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 DNMT3A
Gene summary
Basic gene Info.Gene symbolDNMT3A
Gene nameDNA (cytosine-5-)-methyltransferase 3 alpha
SynonymsDNMT3A2|M.HsaIIIA|TBRS
CytomapUCSC genome browser: 2p23
Type of geneprotein-coding
RefGenesNM_022552.4,
NM_153759.3,NM_175629.2,NM_175630.1,
DescriptionDNA (cytosine-5)-methyltransferase 3ADNA MTase HsaIIIADNA cytosine methyltransferase 3A2
Modification date20141207
dbXrefs MIM : 602769
HGNC : HGNC
Ensembl : ENSG00000119772
HPRD : 04141
Vega : OTTHUMG00000094777
ProteinUniProt: Q9Y6K1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DNMT3A
BioGPS: 1788
PathwayNCI Pathway Interaction Database: DNMT3A
KEGG: DNMT3A
REACTOME: DNMT3A
Pathway Commons: DNMT3A
ContextiHOP: DNMT3A
ligand binding site mutation search in PubMed: DNMT3A
UCL Cancer Institute: DNMT3A
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
GO:0006306DNA methylation12138111
GO:0090116C-5 methylation of cytosine12138111


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Ligand binding site mutations for DNMT3A

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
R891G890DBRCA1
R688S689CHNSC1
C557R556MHNSC1
L730R729QHNSC1
L730R729QLAML1
L730R729WLAML1
C497C497YLAML1
T645G646VLAML1
R891G890CLUAD1
P709P709LLUAD1
Y533Y533CLUSC1
D686G685ESKCM1
C524E523VSTAD1
C524A525VSTAD1
E664E664DSTAD1
L730R729WSTAD1
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 DNMT3A
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
T645G646V0.34857624
L730R729Q-1.3317653
L730R729W-1.009086
C557R556M-0.86329103
C524A525V-0.78072899
C524E523V-0.77754141
R891G890D-0.72435147
Y533Y533C-0.69963674
E664E664D-0.64405454
R891G890C-0.5429574
D686G685E-0.44064175
R688S689C-0.29054329
C497C497Y-0.17571357
P709P709L-0.17446995
(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 DNMT3A from PDB

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Differential gene expression and gene-gene network for DNMT3A
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 DNMT3A and the right PPI network was created from samples without mutations in the LBS of DNMT3A. 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 DNMT3A
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0020981Immunoblastic Lymphadenopathy2Biomarker, GeneticVariation
umls:C0079774Lymphoma, T-Cell, Peripheral2Biomarker
umls:C0010346Crohn Disease1Biomarker, GeneticVariation
umls:C3714756Intellectual Disability1Biomarker
umls:C0023465Leukemia, Monocytic, Acute1Biomarker
umls:C1458155Breast Neoplasms1Biomarker
umls:C0376634Craniofacial Abnormalities1Biomarker
umls:C0282631Facies1Biomarker
umls:C0018273Growth Disorders1Biomarker

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

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Pharmacological information for DNMT3A
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 DNMT3A go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)3a1aAC497
ZNZINC(2+)4u7pAC497
ZNZINC(2+)4u7tAC497
ZNZINC(2+)4u7tCC497
ZNZINC(2+)4qbqAC497
ZNZINC(2+)4qbqCC497
ZNZINC(2+)4qbrAC497
ZNZINC(2+)4qbrCC497
ZNZINC(2+)4qbsAC497
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA,ARG,LYS,SER)4u7tAC524
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA,ARG,LYS,SER)4u7tCC524 Y533
SAHS-ADENOSYL-L-HOMOCYSTEINE4u7pAT645 E664 D686 P709 L730 R891
SAHS-ADENOSYL-L-HOMOCYSTEINE4u7tAT645 E664 D686 R688 L730 R891
SAHS-ADENOSYL-L-HOMOCYSTEINE4u7tCT645 E664 D686 R688 L730 R891
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA)4qbrAY533
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA)4qbrCY533
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA)4qbsAY533 C557


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Conservation information for LBS of DNMT3A
Multiple alignments for Q9Y6K1 in multiple species
LBSAA sequence# speciesSpecies
A575GAAQAAIKEDP4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C494NIEDICISCGS4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C497DICISCGSLNV4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C514FIGGMCQNCKN3Gallus gallus, Mus musculus, Rattus norvegicus
C514FVGGMCQNCKN1Homo sapiens
C517GMCQNCKNCFL4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C520QNCKNCFLECA4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C524NCFLECAYQYD4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C537GYQSYCTICCG4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C540SYCTICCGGRE4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C541YCTICCGGREV4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C557NNCCRCFCVEC4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C559CCRCFCVECVD4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C562CFCVECVDLLV4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
C666IASEVCEDSIT4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
D529CAYQYDDDGYQ4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
D531YQYDDDGYQSY4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
D579AAIKEDPWNCY4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
D641VLSLFDGIATG4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
D686IMYVGDVRSVT3Homo sapiens, Mus musculus, Rattus norvegicus
D686IMYVGDVRNVT1Gallus gallus
E545CCGGREVLMCG4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
E578QAAIKEDPWNC4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
E664RYIASEVCEDS4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
F640RVLSLFDGIAT4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
G542CTICCGGREVL4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
G543TICCGGREVLM4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
G642LSLFDGIATGL4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
G707DLVIGGSPCND4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I576AAQAAIKEDPW4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I643SLFDGIATGLL4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L547GGREVLMCGNN4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L730EGTGRLFFEFY4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
M548GREVLMCGNNN4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
P709VIGGSPCNDLS4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
Q534DDDGYQSYCTI4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
R544ICCGGREVLMC4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
R688YVGDVRSVTQK3Homo sapiens, Mus musculus, Rattus norvegicus
R688YVGDVRNVTQK1Gallus gallus
R891QRLLGRSWSVP4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
S535DDGYQSYCTIC4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
S663DRYIASEVCED4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
S892RLLGRSWSVPV4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
T645FDGIATGLLVL4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
V546CGGREVLMCGN4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
V665YIASEVCEDSI4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
V687MYVGDVRSVTQ3Homo sapiens, Mus musculus, Rattus norvegicus
V687MYVGDVRNVTQ1Gallus gallus
W581IKEDPWNCYMC4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
W893LLGRSWSVPVI4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
Y533YDDDGYQSYCT4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
Y536DGYQSYCTICC4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus


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