mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 KMT2D
Gene summary
Basic gene Info.Gene symbolKMT2D
Gene namelysine (K)-specific methyltransferase 2D
SynonymsAAD10|ALR|CAGL114|KABUK1|KMS|MLL2|MLL4|TNRC21
CytomapUCSC genome browser: 12q13.12
Type of geneprotein-coding
RefGenesNM_003482.3,
DescriptionALL1-related proteinKabuki make-up syndromeKabuki mental retardation syndromehistone-lysine N-methyltransferase 2Dhistone-lysine N-methyltransferase MLL2lysine N-methyltransferase 2Dmyeloid/lymphoid or mixed-lineage leukemia 2trinucleotide repeat c
Modification date20141219
dbXrefs MIM : 602113
HGNC : HGNC
Ensembl : ENSG00000167548
HPRD : 03664
Vega : OTTHUMG00000166524
ProteinUniProt: O14686
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KMT2D
BioGPS: 8085
PathwayNCI Pathway Interaction Database: KMT2D
KEGG: KMT2D
REACTOME: KMT2D
Pathway Commons: KMT2D
ContextiHOP: KMT2D
ligand binding site mutation search in PubMed: KMT2D
UCL Cancer Institute: KMT2D
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:0043627response to estrogen16603732


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Ligand binding site mutations for KMT2D
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
C5525C5525SCOAD1
C5477C5477GSTAD1
Y5512D5511AUCEC1
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 KMT2D
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
C5525C5525S-1.404374
Y5512D5511A-1.3919313
C5477C5477G-1.0716764
(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 KMT2D from PDB

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Differential gene expression and gene-gene network for KMT2D
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 KMT2D and the right PPI network was created from samples without mutations in the LBS of KMT2D. 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 KMT2D
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0796004Kabuki syndrome22Biomarker, GeneticVariation
umls:C0079744Lymphoma, Large B-Cell, Diffuse2Biomarker
umls:C0024301Lymphoma, Follicular2Biomarker
umls:C0279626Esophageal Squamous Cell Carcinoma1Biomarker
umls:C0021364Infertility, Male1Biomarker

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

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Pharmacological information for KMT2D
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 KMT2D go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)4z4pAC5477 C5525
SAHS-ADENOSYL-L-HOMOCYSTEINE4z4pAY5512 C5525


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Conservation information for LBS of KMT2D
Multiple alignments for O14686 in multiple species
LBSAA sequence# speciesSpecies


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