mutLBSgeneDB

mutLBSgeneDB
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 RB1
Gene summary
Basic gene Info.Gene symbolRB1
Gene nameretinoblastoma 1
SynonymsOSRC|PPP1R130|RB|p105-Rb|pRb|pp110
CytomapUCSC genome browser: 13q14.2
Type of geneprotein-coding
RefGenesNM_000321.2,
Descriptionprepro-retinoblastoma-associated proteinprotein phosphatase 1, regulatory subunit 130retinoblastoma suspectibility proteinretinoblastoma-associated protein
Modification date20141219
dbXrefs MIM : 614041
HGNC : HGNC
Ensembl : ENSG00000139687
HPRD : 01574
Vega : OTTHUMG00000016900
ProteinUniProt: P06400
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RB1
BioGPS: 5925
PathwayNCI Pathway Interaction Database: RB1
KEGG: RB1
REACTOME: RB1
Pathway Commons: RB1
ContextiHOP: RB1
ligand binding site mutation search in PubMed: RB1
UCL Cancer Institute: RB1
Assigned class in mutLBSgeneDBA: This gene has a literature evidence and it belongs to targetable_mutLBSgenes.
References showing study about ligand binding site mutation for RB1.1. "Baillie RA, Sha X, Thuillier P, Clarke SD. A novel 3T3-L1 preadipocyte variant that expresses PPARgamma2 and RXRalpha but does not undergo differentiation. J Lipid Res. 1998 Oct;39(10):2048-53." 9788251

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0043550regulation of lipid kinase activity16286473
GO:0045892negative regulation of transcription, DNA-templated10783144


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Ligand binding site mutations for RB1

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
N716,K720D718GCOAD4
E533E533GCOAD3
N716,V714K715ECOAD2
H555R556QCOAD2
Y756Y756CCOAD2
M761M761LBLCA1
E551L550IBRCA1
N716,K720D718NCOAD1
I66K65NCOAD1
L660Y659HCOAD1
L660R661WCOAD1
H555R556LCOAD1
N716,V714K715RCOAD1
L660R661LCOAD1
L660Y659FGBM1
K653V654LGBM1
L660R661WGBM1
K653V654MKIRC1
Y756Y756CLUAD1
I66D68GLUSC1
M761,K765R763TOV1
M460L461PSKCM1
Y756F755IUCEC1
N757S758LUCEC1
I752S751YUCEC1
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.

Clinical information for RB1 from My Cancer Genome.
Retinoblastoma 1 (RB1) is a gene that encodes a protein that is a negative regulator of the cell cycle as well as a tumor suppressor. Missense mutations, nonsense mutations, silent mutations, frameshift deletions and insertions, and in-frame deletions are observed in cancers such as cancers of the fallopian tubes, cancers of the eye, and intestinal cancer.Related Pathways: Cell cycle control.Modified: December 4, 2015

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Protein structure related information for RB1
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
N757S758L0.016335882
E533E533G-1.5622795
K720D718G-1.4526905
N716D718G-1.4526905
M460L461P-1.3971126
I66D68G-1.3286123
K720D718N-1.3272052
N716D718N-1.3272052
M761R763T-1.3259044
K765R763T-1.3259044
I66K65N-1.2897835
L660Y659H-1.0313084
Y756F755I-1.0067972
K653V654M-0.92793829
L660R661W-0.90906764
H555R556Q-0.89148432
V714K715R-0.82529546
N716K715R-0.82529546
N716K715E-0.78224004
V714K715E-0.78224004
Y756Y756C-0.69245694
K653V654L-0.69093928
I752S751Y-0.6822503
L660R661L-0.67768182
L660Y659F-0.61288987
E551L550I-0.51137438
H555R556L-0.35363539
M761M761L-0.098350003
(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 RB1 from PDB
PDB IDPDB titlePDB structure
1AD6DOMAIN A OF HUMAN RETINOBLASTOMA TUMOR SUPPRESSOR

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Differential gene expression and gene-gene network for RB1
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types
RB1_COAD_DE

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 RB1 and the right PPI network was created from samples without mutations in the LBS of RB1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

