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 VCL

Gene summary

Basic gene Info.	Gene symbol	VCL
	Gene name	vinculin
	Synonyms	CMD1W\|CMH15\|HEL114\|MV\|MVCL
	Cytomap	UCSC genome browser: 10q22.2
	Type of gene	protein-coding
	RefGenes	NM_003373.3, NM_014000.2,
	Description	epididymis luminal protein 114metavinculin
	Modification date	20141222
dbXrefs	MIM : 193065
	HGNC : HGNC
	Ensembl : ENSG00000035403
	HPRD : 01900
	Vega : OTTHUMG00000018498
Protein	UniProt: P18206 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_VCL
	BioGPS: 7414
Pathway	NCI Pathway Interaction Database: VCL
	KEGG: VCL
	REACTOME: VCL
	Pathway Commons: VCL
Context	iHOP: VCL
	ligand binding site mutation search in PubMed: VCL
	UCL Cancer Institute: VCL
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

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Ligand binding site mutations for VCL

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
K133	K133T	COAD	1
K133	R132C	SKCM	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.

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Protein structure related information for VCL

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
K133	R132C	-0.79888841
K133	K133T	-0.58575399

(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 VCL from PDB

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Differential gene expression and gene-gene network for VCL

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

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0007193	Cardiomyopathy, Dilated	7	Biomarker, GeneticVariation
umls:C0948089	Acute Coronary Syndrome	1	Biomarker
umls:C0029456	Osteoporosis	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for VCL

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 status

DrugBank ID

Name

Type

Drug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of VCL go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
III		Peptide ligand (TYR,THR,LYS,LYS,GLU,LEU,ILE,GLU,SER,ALA,ARG,LYS,VAL,SER,GLU,LYS,VAL,SER,HIS,VAL,LEU,ALA,ALA,LEU,GLN,ALA)	1rkc	A	K133

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Conservation information for LBS of VCL

Multiple alignments for P18206 in multiple species

LBS	AA sequence	# species	Species
A46	TAPVAAVQAAV	3	Homo sapiens, Mus musculus, Rattus norvegicus
A46	TAPVSAVQAAV	1	Gallus gallus
A50	AAVQAAVSNLV	3	Homo sapiens, Mus musculus, Rattus norvegicus
A50	SAVQAAVSNLV	1	Gallus gallus
D127	LLLTFDEAEVR	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
D39	GKAIPDLTAPV	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
E130	TFDEAEVRKII	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
E14	IESILEPVAQQ	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
E155	VVETMEDLVTY	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
E181	DERQQELTHQE	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
E31	MHEEGEVDGKA	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
E60	VRVGKETVQTT	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
F126	DLLLTFDEAEV	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
G165	YTKNLGPGMTK	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
G58	NLVRVGKETVQ	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
H22	AQQISHLVIMH	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I109	ARDYLIDGSRG	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I115	DGSRGILSGTS	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I12	RTIESILEPVA	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I20	PVAQQISHLVI	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I206	LLPVLISAMKI	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I37	VDGKAIPDLTA	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I9	FHTRTIESILE	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
K1012	GGSGTKRALIQ	3	Homo sapiens, Mus musculus, Rattus norvegicus
K1012	GGSGNKRALIQ	1	Gallus gallus
K1129	LRWVRKTPWYQ	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
K133	EAEVRKIIRVC	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
K162	LVTYTKNLGPG	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
K199	SMNTVKELLPV	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
K210	LISAMKIFVTT	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
K35	GEVDGKAIPDL	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
K983	TKWSSKGNDII	2	Homo sapiens, Gallus gallus
K983	-KWSSKGNDII	2	Mus musculus, Rattus norvegicus
L108	PARDYLIDGSR	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L116	GSRGILSGTSD	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L122	SGTSDLLLTFD	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L123	GTSDLLLTFDE	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L13	TIESILEPVAQ	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L157	ETMEDLVTYTK	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L23	QQISHLVIMHE	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L40	KAIPDLTAPVA	3	Homo sapiens, Mus musculus, Rattus norvegicus
L40	KAIPDLTAPVS	1	Gallus gallus
L54	AAVSNLVRVGK	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L70	TEDQILKRDMP	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
L88	NACTKLVQAAQ	3	Homo sapiens, Mus musculus, Rattus norvegicus
L88	NACTKLVRAAQ	1	Gallus gallus
M154	EVVETMEDLVT	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
M168	NLGPGMTKMAK	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
M26	SHLVIMHEEGE	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
M74	ILKRDMPPAFI	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
N53	QAAVSNLVRVG	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
P15	ESILEPVAQQI	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
P38	DGKAIPDLTAP	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
P43	PDLTAPVAAVQ	3	Homo sapiens, Mus musculus, Rattus norvegicus
P43	PDLTAPVSAVQ	1	Gallus gallus
Q180	IDERQQELTHQ	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
Q185	QELTHQEHRVM	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
Q19	EPVAQQISHLV	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
R1013	GSGTKRALIQC	3	Homo sapiens, Mus musculus, Rattus norvegicus
R1013	GSGNKRALIQC	1	Gallus gallus
R105	YSVPARDYLID	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
R188	THQEHRVMLVN	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
R56	VSNLVRVGKET	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
R7	PVFHTRTIESI	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
S11	TRTIESILEPV	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
S112	YLIDGSRGILS	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
S981	EATKWSSKGND	2	Homo sapiens, Gallus gallus
S981	---KWSSKGND	2	Mus musculus, Rattus norvegicus
S982	ATKWSSKGNDI	2	Homo sapiens, Gallus gallus
S982	--KWSSKGNDI	2	Mus musculus, Rattus norvegicus
T119	GILSGTSDLLL	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
T161	DLVTYTKNLGP	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
T169	LGPGMTKMAKM	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
T61	RVGKETVQTTE	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
T8	VFHTRTIESIL	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
V158	TMEDLVTYTKN	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
V16	SILEPVAQQIS	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
V44	DLTAPVAAVQA	3	Homo sapiens, Mus musculus, Rattus norvegicus
V44	DLTAPVSAVQA	1	Gallus gallus
V47	APVAAVQAAVS	3	Homo sapiens, Mus musculus, Rattus norvegicus
V47	APVSAVQAAVS	1	Gallus gallus
V51	AVQAAVSNLVR	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
V57	SNLVRVGKETV	4	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus