mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 VWF
Gene summary
Basic gene Info.Gene symbolVWF
Gene namevon Willebrand factor
SynonymsF8VWF|VWD
CytomapUCSC genome browser: 12p13.3
Type of geneprotein-coding
RefGenesNM_000552.3,
Descriptioncoagulation factor VIII VWF
Modification date20141222
dbXrefs MIM : 613160
HGNC : HGNC
Ensembl : ENSG00000110799
HPRD : 01906
Vega : OTTHUMG00000168265
ProteinUniProt: P04275
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_VWF
BioGPS: 7450
PathwayNCI Pathway Interaction Database: VWF
KEGG: VWF
REACTOME: VWF
Pathway Commons: VWF
ContextiHOP: VWF
ligand binding site mutation search in PubMed: VWF
UCL Cancer Institute: VWF
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0007155cell adhesion10764791
GO:0030168platelet activation8565074
GO:0031589cell-substrate adhesion9079671
GO:0051260protein homooligomerization8874190


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Ligand binding site mutations for VWF
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
K1751P1749TLUAD1
H2748H2748NLUSC1
H2748H2748YSKCM1
Y1400Q1402PSTAD1
D2746D2746ESTAD1
R1395R1395WTHCA1
R1392R1392WUCEC1
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 VWF
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
Y1400Q1402P0.50421876
H2748H2748N-1.629445
H2748H2748Y-1.2680594
R1392R1392W-1.1875335
R1395R1395W-0.80534595
K1751P1749T-0.56132889
D2746D2746E-0.26264431
(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 VWF from PDB

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Differential gene expression and gene-gene network for VWF
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 VWF and the right PPI network was created from samples without mutations in the LBS of VWF. 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 VWF
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1264039von Willebrand Disease, Type 196Biomarker, GeneticVariation
umls:C1264041von Willebrand Disease, Type 343Biomarker, GeneticVariation
umls:C1282971von Willebrand disease type 2B34Biomarker, GeneticVariation
umls:C1264040von Willebrand Disease, Type 226Biomarker, GeneticVariation
umls:C1282968von Willebrand disease type 2A22Biomarker, GeneticVariation
umls:C1282975von Willebrand disease type 2N13Biomarker, GeneticVariation
umls:C0007222Cardiovascular Diseases12Biomarker, GeneticVariation
umls:C1282974von Willebrand disease type 2M11Biomarker, GeneticVariation
umls:C0040053Thrombosis8Biomarker, GeneticVariation
umls:C0020538Hypertension8Biomarker, GeneticVariation
umls:C0004238Atrial Fibrillation2AlteredExpression, Biomarker
umls:C0018801Heart Failure1Biomarker
umls:C0752143Intracranial Thrombosis1Biomarker
umls:C0031117Peripheral Nervous System Diseases1Biomarker

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

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Pharmacological information for VWF
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|investigationalDB00025Antihemophilic Factor (Recombinant)Biotech
InvestigationalDB05202ARC1779Biotech

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of VWF go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)4nt5AD2746 H2748


