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 PRPS1
Gene summary
Basic gene Info.Gene symbolPRPS1
Gene namephosphoribosyl pyrophosphate synthetase 1
SynonymsARTS|CMTX5|DFN2|DFNX1|PPRibP|PRS-I|PRSI
CytomapUCSC genome browser: Xq22.3
Type of geneprotein-coding
RefGenesNM_001204402.1,
NM_002764.3,
DescriptiondJ1070B1.2 (phosphoribosyl pyrophosphate synthetase 1)deafness 2, perceptive, congenitaldeafness, X-linked 2, perceptive, congenitalphosphoribosyl pyrophosphate synthase Iribose-phosphate diphosphokinase 1ribose-phosphate pyrophosphokinase 1
Modification date20141219
dbXrefs MIM : 311850
HGNC : HGNC
Ensembl : ENSG00000147224
HPRD : 02413
Vega : OTTHUMG00000022167
ProteinUniProt: P60891
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRPS1
BioGPS: 5631
PathwayNCI Pathway Interaction Database: PRPS1
KEGG: PRPS1
REACTOME: PRPS1
Pathway Commons: PRPS1
ContextiHOP: PRPS1
ligand binding site mutation search in PubMed: PRPS1
UCL Cancer Institute: PRPS1
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 PRPS1
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
R96A95VKIRC1
K102S103NSKCM1
D101D101YUCEC1
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 PRPS1
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
K102S103N-1.072272
R96A95V-0.71179315
D101D101Y-0.58536491
(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 PRPS1 from PDB

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Differential gene expression and gene-gene network for PRPS1
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 PRPS1 and the right PPI network was created from samples without mutations in the LBS of PRPS1. 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 PRPS1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0796028Arts syndrome1Biomarker, GeneticVariation
umls:C1839566Optic atrophy polyneuropathy deafness1Biomarker, GeneticVariation
umls:C0043094Weight Gain1Biomarker

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

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Pharmacological information for PRPS1
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 PRPS1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
SO4SULFATE2hcrAD101 K102
AMPAMP2hcrAR96
AMPAMP2hcrBR96 D101


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Conservation information for LBS of PRPS1
Multiple alignments for P60891 in multiple species
LBSAA sequence# speciesSpecies
D101RQDKKDKSRAP4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
D101RADRKTQGRES3Arabidopsis thaliana, Arabidopsis thaliana, Arabidopsis thaliana
D101RADRKSQGRES1Oryza sativa subsp. japonica
H130ITMDLHASQIQ4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
H130LACDLHSGQSM3Arabidopsis thaliana, Arabidopsis thaliana, Arabidopsis thaliana
H130LVCDLHSSQAM1Oryza sativa subsp. japonica
H304AIRRTHNGESV4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
H304TIWRVHDDSSV2Arabidopsis thaliana, Arabidopsis thaliana
H304TIWRVHDDCSV1Oryza sativa subsp. japonica
H304TIWRVHDDCSG1Arabidopsis thaliana
K102QDKKDKSRAPI4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
K102ADRKTQGRESI3Arabidopsis thaliana, Arabidopsis thaliana, Arabidopsis thaliana
K102ADRKSQGRESI1Oryza sativa subsp. japonica
K99YARQDKKDKSR4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
K99YARADRKTQGR3Arabidopsis thaliana, Arabidopsis thaliana, Arabidopsis thaliana
K99YARADRKSQGR1Oryza sativa subsp. japonica
N144DIPVDNLYAEP4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
N144DIPVDHVYGQP2Oryza sativa subsp. japonica, Arabidopsis thaliana
N144DIPVDHVYCQP2Arabidopsis thaliana, Arabidopsis thaliana
Q135HASQIQGFFDI4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q135HSGQSMGYFDI3Arabidopsis thaliana, Arabidopsis thaliana, Arabidopsis thaliana
Q135HSSQAMGYFDI1Oryza sativa subsp. japonica
Q97FPYARQDKKDK4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q97FGYARADRKTQ3Arabidopsis thaliana, Arabidopsis thaliana, Arabidopsis thaliana
Q97FGYARADRKSQ1Oryza sativa subsp. japonica
R96CFPYARQDKKD4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
R96YFGYARADRKT3Arabidopsis thaliana, Arabidopsis thaliana, Arabidopsis thaliana
R96YFGYARADRKS1Oryza sativa subsp. japonica
S132MDLHASQIQGF4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
S132CDLHSGQSMGY3Arabidopsis thaliana, Arabidopsis thaliana, Arabidopsis thaliana
S132CDLHSSQAMGY1Oryza sativa subsp. japonica
Y146PVDNLYAEPAV4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Y146PVDHVYGQPVI2Oryza sativa subsp. japonica, Arabidopsis thaliana
Y146PVDHVYCQPVI2Arabidopsis thaliana, Arabidopsis thaliana
Y54RGEDVYIVQSG4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Y54RGCDVFLVQPT3Oryza sativa subsp. japonica, Arabidopsis thaliana, Arabidopsis thaliana
Y54RGCDVYLVQPT1Arabidopsis thaliana


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