GeneticVariation
umls:C0018923Hemangiosarcoma7Biomarker
umls:C0024115Lung Diseases7Biomarker
umls:C0014170Endometrial Neoplasms6AlteredExpression, Biomarker, GeneticVariation
umls:C0035412Rhabdomyosarcoma6Biomarker
umls:C0032927Precancerous Conditions6Biomarker, GeneticVariation
umls:C0023470Leukemia, Myeloid4Biomarker
umls:C0020541Hypertension, Portal4Biomarker, Therapeutic
umls:C0035328Retinal Vein Occlusion3AlteredExpression, Biomarker
umls:C0600518Choroidal Neovascularization3Biomarker, GeneticVariation
umls:C0011853Diabetes Mellitus, Experimental3Biomarker
umls:C0018671Head and Neck Neoplasms3Biomarker, GeneticVariation
umls:C0242350Erectile Dysfunction3Biomarker, GeneticVariation
umls:C2717961Thrombotic Microangiopathies3Biomarker
umls:C0027659Neoplasms, Experimental3Biomarker, Therapeutic
umls:C0270611Brain Injuries2Biomarker, Therapeutic
umls:C0008677Bronchitis, Chronic2Biomarker
umls:C0887833Carcinoma, Pancreatic Ductal2Biomarker
umls:C0018799Heart Diseases2Biomarker
umls:C2609414Acute Kidney Injury2Biomarker, Therapeutic
umls:C0023893Liver Cirrhosis, Experimental2Biomarker, Therapeutic
umls:C0037929Spinal Cord Injuries1Biomarker
umls:C0993582Arthritis, Experimental1Biomarker
umls:C2937358Cerebral Hemorrhage1Biomarker
umls:C0014556Epilepsy, Temporal Lobe1Biomarker
umls:C0206726Gliosarcoma1Biomarker
umls:C0023186Learning Disorders1Therapeutic
umls:C0085605Liver Failure1Therapeutic
umls:C0025261Memory Disorders1Therapeutic
umls:C0027055Myocardial Reperfusion Injury1Biomarker
umls:C0029422Osteochondrodysplasias1Therapeutic
umls:C0033687Proteinuria1Biomarker
umls:C0038220Status Epilepticus1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for VEGFA
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
Approved|investigationalDB00112BevacizumabBiotech
Approved|investigationalDB01017MinocyclineSmall molecule
ApprovedDB01120GliclazideSmall molecule
Approved|investigationalDB01136CarvedilolSmall molecule
ApprovedDB01270RanibizumabBiotech
ExperimentalDB03088Pyroglutamic AcidSmall molecule
ApprovedDB03754TrisSmall molecule
ApprovedDB05294VandetanibSmall molecule
InvestigationalDB05434ABT-510Small molecule
InvestigationalDB05890VEGF-ASSmall molecule
ApprovedDB06779DalteparinSmall molecule
ApprovedDB08885AfliberceptBiotech

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of VEGFA go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of VEGFA
Multiple alignments for P15692 in multiple species
LBSAA sequence# speciesSpecies
C130HNKCECRPKKD2Homo sapiens, Bos taurus
C130HSRCECRPKKD2Mus musculus, Rattus norvegicus
C130HSKCDCRPKKD1Gallus gallus
C130HSKCECRPKKD1Canis lupus familiaris
D67FQEYPDEIEYI4Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris
D67FQEYPDEVEYI1Gallus gallus
D67FQEYPDEIEFI1Bos taurus
D89GGCCNDEGLEC2Homo sapiens, Canis lupus familiaris
D89AGCCNDEALEC2Mus musculus, Rattus norvegicus
D89AGCCGDEGLEC1Gallus gallus
D89GGCCNDESLEC1Bos taurus
E119SQHIGEMSFLQ3Mus musculus, Rattus norvegicus, Bos taurus
E119GQHIGEMSFLQ2Homo sapiens, Canis lupus familiaris
E119SQHIAHMSFLQ1Gallus gallus
E129QHNKCECRPKK2Homo sapiens, Bos taurus
E129QHSRCECRPKK2Mus musculus, Rattus norvegicus
E129QHSKCDCRPKK1Gallus gallus
E129QHSKCECRPKK1Canis lupus familiaris
E64VDIFQEYPDEI5Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Canis lupus familiaris
E64VDIFQEYPDEV1Gallus gallus
F43HEVVKFMDVYQ4Homo sapiens, Rattus norvegicus, Bos taurus, Canis lupus familiaris
F43NEVIKFLEVYE1Gallus gallus
F43HEVIKFMDVYQ1Mus musculus