* In COAD


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Phenotype information for RB1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0035335Retinoblastoma273AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification
umls:C0029463Osteosarcoma41AlteredExpression, Biomarker, GeneticVariation
umls:C0007097Carcinoma40AlteredExpression, Biomarker, GeneticVariation
umls:C2239176Carcinoma, Hepatocellular23Biomarker, GeneticVariation, PostTranslationalModification
umls:C0149925Small Cell Lung Carcinoma19AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification
umls:C1458155Breast Neoplasms17AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification
umls:C0005684Malignant neoplasm of bladder12AlteredExpression, Biomarker, GeneticVariation
umls:C0007131Carcinoma, Non-Small-Cell Lung9AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification
umls:C0080113Retinoblastoma Protein9GeneticVariation
umls:C0005695Urinary Bladder Neoplasms6AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification
umls:C0279626Esophageal Squamous Cell Carcinoma6AlteredExpression, Biomarker, GeneticVariation
umls:C1961102Precursor Cell Lymphoblastic Leukemia-Lymphoma5AlteredExpression, Biomarker, GeneticVariation
umls:C0030297Pancreatic Neoplasms3AlteredExpression, Biomarker, GeneticVariation
umls:C0206686Adrenocortical Carcinoma2Biomarker
umls:C0001624Adrenal Gland Neoplasms1Biomarker
umls:C0007786Brain Ischemia1Biomarker
umls:C0017661Glomerulonephritis, IGA1Biomarker
umls:C0023904Liver Neoplasms, Experimental1Biomarker
umls:C0024667Mammary Neoplasms, Animal1Biomarker
umls:C0024668Mammary Neoplasms, Experimental1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs
28126R661WPathogenicGermline;somaticGeneReviews:NBK1452
MedGen:C0035335
OMIM:180200
Orphanet:ORPHA790
MedGen:CN221809
106668V654MLikely pathogenic;Uncertain significanceSomaticMedGen:CN221809

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Pharmacological information for RB1
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

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RB1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (LEU,ASP,TYR,HIS,PHE,GLY,LEU,GLU,GLU,GLY,GLU,GLY,ILE,ARG,ASP,LEU,PHE,ASP)1o9kAE533
IIIPeptide ligand (LEU,ASP,TYR,HIS,PHE,GLY,LEU,GLU,GLU,GLY,GLU,GLY,ILE,ARG,ASP,LEU,PHE,ASP)1o9kCE533 E551
IIIPeptide ligand (LEU,ASP,TYR,HIS,PHE,GLY,LEU,GLU,GLU,GLY,GLU,GLY,ILE,ARG,ASP,LEU,PHE,ASP)1o9kEE533 E551
IIIPeptide ligand (LEU,ASP,TYR,HIS,PHE,GLY,LEU,GLU,GLU,GLY,GLU,GLY,ILE,ARG,ASP,LEU,PHE,ASP)1o9kGE533 E551
IIIPeptide ligand (ASP,ASP,TYR,LEU,TRP,GLY,LEU,GLU,ALA,GLY,GLU,GLY,ILE,SER,ASP,LEU,PHE,ASP)1n4mAE533 E551 H555 K653 L660
IIIPeptide ligand (LEU,ASP,TYR,HIS,PHE,GLY,LEU,GLU,GLU,GLY,GLU,GLY,ILE,ARG,ASP,LEU,PHE,ASP)1o9kBK653
IIIPeptide ligand (LEU,ASP,TYR,HIS,PHE,GLY,LEU,GLU,GLU,GLY,GLU,GLY,ILE,ARG,ASP,LEU,PHE,ASP)1o9kDK653
IIIPeptide ligand (LEU,ASP,TYR,HIS,PHE,GLY,LEU,GLU,GLU,GLY,GLU,GLY,ILE,ARG,ASP,LEU,PHE,ASP)1o9kFK653
IIIPeptide ligand (LEU,ASP,TYR,HIS,PHE,GLY,LEU,GLU,GLU,GLY,GLU,GLY,ILE,ARG,ASP,LEU,PHE,ASP)1o9kHK653
IIIPeptide ligand (PRO,PRO,THR,LEU,HIS,GLU,LEU,TYR,ASP,LEU)2r7gAM460 E533
IIIPeptide ligand (PRO,PRO,THR,LEU,HIS,GLU,LEU,TYR,ASP,LEU)2r7gCM460 E533
IIIPeptide ligand (ASP,ASP,TYR,LEU,TRP,GLY,LEU,GLU,ALA,GLY,GLU,GLY,ILE,SER,ASP,LEU,PHE,ASP)1n4mBM460 E533 E551 H555 K653 L660
IIIPeptide ligand (ASP,LEU,TYR,CYS,TYR,GLU,GLN,LEU,ASN)1guxBV714 K720 I752 Y756 N757 M761 K765
IIIPeptide ligand (PRO,PRO,THR,LEU,HIS,GLU,LEU,TYR,ASP)2r7gAV714 K720 Y756 N757 M761
IIIPeptide ligand (ASP,ASP,TYR,LEU,TRP,GLY,LEU,GLU,ALA,GLY,GLU,GLY)1n4mBV714 N716 Y756 N757 M761 K765


