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 LRP2
Gene summary
Basic gene Info.Gene symbolLRP2
Gene namelow density lipoprotein receptor-related protein 2
CytomapUCSC genome browser: 2q31.1
Type of geneprotein-coding
DescriptionHeymann nephritis antigen homologLRP-2calcium sensor proteinglycoprotein 330low-density lipoprotein receptor-related protein 2megalin
Modification date20141219
dbXrefs MIM : 600073
Ensembl : ENSG00000081479
HPRD : 02509
Vega : OTTHUMG00000132179
ProteinUniProt: P98164
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LRP2
BioGPS: 4036
PathwayNCI Pathway Interaction Database: LRP2
Pathway Commons: LRP2
ContextiHOP: LRP2
ligand binding site mutation search in PubMed: LRP2
UCL Cancer Institute: LRP2
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for LRP2
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 LRP2
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 LRP2 from PDB

Differential gene expression and gene-gene network for LRP2
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 LRP2 and the right PPI network was created from samples without mutations in the LBS of LRP2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for LRP2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1857277Donnai-Barrow syndrome2Biomarker, GeneticVariation
umls:C0033578Prostatic Neoplasms2Biomarker, GeneticVariation
umls:C0042870Vitamin D Deficiency1Biomarker
umls:C0005944Bone Diseases, Metabolic1Biomarker
umls:C0376634Craniofacial Abnormalities1Biomarker
umls:C0008073Developmental Disabilities1Biomarker
umls:C0015398Eye Diseases, Hereditary1Biomarker
umls:C0018784Hearing Loss, Sensorineural1Biomarker
umls:C0019284Hernia, Diaphragmatic1Biomarker
umls:C0022658Kidney Diseases1Biomarker

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

Pharmacological information for LRP2
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|investigationalDB00030Insulin HumanBiotech
ApprovedDB00071Insulin PorkBiotech
Approved|vet_approvedDB00798GentamicinSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of LRP2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
CACALCIUM(2+)2m0pAW1126 D1139

Conservation information for LBS of LRP2
Multiple alignments for P98164 in multiple species
LBSAA sequence# speciesSpecies
D1129KNWVCDTDNDC1Homo sapiens
D1129EQWKCDSDNDC1Caenorhabditis elegans
D1129KEWVCDTDNDC1Mus musculus
D1129KDWVCDTDNDC1Rattus norvegicus
D1131WVCDTDNDCSD2Mus musculus, Rattus norvegicus
D1131WVCDTDNDCGD1Homo sapiens
D1131WKCDSDNDCGD1Caenorhabditis elegans
D1133CDTDNDCSDGS2Mus musculus, Rattus norvegicus
D1133CDTDNDCGDGS1Homo sapiens
D1133CDSDNDCGDGS1Caenorhabditis elegans
D1139CSDGSDEK-NC2Mus musculus, Rattus norvegicus
D1139CGDGSDEK-NC1Homo sapiens
D1139CGDGSDEKLEM1Caenorhabditis elegans
E1140SDGSDEK-NCQ2Mus musculus, Rattus norvegicus
E1140GDGSDEK-NCN1Homo sapiens
E1140GDGSDEKLEMC1Caenorhabditis elegans
W1126CISKNWVCDTD1Homo sapiens
W1126CIPEQWKCDSD1Caenorhabditis elegans
W1126CIPKEWVCDTD1Mus musculus
W1126CIPKDWVCDTD1Rattus norvegicus

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