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 KDM7A
Gene summary
Basic gene Info.Gene symbolKDM7A
Gene namelysine (K)-specific demethylase 7A
SynonymsJHDM1D
CytomapUCSC genome browser: 7q34
Type of geneprotein-coding
RefGenesNM_030647.1,
Descriptionhistone lysine demethylase JHDM1DjmjC domain-containing histone demethylation protein 1Djumonji C domain containing histone demethylase 1 homolog Djumonji C domain-containing histone demethylase 1 homolog Dlysine-specific demethylase 7lysine-specific
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000006459
Vega : OTTHUMG00000157327
ProteinUniProt: Q6ZMT4
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KDM7A
BioGPS: 80853
PathwayNCI Pathway Interaction Database: KDM7A
KEGG: KDM7A
REACTOME: KDM7A
Pathway Commons: KDM7A
ContextiHOP: KDM7A
ligand binding site mutation search in PubMed: KDM7A
UCL Cancer Institute: KDM7A
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:0033169histone H3-K9 demethylation20023638
GO:0035574histone H4-K20 demethylation20622853
GO:0070544histone H3-K36 demethylation20622853
GO:0071557histone H3-K27 demethylation20023638


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Ligand binding site mutations for KDM7A
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
L93S91YBLCA1
C58D60YCOAD1
V251V251EGBM1
Q200D202ESKCM1
D284D284ESKCM1
D280D280VSTAD1
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 KDM7A
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
V251V251E-1.0974995
D284D284E-0.7657534
Q200D202E-0.51053963
C58D60Y-0.39216807
D280D280V-0.36392011
L93S91Y-0.28265761
(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 KDM7A from PDB

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Differential gene expression and gene-gene network for KDM7A
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 KDM7A and the right PPI network was created from samples without mutations in the LBS of KDM7A. 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 KDM7A
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for KDM7A
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 KDM7A go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)3kv5DC58
ZNZINC(2+)3kv5AC58
ZNZINC(2+)3kv6AC58
ZNZINC(2+)3kv6DC58
FE2IRON(2+)3kv5DD284
FE2IRON(2+)3kv5AD284
OGAN-OXALYLGLYCINE3kv5AD284
FE2IRON(2+)3kv6AD284
FE2IRON(2+)3kv6DD284
AKG2-OXOGLUTARIC ACID3kv6DD284
FE2IRON(2+)3kv9AD284
FE2IRON(2+)3kvaAD284
AKG2-OXOGLUTARIC ACID3kvaAD284
OGAN-OXALYLGLYCINE3kvbAD284
AKG2-OXOGLUTARIC ACID3u78AD284
FE2IRON(2+)3kv5AL93
E677-[(5-AMINOPENTYL)OXY]-N~4~-(1-BENZYLPIPERIDIN-4-YL)-N~2~-[3-(DIMETHYLAMINO)PROPYL]-6-METHOXYQUINAZOLINE-2,4-DIAMINE3u78AQ200 D280 D284
FE2IRON(2+)3kv9AV251
FE2IRON(2+)3kvaAV251


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Conservation information for LBS of KDM7A
Multiple alignments for Q6ZMT4 in multiple species
LBSAA sequence# speciesSpecies
C40PPPVYCVCRQP2Homo sapiens, Mus musculus
C40--PVYCVCRQP1Xenopus tropicalis
C42PVYCVCRQPYD3Homo sapiens, Xenopus tropicalis, Mus musculus
C55RFMIECDICKD2Homo sapiens, Xenopus tropicalis
C55RFMIECDVCKD1Mus musculus
C58IECDICKDWFH2Homo sapiens, Xenopus tropicalis
C58IECDVCKDWFH1Mus musculus
C66WFHGSCVGVEE2Homo sapiens, Mus musculus
C66WFHSSCVKVEE1Xenopus tropicalis
C82IDLYHCPNCAV1Homo sapiens
C82IDLYHCPNCEV1Xenopus tropicalis
C82IDLYHCPDCAA1Mus musculus
C85YHCPNCAVLHG1Homo sapiens
C85YHCPNCEVLHG1Xenopus tropicalis
C85YHCPDCAALHG1Mus musculus
D280QDSYTDFHIDF3Homo sapiens, Xenopus tropicalis, Mus musculus
D284TDFHIDFGGTS3Homo sapiens, Xenopus tropicalis, Mus musculus
D392RLKTPDLFKFP3Homo sapiens, Xenopus tropicalis, Mus musculus
D56FMIECDICKDW2Homo sapiens, Xenopus tropicalis
D56FMIECDVCKDW1Mus musculus
F285DFHIDFGGTSV3Homo sapiens, Xenopus tropicalis, Mus musculus
F369AFGGNFLHNLN3Homo sapiens, Xenopus tropicalis, Mus musculus
H282SYTDFHIDFGG3Homo sapiens, Xenopus tropicalis, Mus musculus
H354PTGWIHAVLTS3Homo sapiens, Xenopus tropicalis, Mus musculus
H63CKDWFHGSCVG2Homo sapiens, Mus musculus
H63CKDWFHSSCVK1Xenopus tropicalis
H81DIDLYHCPNCA1Homo sapiens
H81DIDLYHCPNCE1Xenopus tropicalis
H81DIDLYHCPDCA1Mus musculus
I226KVLNVISLEFS3Homo sapiens, Xenopus tropicalis, Mus musculus
I57MIECDICKDWF2Homo sapiens, Xenopus tropicalis
I57MIECDVCKDWF1Mus musculus
K299VLWGEKIFYLI2Homo sapiens, Mus musculus
K299VLWGEKVFYLI1Xenopus tropicalis
L271VQKYCLMGVQD3Homo sapiens, Xenopus tropicalis, Mus musculus
L370FGGNFLHNLNI3Homo sapiens, Xenopus tropicalis, Mus musculus
L79AVDIDLYHCPN1Homo sapiens
L79AADIDLYHCPN1Xenopus tropicalis
L79AVDIDLYHCPD1Mus musculus
L93LHGSSLMKKRR2Homo sapiens, Mus musculus
L93LHGPSQLKKRR1Xenopus tropicalis
N224RPKVLNVISLE3Homo sapiens, Xenopus tropicalis, Mus musculus
N368MAFGGNFLHNL3Homo sapiens, Xenopus tropicalis, Mus musculus
P391KRLKTPDLFKF3Homo sapiens, Xenopus tropicalis, Mus musculus
Q200IDVARQADSKM3Homo sapiens, Xenopus tropicalis, Mus musculus
S249IAKKLSWVENY1Homo sapiens
S249ISKKLSWVENY1Xenopus tropicalis
S249IARKLSWVENY1Mus musculus
T279VQDSYTDFHID3Homo sapiens, Xenopus tropicalis, Mus musculus
T358IHAVLTSQDCM3Homo sapiens, Xenopus tropicalis, Mus musculus
V251KKLSWVENYWP2Homo sapiens, Xenopus tropicalis
V251RKLSWVENYWP1Mus musculus
V290FGGTSVWYHVL3Homo sapiens, Xenopus tropicalis, Mus musculus
V356GWIHAVLTSQD3Homo sapiens, Xenopus tropicalis, Mus musculus
W250AKKLSWVENYW1Homo sapiens
W250SKKLSWVENYW1Xenopus tropicalis
W250ARKLSWVENYW1Mus musculus
Y292GTSVWYHVLWG3Homo sapiens, Xenopus tropicalis, Mus musculus


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