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 LDLR
Gene summary
Basic gene Info.Gene symbolLDLR
Gene namelow density lipoprotein receptor
SynonymsFH|FHC|LDLCQ2
CytomapUCSC genome browser: 19p13.2
Type of geneprotein-coding
RefGenesNM_000527.4,
NM_001195798.1,NM_001195799.1,NM_001195800.1,NM_001195803.1,
NM_001195802.1,
DescriptionLDL receptorlow-density lipoprotein receptorlow-density lipoprotein receptor class A domain-containing protein 3
Modification date20141222
dbXrefs MIM : 606945
HGNC : HGNC
Ensembl : ENSG00000130164
HPRD : 06091
Vega : OTTHUMG00000171935
ProteinUniProt: P01130
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_LDLR
BioGPS: 3949
PathwayNCI Pathway Interaction Database: LDLR
KEGG: LDLR
REACTOME: LDLR
Pathway Commons: LDLR
ContextiHOP: LDLR
ligand binding site mutation search in PubMed: LDLR
UCL Cancer Institute: LDLR
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 LDLR
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
N297N297SCOAD2
E258E258KCOAD1
D100D100HHNSC1
D131,D133R132LLUAD1
D139D139HLUSC1
D131D131HLUSC1
N297N297SOV1
D172E174KSKCM1
E228E229KSKCM1
R124R124WSKCM1
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 LDLR
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
D100D100H0.13713635
D139D139H0.080653682
E258E258K-1.5453487
D172E174K-1.5334091
E228E229K-1.4837356
N297N297S-1.0101734
D133R132L-0.95689281
D131R132L-0.95689281
R124R124W-0.89863323
D131D131H-0.78369326
(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 LDLR from PDB
PDB IDPDB titlePDB structure
1F5YNMR STRUCTURE OF A CONCATEMER OF THE FIRST AND SECOND LIGAND-BINDING MODULES OF THE HUMAN LDL RECEPTOR

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Differential gene expression and gene-gene network for LDLR
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 LDLR and the right PPI network was created from samples without mutations in the LBS of LDLR. 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 LDLR
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0020445Hyperlipoproteinemia Type II693AlteredExpression, Biomarker, GeneticVariation
umls:C0020443Hypercholesterolemia146AlteredExpression, Biomarker, GeneticVariation
umls:C0004153Atherosclerosis131AlteredExpression, Biomarker, GeneticVariation, Therapeutic
umls:C0010068Coronary Disease82Biomarker, GeneticVariation
umls:C0745103HYPERCHOLESTEROLEMIA, FAMILIAL60Biomarker, GeneticVariation
umls:C1956346Coronary Artery Disease45Biomarker, GeneticVariation
umls:C0020473Hyperlipidemias19Biomarker, GeneticVariation
umls:C0242339Dyslipidemias9Biomarker, GeneticVariation
umls:C0400966Non-alcoholic Fatty Liver Disease8Biomarker
umls:C1862939Amyotrophic lateral sclerosis 11Biomarker
umls:C0020507Hyperplasia1Biomarker

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

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Pharmacological information for LDLR
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|investigationalDB00707PorfimerSmall molecule

