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 USP13
Gene summary
Basic gene Info.Gene symbolUSP13
Gene nameubiquitin specific peptidase 13 (isopeptidase T-3)
CytomapUCSC genome browser: 3q26.2-q26.3
Type of geneprotein-coding
Descriptiondeubiquitinating enzyme 13isopeptidase T-3ubiquitin carboxyl-terminal hydrolase 13ubiquitin specific protease 13 (isopeptidase T-3)ubiquitin thioesterase 13ubiquitin thiolesterase 13ubiquitin-specific-processing protease 13
Modification date20141207
dbXrefs MIM : 603591
Ensembl : ENSG00000058056
HPRD : 04666
Vega : OTTHUMG00000157783
ProteinUniProt: Q92995
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_USP13
BioGPS: 8975
PathwayNCI Pathway Interaction Database: USP13
Pathway Commons: USP13
ContextiHOP: USP13
ligand binding site mutation search in PubMed: USP13
UCL Cancer Institute: USP13
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0010506regulation of autophagy21962518
GO:0050821protein stabilization21659512
GO:0070536protein K63-linked deubiquitination22216260

Ligand binding site mutations for USP13

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for USP13
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
(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 USP13 from PDB

Differential gene expression and gene-gene network for USP13
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 USP13 and the right PPI network was created from samples without mutations in the LBS of USP13. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for USP13
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0311375Arsenic Poisoning1Biomarker
umls:C0037274Skin Diseases1Biomarker

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

Pharmacological information for USP13
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 USP13 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of USP13
Multiple alignments for Q92995 in multiple species
LBSAA sequence# speciesSpecies
C211PSGWKCARCDL3Homo sapiens, Mus musculus, Bos taurus
C211PSGWKCAKCEM1Danio rerio
C214WKCARCDLREN3Homo sapiens, Mus musculus, Bos taurus
C214WKCAKCEMREN1Danio rerio
C231DGSVLCGKWFF4Homo sapiens, Danio rerio, Mus musculus, Bos taurus
H244SGGNGHALEHY4Homo sapiens, Danio rerio, Mus musculus, Bos taurus

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