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 VPS4B
Gene summary
Basic gene Info.Gene symbolVPS4B
Gene namevacuolar protein sorting 4 homolog B (S. cerevisiae)
CytomapUCSC genome browser: 18q21.33
Type of geneprotein-coding
Descriptioncell migration-inducing 1cell migration-inducing gene 1 proteinsuppressor of K(+) transport growth defect 1suppressor of K+ transport defect 1vacuolar protein sorting 4Bvacuolar protein sorting-associated protein 4B
Modification date20141207
dbXrefs MIM : 609983
Ensembl : ENSG00000119541
HPRD : 15653
Vega : OTTHUMG00000132790
ProteinUniProt: O75351
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_VPS4B
BioGPS: 9525
PathwayNCI Pathway Interaction Database: VPS4B
Pathway Commons: VPS4B
ContextiHOP: VPS4B
ligand binding site mutation search in PubMed: VPS4B
UCL Cancer Institute: VPS4B
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0016197endosomal transport11563910
GO:0033993response to lipid16757520

Ligand binding site mutations for VPS4B
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
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.

Protein structure related information for VPS4B
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
(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 VPS4B from PDB

Differential gene expression and gene-gene network for VPS4B
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 VPS4B and the right PPI network was created from samples without mutations in the LBS of VPS4B. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for VPS4B
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for VPS4B
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of VPS4B go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of VPS4B
Multiple alignments for O75351 in multiple species
LBSAA sequence# speciesSpecies
A60KQSIRAKCTEY3Homo sapiens, Mus musculus, Bos taurus
A60REAITQKFTEY1Arabidopsis thaliana
A60KEIIRSKVIEY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A60KDLIRAKFTEY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A69EYLDRAEKLKE3Homo sapiens, Mus musculus, Bos taurus
A69EYLRRAEEIRA1Arabidopsis thaliana
A69EYLDRAEKLKV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A69EYLNRAEQLKK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
C62SIRAKCTEYLD3Homo sapiens, Mus musculus, Bos taurus
C62AITQKFTEYLR1Arabidopsis thaliana
C62IIRSKVIEYLD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C62LIRAKFTEYLN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D67CTEYLDRAEKL3Homo sapiens, Mus musculus, Bos taurus
D67FTEYLRRAEEI1Arabidopsis thaliana
D67VIEYLDRAEKL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D67FTEYLNRAEQL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E70YLDRAEKLKEY3Homo sapiens, Mus musculus, Bos taurus
E70YLRRAEEIRAV1Arabidopsis thaliana
E70YLDRAEKLKVY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
E70YLNRAEQLKKH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K46FLHVVKYEAQG3Homo sapiens, Mus musculus, Bos taurus
K46FKTHLKYE-KN1Arabidopsis thaliana
K46FMMALKYE-KN1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K46LMLALKYE-KN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L31NYEEALQLYQH3Homo sapiens, Mus musculus, Bos taurus
L31NYNKAFPLYMN1Arabidopsis thaliana
L31QYPDAYKYYQS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L31QYEEAYTAYYN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L42AVQYFLHVVKY3Homo sapiens, Mus musculus, Bos taurus
L42ALEYFKTHLKY1Arabidopsis thaliana
L42ALDYFMMALKY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L42GLDYLMLALKY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L66KCTEYLDRAEK3Homo sapiens, Mus musculus, Bos taurus
L66KFTEYLRRAEE1Arabidopsis thaliana
L66KVIEYLDRAEK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L66KFTEYLNRAEQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q35ALQLYQHAVQY3Homo sapiens, Mus musculus, Bos taurus
Q35AFPLYMNALEY1Arabidopsis thaliana
Q35AYKYYQSALDY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q35AYTAYYNGLDY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q39YQHAVQYFLHV3Homo sapiens, Mus musculus, Bos taurus
Q39YMNALEYFKTH1Arabidopsis thaliana
Q39YQSALDYFMMA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q39YYNGLDYLMLA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R59AKQSIRAKCTE3Homo sapiens, Mus musculus, Bos taurus
R59IREAITQKFTE1Arabidopsis thaliana
R59SKEIIRSKVIE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R59SKDLIRAKFTE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T63IRAKCTEYLDR3Homo sapiens, Mus musculus, Bos taurus
T63ITQKFTEYLRR1Arabidopsis thaliana
T63IRSKVIEYLDR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T63IRAKFTEYLNR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V38LYQHAVQYFLH3Homo sapiens, Mus musculus, Bos taurus
V38LYMNALEYFKT1Arabidopsis thaliana
V38YYQSALDYFMM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V38AYYNGLDYLML1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V45YFLHVVKYEAQ3Homo sapiens, Mus musculus, Bos taurus
V45YFKTHLKYE-K1Arabidopsis thaliana
V45YFMMALKYE-K1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V45YLMLALKYE-K1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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