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 RPE
Gene summary
Basic gene Info.Gene symbolRPE
Gene nameribulose-5-phosphate-3-epimerase
SynonymsRPE2-1
CytomapUCSC genome browser: 2q32-q33.3
Type of geneprotein-coding
RefGenesNM_001278282.1,
NM_001278283.1,NM_001278285.1,NM_001278286.1,NM_001278288.1,
NM_001278289.1,NM_006916.2,NM_199229.2,
Descriptionribulose-phosphate 3-epimerase
Modification date20141211
dbXrefs MIM : 180480
HGNC : HGNC
Ensembl : ENSG00000197713
HPRD : 01608
ProteinUniProt: Q96AT9
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPE
BioGPS: 6120
PathwayNCI Pathway Interaction Database: RPE
KEGG: RPE
REACTOME: RPE
Pathway Commons: RPE
ContextiHOP: RPE
ligand binding site mutation search in PubMed: RPE
UCL Cancer Institute: RPE
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
GO:0005975carbohydrate metabolic process20923965
GO:0006098pentose-phosphate shunt20923965


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Ligand binding site mutations for RPE
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
M39M39RLUAD1
D175E173DSTAD1
S198A199DUCEC1
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 RPE
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
D175E173D-1.5654573
M39M39R-1.339508
S198A199D-0.00359384
(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 RPE from PDB

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Differential gene expression and gene-gene network for RPE
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 RPE and the right PPI network was created from samples without mutations in the LBS of RPE. 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 RPE
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0017661Glomerulonephritis, IGA1Biomarker

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

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Pharmacological information for RPE
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 RPE go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
FE2IRON(2+)3ovpAD175
FE2IRON(2+)3ovpBD175
FE2IRON(2+)3ovqAD175
FE2IRON(2+)3ovqBD175
FE2IRON(2+)3ovrAD175
FE2IRON(2+)3ovrBD175
ZNZINC(2+)3qc3AD175
FEIRON(3+)3qc3AD175
ZNZINC(2+)3qc3BD175
FEIRON(3+)3qc3BD175
5RPRIBULOSE-5-PHOSPHATE3ovqAD175 S198
5RPRIBULOSE-5-PHOSPHATE3ovqBM39 D175 S198
5SPD-XYLULOSE 5-PHOSPHATE3ovrAM39 D175 S198
5SPD-XYLULOSE 5-PHOSPHATE3ovrBM39 D175 S198


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Conservation information for LBS of RPE
Multiple alignments for Q96AT9 in multiple species
LBSAA sequence# speciesSpecies
D175LDIEVDGGVGP2Homo sapiens, Mus musculus
D175LNIQVDGGLGK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D175LDIQVDGGLGK1Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
D175LNVEVDGGLSL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D175LDIEVDGGLGP1Oryza sativa subsp. japonica
D37DYLHLDVMDGH2Homo sapiens, Mus musculus
D37DWLHIDVMDGH1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D37EWLHIDVMDGH1Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
D37DWLHVDVMDAQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D37DWLHMDIMDGH1Oryza sativa subsp. japonica
F147TVEPGFGGQKF5Homo sapiens, Mus musculus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056), Oryza sativa subsp. japonica
F147TVEPGKGGQSF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G146MTVEPGFGGQK5Homo sapiens, Mus musculus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056), Oryza sativa subsp. japonica
G146MTVEPGKGGQS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G148VEPGFGGQKFM5Homo sapiens, Mus musculus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056), Oryza sativa subsp. japonica
G148VEPGKGGQSFM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G149EPGFGGQKFME3Homo sapiens, Mus musculus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G149EPGFGGQKFMP2Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056), Oryza sativa subsp. japonica
G149EPGKGGQSFMP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G176DIEVDGGVGPD2Homo sapiens, Mus musculus
G176NIQVDGGLGKE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G176DIQVDGGLGKE1Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
G176NVEVDGGLSLK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G176DIEVDGGLGPS1Oryza sativa subsp. japonica
G177IEVDGGVGPDT2Homo sapiens, Mus musculus
G177IQVDGGLGKET2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
G177VEVDGGLSLKT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G177IEVDGGLGPST1Oryza sativa subsp. japonica
G197NMIVSGSAIMR2Homo sapiens, Mus musculus
G197NVIVAGTSVFT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G197NVIVAGTSVFA1Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
G197NVIVAGTAVFH1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G197NCIVAGSSIFG1Oryza sativa subsp. japonica
H35GADYLHLDVMD2Homo sapiens, Mus musculus
H35GADWLHIDVMD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H35GAEWLHIDVMD1Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H35GSDWLHVDVMD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H35GADWLHMDIMD1Oryza sativa subsp. japonica
H70PFFDMHMMVSK1Homo sapiens
H70PFFDMHMMVSR1Mus musculus
H70AFFDCHMMVEN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H70AFFDCHMMVAE1Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
H70AFFDCHLMVIE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H70AYLDCHLMVTN1Oryza sativa subsp. japonica
L12IGPSILNSDLA2Homo sapiens, Mus musculus
L12IAPSILASDFA2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
L12IAPSLLAGDFA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L12IAPSMLSSDFA1Oryza sativa subsp. japonica
M39LHLDVMDGHFV2Homo sapiens, Mus musculus
M39LHIDVMDGHFV2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
M39LHVDVMDAQFV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M39LHMDIMDGHFV1Oryza sativa subsp. japonica
M72FDMHMMVSKPE1Homo sapiens
M72FDMHMMVSRPE1Mus musculus
M72FDCHMMVENPE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M72FDCHMMVAEPE1Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
M72FDCHLMVIEPE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M72LDCHLMVTNPS1Oryza sativa subsp. japonica
P145VMTVEPGFGGQ5Homo sapiens, Mus musculus, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056), Oryza sativa subsp. japonica
P145VMTVEPGKGGQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S10CKIGPSILNSD2Homo sapiens, Mus musculus
S10PIIAPSILASD2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
S10AKIAPSLLAGD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S10AKIAPSMLSSD1Oryza sativa subsp. japonica
S198MIVSGSAIMRS2Homo sapiens, Mus musculus
S198VIVAGTSVFTA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S198VIVAGTSVFAA1Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
S198VIVAGTAVFHA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S198CIVAGSSIFGA1Oryza sativa subsp. japonica


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