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Conservation information for LBS of RB1
Multiple alignments for P06400 in multiple species
LBSAA sequence# speciesSpecies
A772NILQYASTRPP3Homo sapiens, Mus musculus, Rattus norvegicus
A772NILQYASNRPP1Gallus gallus
D479SKLLNDNIFHM3Homo sapiens, Mus musculus, Rattus norvegicus
D479SKLLNDNIFHT1Gallus gallus
E464SMLKSEEERLS4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
E533FYKVIESFIKV3Gallus gallus, Mus musculus, Rattus norvegicus
E533FYKVIESFIKA1Homo sapiens
E551MIKHLERCEHR4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
E554HLERCEHRIME4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
F482LNDNIFHMSLL3Homo sapiens, Mus musculus, Rattus norvegicus
F482LNDNIFHTSLL1Gallus gallus
F721NIDLKFKIIVT3Homo sapiens, Mus musculus, Rattus norvegicus
F721NVDLRFKTIVS1Gallus gallus
H555LERCEHRIMES4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I470EERLSIQNFSK3Homo sapiens, Mus musculus, Rattus norvegicus
I470EERLSVHNFSK1Gallus gallus
I481LLNDNIFHMSL3Homo sapiens, Mus musculus, Rattus norvegicus
I481LLNDNIFHTSL1Gallus gallus
I536VIESFIKVEAN2Mus musculus, Rattus norvegicus
I536VIESFIKAEGN1Homo sapiens
I536VIESFIKVEPS1Gallus gallus
I66CQKLKVPDHVR2Mus musculus, Rattus norvegicus
I66CQKLKIPDHVR1Homo sapiens
I66CDALKAPDSVR1Gallus gallus
I752EEFDSIIVFYN2Mus musculus, Rattus norvegicus
I752EEYDSIIVFYN1Homo sapiens
I752EQYDSIIVFYN1Gallus gallus
I753EFDSIIVFYNS2Mus musculus, Rattus norvegicus
I753EYDSIIVFYNS1Homo sapiens
I753QYDSIIVFYNL1Gallus gallus
I768RLKTNILQYAS3Homo sapiens, Mus musculus, Rattus norvegicus
I768KLKTNILQYAS1Gallus gallus
K475IQNFSKLLNDN3Homo sapiens, Mus musculus, Rattus norvegicus
K475VHNFSKLLNDN1Gallus gallus
K530AFDFYKVIESF4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
K537IESFIKVEANL2Mus musculus, Rattus norvegicus
K537IESFIKAEGNL1Homo sapiens
K537IESFIKVEPSL1Gallus gallus
K548TREMIKHLERC3Homo sapiens, Mus musculus, Rattus norvegicus
K548TRDMIKHLERC1Gallus gallus
K652LSLFYKKVYRL2Homo sapiens, Rattus norvegicus
K652LSLFYKKVFRL1Gallus gallus
K652LALFYKKVYRL1Mus musculus
K653SLFYKKVYRLA2Homo sapiens, Rattus norvegicus
K653SLFYKKVFRLA1Gallus gallus
K653ALFYKKVYRLA1Mus musculus
K713MYGICKVKNID3Homo sapiens, Mus musculus, Rattus norvegicus
K713MYGICKVKNVD1Gallus gallus
K720KNIDLKFKIIV3Homo sapiens, Mus musculus, Rattus norvegicus
