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 VLDLR
Gene summary
Basic gene Info.Gene symbolVLDLR
Gene namevery low density lipoprotein receptor
CytomapUCSC genome browser: 9p24
Type of geneprotein-coding
DescriptionVLDL receptorVLDL-Rvery low-density lipoprotein receptor
Modification date20141219
dbXrefs MIM : 192977
Ensembl : ENSG00000147852
HPRD : 01895
Vega : OTTHUMG00000019447
ProteinUniProt: P98155
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_VLDLR
BioGPS: 7436
PathwayNCI Pathway Interaction Database: VLDLR
Pathway Commons: VLDLR
ContextiHOP: VLDLR
ligand binding site mutation search in PubMed: VLDLR
UCL Cancer Institute: VLDLR
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0006898receptor-mediated endocytosis10571240
GO:0034436glycoprotein transport10571240
GO:0034447very-low-density lipoprotein particle clearance8083232

Ligand binding site mutations for VLDLR
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 VLDLR
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 VLDLR from PDB

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


Phenotype information for VLDLR
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0394006Dysequilibrium syndrome6Biomarker, GeneticVariation
umls:C0004352Autistic Disorder2Biomarker

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

Pharmacological information for VLDLR
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 VLDLR go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
CACALCIUM(2+)1v9u5D139 D145

Conservation information for LBS of VLDLR
Multiple alignments for P98155 in multiple species
LBSAA sequence# speciesSpecies
D135VSWRCDGENDC2Homo sapiens, Mus musculus
D135VSWKCDGEKDC1Gallus gallus
D139CDGENDCDSGE1Homo sapiens
D139CDGEKDCDSGE1Gallus gallus
D139CDGENDCDNGE1Mus musculus
D145CDSGEDEENCG2Homo sapiens, Gallus gallus
D145CDNGEDEENCG1Mus musculus
E137WRCDGENDCDS1Homo sapiens
E137WKCDGEKDCDS1Gallus gallus
E137WRCDGENDCDN1Mus musculus
E146DSGEDEENCGN2Homo sapiens, Gallus gallus
E146DNGEDEENCGN1Mus musculus
N138RCDGENDCDSG1Homo sapiens
N138KCDGEKDCDSG1Gallus gallus
N138RCDGENDCDNG1Mus musculus
W132CIPVSWRCDGE2Homo sapiens, Mus musculus
W132CIPVSWKCDGE1Gallus gallus

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