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 DNMT3L
Gene summary
Basic gene Info.Gene symbolDNMT3L
Gene nameDNA (cytosine-5-)-methyltransferase 3-like
CytomapUCSC genome browser: 21q22.3
Type of geneprotein-coding
DescriptionDNA (cytosine-5)-methyltransferase 3-likecytosine-5-methyltransferase 3-like proteinhuman cytosine-5-methyltransferase 3-like protein
Modification date20141207
dbXrefs MIM : 606588
Ensembl : ENSG00000142182
HPRD : 09417
Vega : OTTHUMG00000086914
ProteinUniProt: Q9UJW3
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DNMT3L
BioGPS: 29947
PathwayNCI Pathway Interaction Database: DNMT3L
Pathway Commons: DNMT3L
ContextiHOP: DNMT3L
ligand binding site mutation search in PubMed: DNMT3L
UCL Cancer Institute: DNMT3L
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0043085positive regulation of catalytic activity16543361
GO:0045892negative regulation of transcription, DNA-templated12202768

Ligand binding site mutations for DNMT3L

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 DNMT3L
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 DNMT3L from PDB

Differential gene expression and gene-gene network for DNMT3L
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 DNMT3L and the right PPI network was created from samples without mutations in the LBS of DNMT3L. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for DNMT3L
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for DNMT3L
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 DNMT3L go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA)2pvcBV134
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA)2pvcCV134

Conservation information for LBS of DNMT3L
Multiple alignments for Q9UJW3 in multiple species
LBSAA sequence# speciesSpecies
C118CTRCYCFECVD3Homo sapiens, Mus musculus, Rattus norvegicus
C121CYCFECVDILV2Mus musculus, Rattus norvegicus
C121CYCFECVDSLV1Homo sapiens
C96GHQSYCTICCS2Mus musculus, Rattus norvegicus
C96GYQSYCSICCS1Homo sapiens
C99SYCSICCSGET1Homo sapiens
C99SYCTICCSGGT1Mus musculus
C99SYCTICCSGHT1Rattus norvegicus
D88ALFLYDDDGYQ1Homo sapiens
D88SLFLYDDDGHQ1Mus musculus
D88TLFLYDEDGHQ1Rattus norvegicus
D90FLYDDDGYQSY1Homo sapiens
D90FLYDDDGHQSY1Mus musculus
D90FLYDEDGHQSY1Rattus norvegicus
E103ICCSGETLLIC1Homo sapiens
E103ICCSGGTLFIC1Mus musculus
E103ICCSGHTLFIC1Rattus norvegicus
G102SICCSGETLLI1Homo sapiens
G102TICCSGGTLFI1Mus musculus
G102TICCSGHTLFI1Rattus norvegicus
H135TSERINAMACW2Mus musculus, Rattus norvegicus
H135TSGKVHAMSNW1Homo sapiens
I107GETLLICGNPD1Homo sapiens
I107GGTLFICESPD1Mus musculus
I107GHTLFICESPD1Rattus norvegicus
L105CSGETLLICGN1Homo sapiens
L105CSGGTLFICES1Mus musculus
L105CSGHTLFICES1Rattus norvegicus
L106SGETLLICGNP1Homo sapiens
L106SGGTLFICESP1Mus musculus
L106SGHTLFICESP1Rattus norvegicus
M137ERINAMACWVC2Mus musculus, Rattus norvegicus
M137GKVHAMSNWVC1Homo sapiens
Q93DDDGYQSYCSI1Homo sapiens
Q93DDDGHQSYCTI1Mus musculus
Q93DEDGHQSYCTI1Rattus norvegicus
S138RINAMACWVCF2Mus musculus, Rattus norvegicus
S138KVHAMSNWVCY1Homo sapiens
T104CCSGETLLICG1Homo sapiens
T104CCSGGTLFICE1Mus musculus
T104CCSGHTLFICE1Rattus norvegicus
V134GTSERINAMAC2Mus musculus, Rattus norvegicus
V134GTSGKVHAMSN1Homo sapiens
W140NAMACWVCFLC2Mus musculus, Rattus norvegicus
W140HAMSNWVCYLC1Homo sapiens
Y92YDDDGYQSYCS1Homo sapiens
Y92YDDDGHQSYCT1Mus musculus
Y92YDEDGHQSYCT1Rattus norvegicus

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