K720KNVDLRFKTIV1Gallus gallus
K722IDLKFKIIVTA3Homo sapiens, Mus musculus, Rattus norvegicus
K722VDLRFKTIVSA1Gallus gallus
K765FMQRLKTNILQ3Homo sapiens, Mus musculus, Rattus norvegicus
K765FMQKLKTNILQ1Gallus gallus
L468SEEERLSIQNF3Homo sapiens, Mus musculus, Rattus norvegicus
L468SEEERLSVHNF1Gallus gallus
L476QNFSKLLNDNI3Homo sapiens, Mus musculus, Rattus norvegicus
L476HNFSKLLNDNI1Gallus gallus
L649STSLSLFYKKV3Homo sapiens, Gallus gallus, Rattus norvegicus
L649STSLALFYKKV1Mus musculus
L660YRLAYLRLNTL3Homo sapiens, Mus musculus, Rattus norvegicus
L660FRLAYLRLHTL1Gallus gallus
L769LKTNILQYAST3Homo sapiens, Mus musculus, Rattus norvegicus
L769LKTNILQYASN1Gallus gallus
M460RVMESMLKSEE4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
M761YNSVFMQRLKT3Homo sapiens, Mus musculus, Rattus norvegicus
M761YNLVFMQKLKT1Gallus gallus
N472RLSIQNFSKLL3Homo sapiens, Mus musculus, Rattus norvegicus
N472RLSVHNFSKLL1Gallus gallus
N716ICKVKNIDLKF3Homo sapiens, Mus musculus, Rattus norvegicus
N716ICKVKNVDLRF1Gallus gallus
N757IIVFYNSVFMQ3Homo sapiens, Mus musculus, Rattus norvegicus
N757IIVFYNLVFMQ1Gallus gallus
R467KSEEERLSIQN3Homo sapiens, Mus musculus, Rattus norvegicus
R467KSEEERLSVHN1Gallus gallus
R656YKKVYRLAYLR3Homo sapiens, Mus musculus, Rattus norvegicus
R656YKKVFRLAYLR1Gallus gallus
R775QYASTRPPTLS3Homo sapiens, Mus musculus, Rattus norvegicus
R775QYASNRPPTLS1Gallus gallus
S534YKVIESFIKVE3Gallus gallus, Mus musculus, Rattus norvegicus
S534YKVIESFIKAE1Homo sapiens
S644QKPLKSTSLSL2Homo sapiens, Rattus norvegicus
S644QKPQKSTSLSL1Gallus gallus
S644QKPLKSTSLAL1Mus musculus
S646PLKSTSLSLFY2Homo sapiens, Rattus norvegicus
S646PQKSTSLSLFY1Gallus gallus
S646PLKSTSLALFY1Mus musculus
S773ILQYASTRPPT3Homo sapiens, Mus musculus, Rattus norvegicus
S773ILQYASNRPPT1Gallus gallus
T645KPLKSTSLSLF2Homo sapiens, Rattus norvegicus
T645KPQKSTSLSLF1Gallus gallus
T645KPLKSTSLALF1Mus musculus
T774LQYASTRPPTL3Homo sapiens, Mus musculus, Rattus norvegicus
T774LQYASNRPPTL1Gallus gallus
V531FDFYKVIESFI4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
V714YGICKVKNIDL3Homo sapiens, Mus musculus, Rattus norvegicus
V714YGICKVKNVDL1Gallus gallus
Y709MMCSMYGICKV4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
Y756SIIVFYNSVFM3Homo sapiens, Mus musculus, Rattus norvegicus
Y756SIIVFYNLVFM1Gallus gallus


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