Gene-centered ligand-gene interaction network

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


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Conservation information for LBS of LDLR
Multiple alignments for P01130 in multiple species
LBSAA sequence# speciesSpecies
A299KVCNMARDCRD1Homo sapiens
A299KVCDSARDCQD1Mus musculus
A299KVCNSARDCRD1Rattus norvegicus
C255HGSRQCDREHD2Mus musculus, Rattus norvegicus
C255HGSRQCDREYD1Homo sapiens
C296TLDKVCNMARD1Homo sapiens
C296SLDKVCDSARD1Mus musculus
C296SLDKVCNSARD1Rattus norvegicus
C313EPIKECKTNEC2Mus musculus, Rattus norvegicus
C313EPIKECGTNEC1Homo sapiens
C318CKTNECLDNNG2Mus musculus, Rattus norvegicus
C318CGTNECLDNNG1Homo sapiens
C46SYKWVCDGSAE1Homo sapiens
C46ASKWVCDGSPE1Mus musculus
C46VSKWVCDGSRE1Rattus norvegicus
D100CDNGSDEQGCP1Homo sapiens
D100CENDSDEQGCP1Mus musculus
D100CENGSDELDCS1Rattus norvegicus
D129RQFVCDSDRDC1Homo sapiens
D129PQFVCDGDRDC1Mus musculus
D129RQFVCDQDWDC1Rattus norvegicus
D131FVCDSDRDCLD1Homo sapiens
D131FVCDGDRDCLD1Mus musculus
D131FVCDQDWDCLD1Rattus norvegicus
D133CDSDRDCLDGS1Homo sapiens
D133CDGDRDCLDGS1Mus musculus
D133CDQDWDCLDGS1Rattus norvegicus
D139CLDGSDEASCP1Homo sapiens
D139CLDGSDEAHCQ1Mus musculus
D139CLDGSDEAHCA1Rattus norvegicus
D168QLWACDNDPDC1Homo sapiens
D168SLWACDGDVDC1Mus musculus
D168SLWACDGDRDC1Rattus norvegicus
D170WACDNDPDCED1Homo sapiens
D170WACDGDVDCVD1Mus musculus
D170WACDGDRDCDD1Rattus norvegicus
D172CDNDPDCEDGS1Homo sapiens
D172CDGDVDCVDGS1Mus musculus
D172CDGDRDCDDGS1Rattus norvegicus
D178CEDGSDEWPQR1Homo sapiens
D178CVDGSDEWPQN1Mus musculus
D178CDDGSDEWPQN1Rattus norvegicus
D217SSWRCDGGPDC1Homo sapiens
D217RSWVCDGEADC1Mus musculus
D217RSWVCDGAADC1Rattus norvegicus
D221CDGGPDCKDKS1Homo sapiens
D221CDGEADCKDKS1Mus musculus
D221CDGAADCKDKS1Rattus norvegicus
D227CKDKSDEENCA2Homo sapiens, Rattus norvegicus
D227CKDKSDEEHCA1Mus musculus
D256GSRQCDREHDC2Mus musculus, Rattus norvegicus
D256GSRQCDREYDC1Homo sapiens
D260CDREHDCKDMS2Mus musculus, Rattus norvegicus
D260CDREYDCKDMS1Homo sapiens
D266CKDMSDEVGCV1Homo sapiens
D266CKDMSDELGCV1Mus musculus
D266CKDMSDELGCI1Rattus norvegicus
D301CNMARDCRDWS1Homo sapiens
D301CDSARDCQDWS1Mus musculus
D301CNSARDCRDWS1Rattus norvegicus
D307CRDWSDEPIKE2Homo sapiens, Rattus norvegicus
D307CQDWSDEPIKE1Mus musculus
D331SHVCNDLKIGY1Homo sapiens
D331SHICKDLKIGS1Mus musculus
D331SHICKDLKIGY1Rattus norvegicus
D354QRRCEDIDECQ1Homo sapiens
D354LHRCEDIDECQ1Mus musculus
D354GHQCEDIDECQ1Rattus norvegicus
D356RCEDIDECQDP1Homo sapiens
D356RCEDIDECQEP1Mus musculus
D356QCEDIDECQEP1Rattus norvegicus
D47YKWVCDGSAEC1Homo sapiens
D47SKWVCDGSPEC1Mus musculus
D47SKWVCDGSREC1Rattus norvegicus
D57CPDGSDESPET2Mus musculus, Rattus norvegicus
D57CQDGSDESQET1Homo sapiens
D90QFWRCDGQVDC1Homo sapiens
D90DSWRCDGQVDC1Mus musculus
D90DSWRCDGRTDC1Rattus norvegicus
D94CDGQVDCDNGS1Homo sapiens
D94CDGQVDCENDS1Mus musculus
D94CDGRTDCENGS1Rattus norvegicus
E101DNGSDEQGCPP1Homo sapiens
E101ENDSDEQGCPP1Mus musculus
E101ENGSDELDCSP1Rattus norvegicus
E140LDGSDEASCPV1Homo sapiens
E140LDGSDEAHCQA1Mus musculus
E140LDGSDEAHCAA1Rattus norvegicus
E179EDGSDEWPQRC1Homo sapiens
E179VDGSDEWPQNC1Mus musculus
E179DDGSDEWPQNC1Rattus norvegicus
E228KDKSDEENCAV2Homo sapiens, Rattus norvegicus
E228KDKSDEEHCAV1Mus musculus
E258RQCDREHDCKD2Mus musculus, Rattus norvegicus
E258RQCDREYDCKD1Homo sapiens
E267KDMSDEVGCVN1Homo sapiens
E267KDMSDELGCVN1Mus musculus
E267KDMSDELGCIN1Rattus norvegicus
