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 HDAC6
Gene summary
Basic gene Info.Gene symbolHDAC6
Gene namehistone deacetylase 6
SynonymsCPBHM|HD6|PPP1R90
CytomapUCSC genome browser: Xp11.23
Type of geneprotein-coding
RefGenesNM_006044.2,
Descriptionprotein phosphatase 1, regulatory subunit 90
Modification date20141207
dbXrefs MIM : 300272
HGNC : HGNC
Ensembl : ENSG00000094631
HPRD : 02228
Vega : OTTHUMG00000034496
ProteinUniProt: Q9UBN7
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HDAC6
BioGPS: 10013
PathwayNCI Pathway Interaction Database: HDAC6
KEGG: HDAC6
REACTOME: HDAC6
Pathway Commons: HDAC6
ContextiHOP: HDAC6
ligand binding site mutation search in PubMed: HDAC6
UCL Cancer Institute: HDAC6
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0016575histone deacetylation10220385
GO:0090042tubulin deacetylation19228685
GO:1901300positive regulation of hydrogen peroxide-mediated programmed cell death18606987


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Ligand binding site mutations for HDAC6
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
H1115H1115RBLCA1
Y1156I1157VBRCA1
R1155R1155CCOAD1
H1170P1171LUCEC1
W1182A1181VUCEC1
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 HDAC6
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
H1170P1171L0.34491491
Y1156I1157V-1.2336567
R1155R1155C-1.1814029
W1182A1181V-0.72036106
H1115H1115R-0.047841821
(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 HDAC6 from PDB

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Differential gene expression and gene-gene network for HDAC6
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 HDAC6 and the right PPI network was created from samples without mutations in the LBS of HDAC6. 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 HDAC6
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0025202Melanoma2Biomarker
umls:C0919267Ovarian Neoplasms1Biomarker

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

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Pharmacological information for HDAC6
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|investigationalDB02546VorinostatSmall molecule
InvestigationalDB05223SB939Small molecule
Approved|investigationalDB06176RomidepsinSmall molecule
Approved|investigationalDB06603PanobinostatSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of HDAC6 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of HDAC6
Multiple alignments for Q9UBN7 in multiple species
LBSAA sequence# speciesSpecies
C1113TPLPWCPHLVA1Homo sapiens
C1113VPLATCPHLKE1Caenorhabditis elegans
C1113TPLSWCPHLMA1Mus musculus
C1133DVTQPCGDCGT1Homo sapiens
C1133NARTACSECQI1Caenorhabditis elegans
C1133DVSQPCKTCGT1Mus musculus
C1136QPCGDCGTIQE1Homo sapiens
C1136TACSECQIGAE1Caenorhabditis elegans
C1136QPCKTCGTVQE1Mus musculus
C1145QENWVCLSCYQ1Homo sapiens
C1145AEVWTCLTCYK1Caenorhabditis elegans
C1145QENWVCLTCYQ1Mus musculus
C1148WVCLSCYQVYC1Homo sapiens
C1148WTCLTCYKYNC1Caenorhabditis elegans
C1148WVCLTCYQVYC1Mus musculus
C1153CYQVYCGRYIN1Homo sapiens
C1153CYKYNCGRFVN1Caenorhabditis elegans
C1153CYQVYCSRYVN1Mus musculus
C1183DLSAWCYYCQA1Homo sapiens
C1183DLSVWCYPCDS1Caenorhabditis elegans
C1183DLSTWCYVCQA1Mus musculus
C1186AWCYYCQAYVH1Homo sapiens
C1186VWCYPCDSYVH1Caenorhabditis elegans
C1186TWCYVCQAYVH1Mus musculus
D1178VLSYIDLSAWC1Homo sapiens
D1178ALSMADLSVWC1Caenorhabditis elegans
D1178VLSCVDLSTWC1Mus musculus
E1141CGTIQENWVCL1Homo sapiens
E1141CQIGAEVWTCL1Caenorhabditis elegans
E1141CGTVQENWVCL1Mus musculus
G1154YQVYCGRYING1Homo sapiens
G1154YKYNCGRFVNE1Caenorhabditis elegans
G1154YQVYCSRYVNA1Mus musculus
H1115LPWCPHLVAVC1Homo sapiens
H1115LATCPHLKEVK1Caenorhabditis elegans
H1115LSWCPHLMAVC1Mus musculus
H1160RYINGHMLQHH1Homo sapiens
H1160RFVNEHAMMHH1Caenorhabditis elegans
H1160RYVNAHMVCHH1Mus musculus
H1164GHMLQHHGNSG1Homo sapiens
H1164EHAMMHHLSSS1Caenorhabditis elegans
H1164AHMVCHHEASE1Mus musculus
H1170HGNSGHPLVLS1Homo sapiens
H1170HLSSSHPMALS1Caenorhabditis elegans
H1170HEASEHPLVLS1Mus musculus
H1192QAYVHHQALLD1Homo sapiens
H1192DSYVHNPALIG1Caenorhabditis elegans
H1192QAYVHHEDLQD1Mus musculus
I1177LVLSYIDLSAW1Homo sapiens
I1177MALSMADLSVW1Caenorhabditis elegans
I1177LVLSCVDLSTW1Mus musculus
Q1187WCYYCQAYVHH1Homo sapiens
Q1187WCYPCDSYVHN1Caenorhabditis elegans
Q1187WCYVCQAYVHH1Mus musculus
R1155QVYCGRYINGH1Homo sapiens
R1155KYNCGRFVNEH1Caenorhabditis elegans
R1155QVYCSRYVNAH1Mus musculus
W1143TIQENWVCLSC1Homo sapiens
W1143IGAEVWTCLTC1Caenorhabditis elegans
W1143TVQENWVCLTC1Mus musculus
W1182IDLSAWCYYCQ1Homo sapiens
W1182ADLSVWCYPCD1Caenorhabditis elegans
W1182VDLSTWCYVCQ1Mus musculus
Y1156VYCGRYINGHM1Homo sapiens
Y1156YNCGRFVNEHA1Caenorhabditis elegans
Y1156VYCSRYVNAHM1Mus musculus
Y1184LSAWCYYCQAY1Homo sapiens
Y1184LSVWCYPCDSY1Caenorhabditis elegans
Y1184LSTWCYVCQAY1Mus musculus
Y1189YYCQAYVHHQA1Homo sapiens
Y1189YPCDSYVHNPA1Caenorhabditis elegans
Y1189YVCQAYVHHED1Mus musculus


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