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 KMT2C

Gene summary

Basic gene Info.	Gene symbol	KMT2C
	Gene name	lysine (K)-specific methyltransferase 2C
	Synonyms	HALR\|MLL3
	Cytomap	UCSC genome browser: 7q36.1
	Type of gene	protein-coding
	RefGenes	NM_170606.2, NM_021230.2,
	Description	ALR-like proteinhistone-lysine N-methyltransferase 2Chistone-lysine N-methyltransferase MLL3histone-lysine N-methyltransferase, H3 lysine-4 specifichomologous to ALR proteinmyeloid/lymphoid or mixed-lineage leukemia protein 3
	Modification date	20141207
dbXrefs	MIM : 606833
	HGNC : HGNC
	Ensembl : ENSG00000055609
	HPRD : 06016
	Vega : OTTHUMG00000150553
Protein	UniProt: Q8NEZ4 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_KMT2C
	BioGPS: 58508
Pathway	NCI Pathway Interaction Database: KMT2C
	KEGG: KMT2C
	REACTOME: KMT2C
	Pathway Commons: KMT2C
Context	iHOP: KMT2C
	ligand binding site mutation search in PubMed: KMT2C
	UCL Cancer Institute: KMT2C
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO Term	PubMed ID
GO:0051568	histone H3-K4 methylation	17500065

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Ligand binding site mutations for KMT2C

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

LBS	AAchange of nsSNV	Cancer type	# samples
H367	Y366H	COAD	4
C347	C347R	COAD	3
C370	D372N	SKCM	2
H367	G368R	BLCA	1
C388	E387V	BLCA	1
H367	H367Y	BRCA	1
H367	H367D	BRCA	1
H367	Y366N	COAD	1
H367	Y366C	COAD	1
C362	G363C	GBM	1
C359	F358C	KIRC	1
C385	Q384E	LUAD	1
H367	H365N	LUAD	1
C385	W383L	LUAD	1
C370	D372Y	LUAD	1
C347	C347W	LUAD	1
C385	Q384K	LUAD	1
C362	Q364H	LUAD	1
C362	G363R	LUAD	1
H367	G368V	LUSC	1
H367	Y366S	OV	1
C385	C385Y	SKCM	1
H367	H367Y	SKCM	1
C370	D372V	STAD	1

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 KMT2C from My Cancer Genome.

Lysine (K)-specific methyltransferase 2C (KMT2C) is a gene that encodes a nuclear protein that functions in histone methylation and transcriptional coactivation. Missense mutations, nonsense mutations, silent mutations, frameshift deletions and insertions, and in-frame deletions and insertions are observed in cancers such as biliary tract cancer, intestinal cancer, and skin cancer.Modified: July 1, 2015

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Protein structure related information for KMT2C

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.

LBS	AAchange of nsSNV	Relative stability change
C385	Q384E	0.039593459
H367	Y366N	-0.99245375
H367	H365N	-0.97836881
C359	F358C	-0.96410675
H367	Y366S	-0.95712788
H367	Y366H	-0.94428727
H367	H367D	-0.81023075
C385	C385Y	-0.80127336
C388	E387V	-0.7975116
C370	D372N	-0.77612156
C362	Q364H	-0.76687586
H367	Y366C	-0.69913523
H367	G368V	-0.56523735
H367	H367Y	-0.55215346
C362	G363C	-0.54661116
H367	G368R	-0.53301208
C362	G363R	-0.46611903
C347	C347W	-0.38999545
C347	C347R	-0.38532277
C370	D372Y	-0.32256558
C385	W383L	-0.26091176
C370	D372V	-0.17821281
C385	Q384K	-0.15761364

(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 KMT2C from PDB

PDB ID	PDB title	PDB structure
2YSM	Solution structure of the first and second PHD domain from Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog

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Differential gene expression and gene-gene network for KMT2C

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 KMT2C and the right PPI network was created from samples without mutations in the LBS of KMT2C. 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 KMT2C

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C2239176	Carcinoma, Hepatocellular	2	Biomarker
umls:C0001418	Adenocarcinoma	1	Biomarker
umls:C0010606	Carcinoma, Adenoid Cystic	1	Biomarker
umls:C0007138	Carcinoma, Transitional Cell	1	Biomarker
umls:C0206698	Cholangiocarcinoma	1	Biomarker
umls:C0279626	Esophageal Squamous Cell Carcinoma	1	Biomarker
umls:C0023897	Liver Diseases, Parasitic	1	Biomarker
umls:C0038356	Stomach Neoplasms	1	Biomarker
umls:C0005695	Urinary Bladder Neoplasms	1	Biomarker