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 RUNX1T1

Gene summary

Basic gene Info.	Gene symbol	RUNX1T1
	Gene name	runt-related transcription factor 1; translocated to, 1 (cyclin D-related)
	Synonyms	AML1T1\|CBFA2T1\|CDR\|ETO\|MTG8\|ZMYND2
	Cytomap	UCSC genome browser: 8q22
	Type of gene	protein-coding
	RefGenes	NM_001198625.1, NM_001198626.1,NM_001198627.1,NM_001198628.1,NM_001198629.1, NM_001198630.1,NM_001198631.1,NM_001198632.1,NM_001198633.1, NM_001198634.1,NM_001198679.1,NM_004349.3,NM_175634.2, NM_175635.2,NM_175636.2,
	Description	CBFA2T1 isoform r1t1-11a62CBFA2T1 isoform r1t1-11a63CBFA2T1 isoform r1t1-11a64CBFA2T1 isoform r1t1-11a65CBFA2T1 isoform r1t1-7a47CBFA2T1 isoform r1t1-7a48CBFA2T1 isoform r1t1-7a49CBFA2T1 isoform r1t1-7a50CBFA2T1 isoform r1t1-7a52CBFA2T1 isoform r
	Modification date	20141207
dbXrefs	MIM : 133435
	HGNC : HGNC
	Ensembl : ENSG00000079102
	HPRD : 00590
	Vega : OTTHUMG00000164066
Protein	UniProt: Q06455 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RUNX1T1
	BioGPS: 862
Pathway	NCI Pathway Interaction Database: RUNX1T1
	KEGG: RUNX1T1
	REACTOME: RUNX1T1
	Pathway Commons: RUNX1T1
Context	iHOP: RUNX1T1
	ligand binding site mutation search in PubMed: RUNX1T1
	UCL Cancer Institute: RUNX1T1
Assigned class in mutLBSgeneDB	B: This gene belongs to targetable_mutLBSgenes.

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

GO ID

GO Term

PubMed ID

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Ligand binding site mutations for RUNX1T1

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
R128	R128S	LUAD	2
W544	D543H	BLCA	1
K125	S124N	COAD	1
F184	P183T	COAD	1
Y534,N530	A532S	HNSC	1
F184	P183L	HNSC	1
E353	W354C	HNSC	1
C518	R520S	HNSC	1
V181	V181F	LUAD	1
C518	G519C	LUAD	1
C518	G519V	LUAD	1
C526	C526S	LUAD	1
G536	G536V	LUAD	1
V377	T376N	LUAD	1
F184	P183L	LUAD	1
F184	P183R	LUAD	1
C515	C515F	LUSC	1
E353	E352K	SKCM	1
E349	D347N	SKCM	1
Y534	R533Q	SKCM	1
L378	R380W	STAD	1
P176	F175V	STAD	1
W544	D543H	THCA	1
H356	K355T	UCEC	1
H343	R344I	UCEC	1
H343	H343N	UCEC	1
E545	E545D	UCEC	1
S523	A522V	UCEC	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 RUNX1T1 from My Cancer Genome.

Runt-related transcription factor 1; translocated to, 1 (cyclin D-related) (RUNX1T1; also known as ETO) is a gene that encodes a protein that belongs to the myeloid translocation gene family. The protein functions in blocking hematopoietic differentiation by associating with the nuclear corepressor/histone deacetylase complex. Missense mutations, nonsense mutations, silent mutations, frameshift insertions, and in-frame deletions are observed in cancers such as intestinal cancer, skin cancer, and stomach cancer.Modified: July 1, 2015

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Protein structure related information for RUNX1T1

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
Y534	R533Q	-1.9691093
C518	R520S	-1.4342346
E545	E545D	-1.3011755
R128	R128S	-1.0449847
H343	R344I	-0.999524
L378	R380W	-0.99597376
W544	D543H	-0.98757277
V181	V181F	-0.98382495
E353	W354C	-0.9718775
C526	C526S	-0.93014278
V377	T376N	-0.8510067
Y534	A532S	-0.84781308
N530	A532S	-0.84781308
E349	D347N	-0.82752791
E353	E352K	-0.81105157
H343	H343N	-0.70086196
C515	C515F	-0.68363349
H356	K355T	-0.64749992
F184	P183T	-0.61926154
S523	A522V	-0.55696685
G536	G536V	-0.47513195
K125	S124N	-0.42614147
F184	P183R	-0.38530042
P176	F175V	-0.29436777
C518	G519C	-0.27156097
C518	G519V	-0.19198393
F184	P183L	-0.012473221

(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 RUNX1T1 from PDB

PDB ID	PDB title	PDB structure
2PP4	Solution Structure of ETO-TAFH refined in explicit solvent

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Differential gene expression and gene-gene network for RUNX1T1

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 RUNX1T1 and the right PPI network was created from samples without mutations in the LBS of RUNX1T1. 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 RUNX1T1

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0023467	Leukemia, Myeloid, Acute	262	Biomarker, GeneticVariation
umls:C0149925	Small Cell Lung Carcinoma	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for RUNX1T1

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.