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 PTPN5
Gene summary
Basic gene Info.Gene symbolPTPN5
Gene nameprotein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)
SynonymsPTPSTEP|STEP
CytomapUCSC genome browser: 11p15.1
Type of geneprotein-coding
RefGenesNM_001039970.1,
NM_001278236.1,NM_001278238.1,NM_001278239.1,NM_006906.1,
NM_032781.3,
Descriptionneural-specific protein-tyrosine phosphataseprotein-tyrosine phosphatase striatum-enrichedstriatum-enriched protein-tyrosine phosphatasetyrosine-protein phosphatase non-receptor type 5
Modification date20141207
dbXrefs MIM : 176879
HGNC : HGNC
Ensembl : ENSG00000110786
HPRD : 01472
Vega : OTTHUMG00000134304
ProteinUniProt: P54829
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PTPN5
BioGPS: 84867
PathwayNCI Pathway Interaction Database: PTPN5
KEGG: PTPN5
REACTOME: PTPN5
Pathway Commons: PTPN5
ContextiHOP: PTPN5
ligand binding site mutation search in PubMed: PTPN5
UCL Cancer Institute: PTPN5
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 PTPN5

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
Y328K329EOV1
R502G504SUCEC1
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 PTPN5
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
R502G504S-0.93762716
Y328K329E-0.42436001
(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 PTPN5 from PDB

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Differential gene expression and gene-gene network for PTPN5
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 PTPN5 and the right PPI network was created from samples without mutations in the LBS of PTPN5. 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 PTPN5
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0027746Nerve Degeneration1Biomarker

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

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Pharmacological information for PTPN5
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 PTPN5 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of PTPN5
Multiple alignments for P54829 in multiple species
LBSAA sequence# speciesSpecies
A498IVHCSAGIGRT3Homo sapiens, Mus musculus, Rattus norvegicus
G499VHCSAGIGRTG3Homo sapiens, Mus musculus, Rattus norvegicus
G501CSAGIGRTGCF3Homo sapiens, Mus musculus, Rattus norvegicus
I331NRYKTILPNPH3Homo sapiens, Mus musculus, Rattus norvegicus
I500HCSAGIGRTGC3Homo sapiens, Mus musculus, Rattus norvegicus
K463SWPDQKTPDRA3Homo sapiens, Mus musculus, Rattus norvegicus
Q544IQTCEQYQFVH3Homo sapiens, Mus musculus, Rattus norvegicus
R502SAGIGRTGCFI3Homo sapiens, Mus musculus, Rattus norvegicus
S497IIVHCSAGIGR3Homo sapiens, Mus musculus, Rattus norvegicus
W459YWFTSWPDQKT3Homo sapiens, Mus musculus, Rattus norvegicus
Y328VRKNRYKTILP3Homo sapiens, Mus musculus, Rattus norvegicus


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