E308RDWSDEPIKEC2Homo sapiens, Rattus norvegicus
E308QDWSDEPIKEC1Mus musculus
E312DEPIKECKTNE2Mus musculus, Rattus norvegicus
E312DEPIKECGTNE1Homo sapiens
E317ECKTNECLDNN2Mus musculus, Rattus norvegicus
E317ECGTNECLDNN1Homo sapiens
E357CEDIDECQEPD2Mus musculus, Rattus norvegicus
E357CEDIDECQDPD1Homo sapiens
E372LCVNLEGGYKC1Homo sapiens
E372LCVNLEGSYKC1Mus musculus
E372LCVNLEGSFKC1Rattus norvegicus
E51CDGSAECQDGS1Homo sapiens
E51CDGSPECPDGS1Mus musculus
E51CDGSRECPDGS1Rattus norvegicus
E58PDGSDESPETC2Mus musculus, Rattus norvegicus
E58QDGSDESQETC1Homo sapiens
F126CISRQFVCDSD1Homo sapiens
F126CISPQFVCDGD1Mus musculus
F126CISRQFVCDQD1Rattus norvegicus
G219WRCDGGPDCKD1Homo sapiens
G219WVCDGEADCKD1Mus musculus
G219WVCDGAADCKD1Rattus norvegicus
G335NDLKIGYECLC1Homo sapiens
G335KDLKIGSECLC1Mus musculus
G335KDLKIGYECLC1Rattus norvegicus
G373CVNLEGGYKCQ1Homo sapiens
G373CVNLEGSYKCE1Mus musculus
G373CVNLEGSFKCE1Rattus norvegicus
G374VNLEGGYKCQC1Homo sapiens
G374VNLEGSYKCEC1Mus musculus
G374VNLEGSFKCEC1Rattus norvegicus
I334CNDLKIGYECL1Homo sapiens
I334CKDLKIGSECL1Mus musculus
I334CKDLKIGYECL1Rattus norvegicus
I355RRCEDIDECQD1Homo sapiens
I355HRCEDIDECQE1Mus musculus
I355HQCEDIDECQE1Rattus norvegicus
K294CITLDKVCNMA1Homo sapiens
K294CISLDKVCDSA1Mus musculus
K294CISLDKVCNSA1Rattus norvegicus
K333VCNDLKIGYEC1Homo sapiens
K333ICKDLKIGSEC1Mus musculus
K333ICKDLKIGYEC1Rattus norvegicus
K603ILEDEKRLAHP1Homo sapiens
K603ILEDENRLAHP1Mus musculus
K603ILEDEKQLAHP1Rattus norvegicus
L332HVCNDLKIGYE1Homo sapiens
L332HICKDLKIGSE1Mus musculus
L332HICKDLKIGYE1Rattus norvegicus
L371QLCVNLEGGYK1Homo sapiens
L371QLCVNLEGSYK1Mus musculus
L371QLCVNLEGSFK1Rattus norvegicus
N297LDKVCNMARDC1Homo sapiens
N297LDKVCDSARDC1Mus musculus
N297LDKVCNSARDC1Rattus norvegicus
N316KECKTNECLDN2Mus musculus, Rattus norvegicus
N316KECGTNECLDN1Homo sapiens
N370SQLCVNLEGGY1Homo sapiens
N370SQLCVNLEGSY1Mus musculus
N370SQLCVNLEGSF1Rattus norvegicus
P171ACDNDPDCEDG1Homo sapiens
P171ACDGDVDCVDG1Mus musculus
P171ACDGDRDCDDG1Rattus norvegicus
P220RCDGGPDCKDK1Homo sapiens
P220VCDGEADCKDK1Mus musculus
P220VCDGAADCKDK1Rattus norvegicus
Q125KCISRQFVCDS1Homo sapiens
Q125KCISPQFVCDG1Mus musculus
Q125KCISRQFVCDQ1Rattus norvegicus
Q254IHGSRQCDREH2Mus musculus, Rattus norvegicus
Q254IHGSRQCDREY1Homo sapiens
Q92WRCDGQVDCDN1Homo sapiens
Q92WRCDGQVDCEN1Mus musculus
Q92WRCDGRTDCEN1Rattus norvegicus
R124GKCISRQFVCD2Homo sapiens, Rattus norvegicus
R124GKCISPQFVCD1Mus musculus
R253CIHGSRQCDRE3Homo sapiens, Mus musculus, Rattus norvegicus
R257SRQCDREHDCK2Mus musculus, Rattus norvegicus
R257SRQCDREYDCK1Homo sapiens
S49WVCDGSAECQD1Homo sapiens
S49WVCDGSPECPD1Mus musculus
S49WVCDGSRECPD1Rattus norvegicus
T315IKECKTNECLD2Mus musculus, Rattus norvegicus
T315IKECGTNECLD1Homo sapiens
V295ITLDKVCNMAR1Homo sapiens
V295ISLDKVCDSAR1Mus musculus
V295ISLDKVCNSAR1Rattus norvegicus
V45ISYKWVCDGSA1Homo sapiens
V45IASKWVCDGSP1Mus musculus
V45IVSKWVCDGSR1Rattus norvegicus
W165CIPSLWACDGD2Mus musculus, Rattus norvegicus
W165CIPQLWACDND1Homo sapiens
W44CISYKWVCDGS1Homo sapiens
W44CIASKWVCDGS1Mus musculus
W44CIVSKWVCDGS1Rattus norvegicus
W87CIPQFWRCDGQ1Homo sapiens
W87CIPDSWRCDGQ1Mus musculus
W87CIPDSWRCDGR1Rattus norvegicus
Y259QCDREHDCKDM2Mus musculus, Rattus norvegicus
Y259QCDREYDCKDM1Homo sapiens
Y336DLKIGYECLCP2Homo sapiens, Rattus norvegicus
Y336DLKIGSECLCP1Mus musculus


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