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 KDM5A
Gene summary
Basic gene Info.Gene symbolKDM5A
Gene namelysine (K)-specific demethylase 5A
CytomapUCSC genome browser: 12p11
Type of geneprotein-coding
DescriptionJumonji, AT rich interactive domain 1A (RBP2-like)histone demethylase JARID1Ajumonji/ARID domain-containing protein 1Alysine-specific demethylase 5Aretinoblastoma binding protein 2
Modification date20141222
dbXrefs MIM : 180202
Ensembl : ENSG00000073614
HPRD : 08915
Vega : OTTHUMG00000168055
ProteinUniProt: P29375
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KDM5A
BioGPS: 5927
PathwayNCI Pathway Interaction Database: KDM5A
Pathway Commons: KDM5A
ContextiHOP: KDM5A
ligand binding site mutation search in PubMed: KDM5A
UCL Cancer Institute: KDM5A
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0045893positive regulation of transcription, DNA-templated11358960

Ligand binding site mutations for KDM5A
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
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 KDM5A
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 KDM5A from PDB

Differential gene expression and gene-gene network for KDM5A
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 KDM5A and the right PPI network was created from samples without mutations in the LBS of KDM5A. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for KDM5A
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C3714756Intellectual Disability1Biomarker

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

Pharmacological information for KDM5A
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 KDM5A go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA,ARG)3gl6AD1633 E1649

Conservation information for LBS of KDM5A
Multiple alignments for P29375 in multiple species
LBSAA sequence# speciesSpecies
A1648S-PEMAENEDY1Homo sapiens
A1648NRSQIKPDDDY1Drosophila melanogaster
A1648S-AEMAENEDY1Mus musculus
A583YNFAEAVNFCT2Homo sapiens, Mus musculus
A583YNFAEAVNFAP1Drosophila melanogaster
C1610DENAVCAAQNC2Homo sapiens, Mus musculus
C1610DDEEECRAENC1Drosophila melanogaster
C1615CAAQNCQRPCK2Homo sapiens, Mus musculus
C1615CRAENCHKPTG1Drosophila melanogaster
C1619NCQRPCKDKVD2Homo sapiens, Mus musculus
C1619NCHKPTGREVD1Drosophila melanogaster
C1628VDWVQCDGGCD2Homo sapiens, Mus musculus
C1628VDWVQCDGGCN1Drosophila melanogaster
C1632QCDGGCDEWFH2Homo sapiens, Mus musculus
C1632QCDGGCNEWFH1Drosophila melanogaster
C1640WFHQVCVGVS-2Homo sapiens, Mus musculus
C1640WFHMYCVGLNR1Drosophila melanogaster
C1655NEDYICINCAK2Homo sapiens, Mus musculus
C1655DDDYICIRCTK1Drosophila melanogaster
C558YRTNQCAGEFV2Homo sapiens, Mus musculus
C558FRTDQHAGEFV1Drosophila melanogaster
D1621QRPCKDKVDWV2Homo sapiens, Mus musculus
D1621HKPTGREVDWV1Drosophila melanogaster
D1624CKDKVDWVQCD2Homo sapiens, Mus musculus
D1624TGREVDWVQCD1Drosophila melanogaster
D1629DWVQCDGGCDE2Homo sapiens, Mus musculus
D1629DWVQCDGGCNE1Drosophila melanogaster
D1633CDGGCDEWFHQ2Homo sapiens, Mus musculus
D1633CDGGCNEWFHM1Drosophila melanogaster
E1649-PEMAENEDYI1Homo sapiens
E1649RSQIKPDDDYI1Drosophila melanogaster
E1649-AEMAENEDYI1Mus musculus
E1651EMAENEDYICI2Homo sapiens, Mus musculus
E1651QIKPDDDYICI1Drosophila melanogaster
E485FCWHIEDHWSY2Homo sapiens, Mus musculus
E485FCWHNEDHWSY1Drosophila melanogaster
F480MCFSSFCWHIE2Homo sapiens, Mus musculus
F480MCFAAFCWHNE1Drosophila melanogaster
H1637CDEWFHQVCVG2Homo sapiens, Mus musculus
H1637CNEWFHMYCVG1Drosophila melanogaster
H483SSFCWHIEDHW2Homo sapiens, Mus musculus
H483AAFCWHNEDHW1Drosophila melanogaster
H571FPRAYHSGFNQ2Homo sapiens, Mus musculus
H571FPRAYHAGFNQ1Drosophila melanogaster
K1620CQRPCKDKVDW2Homo sapiens, Mus musculus
K1620CHKPTGREVDW1Drosophila melanogaster
K1622RPCKDKVDWVQ2Homo sapiens, Mus musculus
K1622KPTGREVDWVQ1Drosophila melanogaster
K501HWGEPKTWYGV3Homo sapiens, Drosophila melanogaster, Mus musculus
N493WSYSINYLHWG3Homo sapiens, Drosophila melanogaster, Mus musculus
Q1627KVDWVQCDGGC2Homo sapiens, Mus musculus
Q1627EVDWVQCDGGC1Drosophila melanogaster
Q1638DEWFHQVCVGV2Homo sapiens, Mus musculus
Q1638NEWFHMYCVGL1Drosophila melanogaster
S491DHWSYSINYLH3Homo sapiens, Drosophila melanogaster, Mus musculus
V1623PCKDKVDWVQC2Homo sapiens, Mus musculus
V1623PTGREVDWVQC1Drosophila melanogaster
V1626DKVDWVQCDGG2Homo sapiens, Mus musculus
V1626REVDWVQCDGG1Drosophila melanogaster
W1625KDKVDWVQCDG2Homo sapiens, Mus musculus
W1625GREVDWVQCDG1Drosophila melanogaster
W1635GGCDEWFHQVC2Homo sapiens, Mus musculus
W1635GGCNEWFHMYC1Drosophila melanogaster
W503GEPKTWYGVPS2Homo sapiens, Mus musculus
W503GEPKTWYGVPG1Drosophila melanogaster
Y1653AENEDYICINC2Homo sapiens, Mus musculus
Y1653KPDDDYICIRC1Drosophila melanogaster
Y409DVIVEYGADIS2Homo sapiens, Mus musculus
Y409DVTVEYGADLH1Drosophila melanogaster
Y472KVPWLYVGMCF2Homo sapiens, Mus musculus
Y472NAPWMYVGMCF1Drosophila melanogaster

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