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 KMT2A
Gene summary
Basic gene Info.Gene symbolKMT2A
Gene namelysine (K)-specific methyltransferase 2A
SynonymsALL-1|CXXC7|HRX|HTRX1|MLL|MLL/GAS7|MLL1|MLL1A|TET1-MLL|TRX1|WDSTS
CytomapUCSC genome browser: 11q23
Type of geneprotein-coding
RefGenesNM_001197104.1,
NM_005933.3,NM_024891.2,
DescriptionCDK6/MLL fusion proteinCXXC-type zinc finger protein 7MLL-AF4 der(11) fusion proteinMLL/GAS7 fusion proteinMLL/GMPS fusion proteinhistone-lysine N-methyltransferase 2Alysine N-methyltransferase 2Amixed lineage leukemia 1myeloid/lymphoid or mixed-l
Modification date20141207
dbXrefs MIM : 159555
HGNC : HGNC
Ensembl : ENSG00000118058
HPRD : 01162
Vega : OTTHUMG00000166337
ProteinUniProt: Q03164
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_KMT2A
BioGPS: 4297
PathwayNCI Pathway Interaction Database: KMT2A
KEGG: KMT2A
REACTOME: KMT2A
Pathway Commons: KMT2A
ContextiHOP: KMT2A
ligand binding site mutation search in PubMed: KMT2A
UCL Cancer Institute: KMT2A
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:0006461protein complex assembly15199122
GO:0045944positive regulation of transcription from RNA polymerase II promoter20861184
GO:0051568histone H3-K4 methylation19556245
GO:0080182histone H3-K4 trimethylation20861184


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Ligand binding site mutations for KMT2A
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
R3903R3903HCOAD2
C1167E1165KBLCA1
R1154R1154WCOAD1
M1585M1585IHNSC1
V1617A1618SLUAD1
H1596H1596YSKCM1
C3964R3965WSTAD1
W1594R1593HSTAD1
D1573K1574RTHCA1
C1173C1173RUCEC1
S1152S1152LUCEC1
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.

Clinical information for KMT2A from My Cancer Genome.
Lysine (K)-specific methyltransferase 2A (KMT2A; also known as MLL) is a gene that encodes a protein that functions as a transcriptional coactivator. The protein is involved in cellular processes including the regulation of gene expressionand hematopoiesis. Fusions, rearrangements, missense mutations, nonsense mutations, silent mutations, frameshift insertions and deletions, and in-frame deletions are observed in cancers such as intestinal cancer, skin cancer, and stomach cancer.Related Pathways: Chromatin remodeling/DNA methylation. Modified: December 4, 2015

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Protein structure related information for KMT2A
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
S1152S1152L0.11743409
W1594R1593H-1.4070359
V1617A1618S-1.3624322
C1167E1165K-1.2403517
R3903R3903H-1.0966848
C3964R3965W-1.0667599
M1585M1585I-1.04028
R1154R1154W-0.87603008
D1573K1574R-0.7317234
C1173C1173R-0.62562327
H1596H1596Y-0.40761975
(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 KMT2A from PDB
PDB IDPDB titlePDB structure
2J2SSOLUTION STRUCTURE OF THE NONMETHYL-CPG-BINDING CXXC DOMAIN OF THE LEUKAEMIA-ASSOCIATED MLL HISTONE METHYLTRANSFERASE

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Differential gene expression and gene-gene network for KMT2A
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 KMT2A and the right PPI network was created from samples without mutations in the LBS of KMT2A. 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 KMT2A
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0023467Leukemia, Myeloid, Acute339Biomarker, GeneticVariation
umls:C0023418Leukemia327AlteredExpression, Biomarker, GeneticVariation
umls:C0023470Leukemia, Myeloid37Biomarker, GeneticVariation
umls:C0023465Leukemia, Monocytic, Acute30Biomarker, GeneticVariation
umls:C0023448Leukemia, Lymphoid14Biomarker, GeneticVariation
umls:C0023479Leukemia, Myelomonocytic, Acute11Biomarker, GeneticVariation
umls:C2239176Carcinoma, Hepatocellular4Biomarker
umls:C1854630Growth Deficiency and Mental Retardation with Facial Dysmorphism2Biomarker, GeneticVariation
umls:C0001418Adenocarcinoma1Biomarker
umls:C0007138Carcinoma, Transitional Cell1Biomarker
umls:C0149925Small Cell Lung Carcinoma1Biomarker
umls:C0038356Stomach Neoplasms1Biomarker
umls:C0005695Urinary Bladder Neoplasms1Biomarker

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

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Pharmacological information for KMT2A
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 KMT2A go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)2j2sAC1167 C1173
ZNZINC(2+)2jyiAC1167 C1173
ZNZINC(2+)2kkfAC1167 C1173
ZNZINC(2+)4nw3AC1167 C1173
ZNZINC(2+)2w5yAC3964
ZNZINC(2+)2w5zAC3964
ZNZINC(2+)3lqhAH1596
ZNZINC(2+)3lqiAH1596
ZNZINC(2+)3lqiBH1596
ZNZINC(2+)3lqiCH1596
ZNZINC(2+)3lqjAH1596
ZNZINC(2+)3lqjBH1596
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR)3lqiAM1585 W1594 V1617
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA)3lqiBM1585 W1594 V1617
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR,ALA,ARG,LYS)3lqiCM1585 W1594 V1617
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR)3lqjAM1585 W1594 V1617
IIIPeptide ligand (ALA,ARG,THR,LYS,GLN,THR)3lqjBM1585 W1594 V1617
SAHS-ADENOSYL-L-HOMOCYSTEINE2w5yAR3903
IIIPeptide ligand (ARG,THR,LYS,GLN,THR,ALA,ARG,TYR)2w5zAR3903
SAHS-ADENOSYL-L-HOMOCYSTEINE2w5zAR3903
NUCNucleic Acids2kkfAS1152 R1154
NUCNucleic Acids4nw3AS1152 R1154


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Conservation information for LBS of KMT2A
Multiple alignments for Q03164 in multiple species
LBSAA sequence# speciesSpecies


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