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 GC
Gene summary
Basic gene Info.Gene symbolGC
Gene namegroup-specific component (vitamin D binding protein)
SynonymsDBP|DBP/GC|GRD3|HEL-S-51|VDBG|VDBP
CytomapUCSC genome browser: 4q12-q13
Type of geneprotein-coding
RefGenesNM_000583.3,
NM_001204306.1,NM_001204307.1,
DescriptionVDBepididymis secretory protein Li 51gc-globulinvitamin D-binding alpha-globulinvitamin D-binding protein
Modification date20141207
dbXrefs MIM : 139200
HGNC : HGNC
Ensembl : ENSG00000145321
HPRD : 00749
Vega : OTTHUMG00000129915
ProteinUniProt: P02774
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GC
BioGPS: 2638
PathwayNCI Pathway Interaction Database: GC
KEGG: GC
REACTOME: GC
Pathway Commons: GC
ContextiHOP: GC
ligand binding site mutation search in PubMed: GC
UCL Cancer Institute: GC
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


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Ligand binding site mutations for GC

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
K51R50TBLCA1
S95K94MLUAD1
M123C122SLUAD1
L63S61NLUAD1
F52S54RLUSC1
F40E38KSKCM1
E24E24KSKCM1
E24,V28N26TUCEC1
Y48Y48FUCEC1
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 GC
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
K51R50T-1.3456279
E24E24K-1.3367227
M123C122S-1.2047994
F40E38K-1.1113604
S95K94M-0.83725545
V28N26T-0.80012296
E24N26T-0.80012296
Y48Y48F-0.47796368
F52S54R-0.29804406
L63S61N-0.010708316
(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 GC from PDB

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Differential gene expression and gene-gene network for GC
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 GC and the right PPI network was created from samples without mutations in the LBS of GC. 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 GC
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0162557Liver Failure, Acute4AlteredExpression, Biomarker
umls:C0018213Graves Disease3Biomarker, GeneticVariation
umls:C0003873Arthritis, Rheumatoid3Biomarker, GeneticVariation
umls:C0005944Bone Diseases, Metabolic1Biomarker
umls:C0860207Drug-Induced Liver Injury1Biomarker
umls:C0019151Hepatic Encephalopathy1Biomarker
umls:C0023890Liver Cirrhosis1Biomarker
umls:C0024121Lung Neoplasms1Biomarker
umls:C0036983Shock, Septic1Biomarker
umls:C0043251Wounds and Injuries1Biomarker

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

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Pharmacological information for GC
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

Gene-centered ligand-gene interaction network

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


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Conservation information for LBS of GC
Multiple alignments for P02774 in multiple species
LBSAA sequence# speciesSpecies
E24RGRDYEKDKVC2Mus musculus, Bos taurus
E24RGRDYEKNKVC1Homo sapiens
E31NKVCKEFSHLG1Homo sapiens
E31DKVCNELAMLG1Mus musculus
E31DKVCKDLASLG1Bos taurus
F40LGKEDFTSLSL1Homo sapiens
F40LGKEDFRSLSL1Mus musculus
F40LGREDFTSLSM1Bos taurus
F52LYSRKFPSGTF2Homo sapiens, Bos taurus
F52LYSRKFSSSTF1Mus musculus
K51VLYSRKFPSGT2Homo sapiens, Bos taurus
K51ILYSRKFSSST1Mus musculus
L43EDFTSLSLVLY1Homo sapiens
L43EDFRSLSLILY1Mus musculus
L43EDFTSLSMVLY1Bos taurus
L47SLSLVLYSRKF1Homo sapiens
L47SLSLILYSRKF1Mus musculus
L47SLSMVLYSRKF1Bos taurus
L63EQVSQLVKEVV1Homo sapiens
L63EQVNQLVKEVV1Mus musculus
L63EQISHLVNEVV1Bos taurus
L91TRTSALSAKSC1Homo sapiens
L91TRTSELSVKSC1Mus musculus
L91NRTSALSDKSC1Bos taurus
M123ERKLCMAALKH1Homo sapiens
M123ERKLCMAALSH1Mus musculus
M123EKKLCMAALKH1Bos taurus
S44DFTSLSLVLYS1Homo sapiens
S44DFRSLSLILYS1Mus musculus
S44DFTSLSMVLYS1Bos taurus
S92RTSALSAKSCE1Homo sapiens
S92RTSELSVKSCE1Mus musculus
S92RTSALSDKSCE1Bos taurus
S95ALSAKSCESNS1Homo sapiens
S95ELSVKSCESDA1Mus musculus
S95ALSDKSCESNS1Bos taurus
V28YEKNKVCKEFS1Homo sapiens
V28YEKDKVCNELA1Mus musculus
V28YEKDKVCKDLA1Bos taurus
Y48LSLVLYSRKFP1Homo sapiens
Y48LSLILYSRKFS1Mus musculus
Y48LSMVLYSRKFP1Bos taurus
Y84ADPDCYDTRTS1Homo sapiens
Y84ADPTCYDTRTS1Mus musculus
Y84ADPDCYDNRTS1Bos taurus


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