G114IKPHQSQHIGE3Mus musculus, Rattus norvegicus, Bos taurus
G114IKPHQGQHIGE2Homo sapiens, Canis lupus familiaris
G114IKPHQSQHIAH1Gallus gallus
G118QSQHIGEMSFL3Mus musculus, Rattus norvegicus, Bos taurus
G118QGQHIGEMSFL2Homo sapiens, Canis lupus familiaris
G118QSQHIAHMSFL1Gallus gallus
H116PHQSQHIGEMS3Mus musculus, Rattus norvegicus, Bos taurus
H116PHQGQHIGEMS2Homo sapiens, Canis lupus familiaris
H116PHQSQHIAHMS1Gallus gallus
I102TEEFNITMQIM2Bos taurus, Canis lupus familiaris
I102TEESNITMQIM1Homo sapiens
I102VDVYNVTMEIA1Gallus gallus
I102TSESNITMQIM1Mus musculus
I102TSESNVTMQIM1Rattus norvegicus
I106NITMQIMRIKP4Homo sapiens, Mus musculus, Bos taurus, Canis lupus familiaris
I106NVTMEIARIKP1Gallus gallus
I106NVTMQIMRIKP1Rattus norvegicus
I109MQIMRIKPHQS3Mus musculus, Rattus norvegicus, Bos taurus
I109MQIMRIKPHQG2Homo sapiens, Canis lupus familiaris
I109MEIARIKPHQS1Gallus gallus
I117HQSQHIGEMSF3Mus musculus, Rattus norvegicus, Bos taurus
I117HQGQHIGEMSF2Homo sapiens, Canis lupus familiaris
I117HQSQHIAHMSF1Gallus gallus
K74IEYIFKPSCVP4Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris
K74VEYIFRPSCVP1Gallus gallus
K74IEFIFKPSCVP1Bos taurus
L92CNDEGLECVPT2Homo sapiens, Canis lupus familiaris
L92CNDEALECVPT2Mus musculus, Rattus norvegicus
L92CGDEGLECVPV1Gallus gallus
L92CNDESLECVPT1Bos taurus
M107ITMQIMRIKPH4Homo sapiens, Mus musculus, Bos taurus, Canis lupus familiaris
M107VTMEIARIKPH1Gallus gallus
M107VTMQIMRIKPH1Rattus norvegicus
M120QHIGEMSFLQH5Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Canis lupus familiaris
M120QHIAHMSFLQH1Gallus gallus
M44EVVKFMDVYQR4Homo sapiens, Rattus norvegicus, Bos taurus, Canis lupus familiaris
M44EVIKFLEVYER1Gallus gallus
M44EVIKFMDVYQR1Mus musculus
N88CGGCCNDEGLE2Homo sapiens, Canis lupus familiaris
N88CAGCCNDEALE2Mus musculus, Rattus norvegicus
N88CAGCCGDEGLE1Gallus gallus
N88CGGCCNDESLE1Bos taurus
P79KPSCVPLMRCG3Homo sapiens, Bos taurus, Canis lupus familiaris
P79KPSCVPLMRCA2Mus musculus, Rattus norvegicus
P79RPSCVPLMRCA1Gallus gallus
Q105SNITMQIMRIK2Homo sapiens, Mus musculus
Q105FNITMQIMRIK2Bos taurus, Canis lupus familiaris
Q105YNVTMEIARIK1Gallus gallus
Q105SNVTMQIMRIK1Rattus norvegicus
Q113RIKPHQSQHIG3Mus musculus, Rattus norvegicus, Bos taurus
Q113RIKPHQGQHIG2Homo sapiens, Canis lupus familiaris
Q113RIKPHQSQHIA1Gallus gallus
Q115KPHQSQHIGEM3Mus musculus, Rattus norvegicus, Bos taurus
Q115KPHQGQHIGEM2Homo sapiens, Canis lupus familiaris
Q115KPHQSQHIAHM1Gallus gallus
Q124EMSFLQHNKCE2Homo sapiens, Bos taurus
Q124EMSFLQHSRCE2Mus musculus, Rattus norvegicus
Q124HMSFLQHSKCD1Gallus gallus
Q124EMSFLQHSKCE1Canis lupus familiaris
Q48FMDVYQRSYCR3Mus musculus, Rattus norvegicus, Canis lupus familiaris
Q48FMDVYQRSYCH1Homo sapiens
Q48FLEVYERSFCR1Gallus gallus
Q48FMDVYQRSFCR1Bos taurus
R108TMQIMRIKPHQ5Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Canis lupus familiaris
R108TMEIARIKPHQ1Gallus gallus
S121HIGEMSFLQHS3Mus musculus, Rattus norvegicus, Canis lupus familiaris
S121HIGEMSFLQHN2Homo sapiens, Bos taurus
S121HIAHMSFLQHS1Gallus gallus
Y47KFMDVYQRSYC4Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris
Y47KFLEVYERSFC1Gallus gallus
Y47KFMDVYQRSFC1Bos taurus
Y51VYQRSYCRPIE3Mus musculus, Rattus norvegicus, Canis lupus familiaris
Y51VYQRSYCHPIE1Homo sapiens
Y51VYERSFCRTIE1Gallus gallus
Y51VYQRSFCRPIE1Bos taurus
Y65DIFQEYPDEIE5Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Canis lupus familiaris
Y65DIFQEYPDEVE1Gallus gallus


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