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Conservation information for LBS of VWF
Multiple alignments for P04275 in multiple species
LBSAA sequence# speciesSpecies
A1420GIGPHASLKQI2Mus musculus, Canis lupus familiaris
A1420GIGPHANLKQI1Homo sapiens
A1420-----------1Bos taurus
A1600GDREQAPNLVY1Homo sapiens
A1600-----------1Bos taurus
A1600GDRVEAPNLVY1Mus musculus
A1600GDREQVPNLVY1Canis lupus familiaris
A1752VVPEKAHLLSL1Homo sapiens
A1752-----------1Bos taurus
A1752VVQEKAHLQSL1Mus musculus
A1752VAYEKVHLLSL1Canis lupus familiaris
D1498NSMVLDVAFVL1Homo sapiens
D1498-----------1Bos taurus
D1498KSMVLDVVFVL1Mus musculus
D1498NSMVLDVVFVL1Canis lupus familiaris
D1596LVSQGDREQAP1Homo sapiens
D1596-----------1Bos taurus
D1596SPSQGDRVEAP1Mus musculus
D1596SVSQGDREQVP1Canis lupus familiaris
D2746SEVEVDIHYCQ1Homo sapiens
D2746-----------1Bos taurus
D2746SQEEVDIHYCQ1Mus musculus
D2746SEEEVDIHYCE1Canis lupus familiaris
E1389LMASQEPQRMS1Homo sapiens
E1389-----------1Bos taurus
E1389LTASQEPPRMA1Mus musculus
E1389LMASQEPSRLA1Canis lupus familiaris
F1366LKYTLFQIFGK2Mus musculus, Canis lupus familiaris
F1366LKYTLFQIFSK1Homo sapiens
F1366-----------1Bos taurus
H2748VEVDIHYCQGK1Homo sapiens
H2748-----------1Bos taurus
H2748EEVDIHYCQGK1Mus musculus
H2748EEVDIHYCEGK1Canis lupus familiaris
K1362TSEVLKYTLFQ3Homo sapiens, Mus musculus, Canis lupus familiaris
K1362-----------1Bos taurus
K1423PHANLKQIRLI1Homo sapiens
K1423-----------1Bos taurus
K1423PHASLKQIRLI1Mus musculus
K1423PHASLKQIHLI1Canis lupus familiaris
K1751NVVPEKAHLLS1Homo sapiens
K1751-----------1Bos taurus
K1751NVVQEKAHLQS1Mus musculus
K1751NVAYEKVHLLS1Canis lupus familiaris
L1422GPHANLKQIRL1Homo sapiens
L1422-----------1Bos taurus
L1422GPHASLKQIRL1Mus musculus
L1422GPHASLKQIHL1Canis lupus familiaris
N1396QRMSRNFVRYV1Homo sapiens
N1396-----------1Bos taurus
N1396PRMARNLVRYV1Mus musculus
N1396SRLARNLVRYV1Canis lupus familiaris
N1602REQAPNLVYMV1Homo sapiens
N1602-----------1Bos taurus
N1602RVEAPNLVYMV1Mus musculus
N1602REQVPNLVYMV1Canis lupus familiaris
P1390MASQEPQRMSR1Homo sapiens
P1390-----------1Bos taurus
P1390TASQEPPRMAR1Mus musculus
P1390MASQEPSRLAR1Canis lupus familiaris
P1418PVGIGPHASLK2Mus musculus, Canis lupus familiaris
P1418PVGIGPHANLK1Homo sapiens
P1418-----------1Bos taurus
Q1388LLMASQEPQRM1Homo sapiens
Q1388-----------1Bos taurus
Q1388LLTASQEPPRM1Mus musculus
Q1388LLMASQEPSRL1Canis lupus familiaris
Q1391ASQEPQRMSRN1Homo sapiens
Q1391-----------1Bos taurus
Q1391ASQEPPRMARN1Mus musculus
Q1391ASQEPSRLARN1Canis lupus familiaris
R1287LDGSSRLSEAE1Homo sapiens
R1287-----------1Bos taurus
R1287LDGSSMLSEAE1Mus musculus
R1287LDGSSKLSEDE1Canis lupus familiaris
R1392SQEPQRMSRNF1Homo sapiens
R1392-----------1Bos taurus
R1392SQEPPRMARNL1Mus musculus
R1392SQEPSRLARNL1Canis lupus familiaris
R1395PQRMSRNFVRY1Homo sapiens
R1395-----------1Bos taurus
R1395PPRMARNLVRY1Mus musculus
R1395PSRLARNLVRY1Canis lupus familiaris
R1597VSQGDREQAPN1Homo sapiens
R1597-----------1Bos taurus
R1597PSQGDRVEAPN1Mus musculus
R1597VSQGDREQVPN1Canis lupus familiaris
S1394EPQRMSRNFVR1Homo sapiens
S1394-----------1Bos taurus
S1394EPPRMARNLVR1Mus musculus
S1394EPSRLARNLVR1Canis lupus familiaris
Y1400RNLVRYVQGLK2Mus musculus, Canis lupus familiaris
Y1400RNFVRYVQGLK1Homo sapiens
Y1400-----------1Bos taurus


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