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 RAB7A

Gene summary

Basic gene Info.	Gene symbol	RAB7A
	Gene name	RAB7A, member RAS oncogene family
	Synonyms	PRO2706\|RAB7
	Cytomap	UCSC genome browser: 3q21.3
	Type of gene	protein-coding
	RefGenes	NM_004637.5,
	Description	RAB7, member RAS oncogene familyRas-associated protein RAB7ras-related protein Rab-7a
	Modification date	20141219
dbXrefs	MIM : 602298
	HGNC : HGNC
	Ensembl : ENSG00000075785
	HPRD : 03805
	Vega : OTTHUMG00000159812
Protein	UniProt: P51149 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RAB7A
	BioGPS: 7879
Pathway	NCI Pathway Interaction Database: RAB7A
	KEGG: RAB7A
	REACTOME: RAB7A
	Pathway Commons: RAB7A
Context	iHOP: RAB7A
	ligand binding site mutation search in PubMed: RAB7A
	UCL Cancer Institute: RAB7A
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:0006184	GTP catabolic process	18272684
GO:0022615	protein to membrane docking	24344282

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Ligand binding site mutations for RAB7A

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
S34	S34R	HNSC	1
G20	G20A	OV	1
L129	E130K	STAD	1
G66,T64	A65T	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.

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Protein structure related information for RAB7A

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
L129	E130K	-0.80491945
S34	S34R	-0.74778962
G20	G20A	-0.26566068
G66	A65T	-0.2334913
T64	A65T	-0.2334913

(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 RAB7A from PDB

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Differential gene expression and gene-gene network for RAB7A

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 RAB7A and the right PPI network was created from samples without mutations in the LBS of RAB7A. 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 RAB7A

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C1833219	Charcot-Marie-Tooth disease, Type 2B	4	Biomarker, GeneticVariation
umls:C0151744	Myocardial Ischemia	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for RAB7A

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.

Gene-centered drug-gene interaction network

Drug information targeting mutLBSgene (Approved drugs only)

Drug status	DrugBank ID	Name	Type	Drug structure
Experimental	DB04315	Guanosine-5'-Diphosphate	Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RAB7A go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
GTP		GTP	1t91	A	G20 G66 L129
GTP		GTP	1t91	B	G20 G66 L129
GTP		GTP	1t91	C	G20 G66 L129
GTP		GTP	1t91	D	G20 G66 L129
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3law	A	G20 S34 G66
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3law	B	G20 S34 G66
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3law	C	G20 S34 G66
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3law	D	G20 S34 G66
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3law	E	G20 S34 G66
GTP		GTP	1yhn	A	G20 S34 G66 L129
MG		MAGNESIUM(2+)	1yhn	A	T64
MG		MAGNESIUM(2+)	3law	A	T64
MG		MAGNESIUM(2+)	3law	B	T64
MG		MAGNESIUM(2+)	3law	D	T64
MG		MAGNESIUM(2+)	3law	E	T64

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Conservation information for LBS of RAB7A

Multiple alignments for P51149 in multiple species

LBS	AA sequence	# species	Species
A156	YFETSAKEAIN	7	Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
A156	LFLTSAKNAIN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A156	YFETSAKVGTN	1	Arabidopsis thaliana
A156	YYETSAKVGTN	1	Arabidopsis thaliana
A39	SNQYKATIGAD	7	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
A39	SQQYKATIGAD	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A39	SKDYKATIGAD	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A39	SASYKATIGAD	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D128	LGNKIDLEN--	5	Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
D128	LGNKIDAEE-S	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D128	IGNKVDVDDGN	1	Arabidopsis thaliana
D128	IGNKIDVDGGS	1	Arabidopsis thaliana
D128	LGNKVDVEE-Q	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D128	LGNKIDMEE-S	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D16	VIILGDSGVGK	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257
D16	VIILGESGVGK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D63	TMQIWDTAGQE	5	Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
D63	TLQIWDTAGQE	2	Arabidopsis thaliana, Arabidopsis thaliana
D63	TMQVWDTAGQE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D63	TLQLWDTAGQE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D63	TMQLWDTAGQE	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
F33	YVNKKFSNQYK	7	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
F33	YVNDKYSQQYK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F33	YVNRKFSKDYK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F33	YVNKKFSASYK	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G18	ILGDSGVGKTS	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257
G18	ILGESGVGKTS	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G20	GDSGVGKTSLM	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257
G20	GESGVGKTSIM	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G66	IWDTAGQERFQ	7	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
G66	LWDTAGQERFQ	2	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
G66	VWDTAGQERFQ	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K126	VVLGNKIDLEN	5	Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
K126	VILGNKIDAEE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K126	VLIGNKVDVDD	1	Arabidopsis thaliana
K126	VVIGNKIDVDG	1	Arabidopsis thaliana
K126	ILLGNKVDVEE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K126	VVLGNKIDMEE	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
K157	FETSAKEAINV	7	Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
K157	FLTSAKNAINV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K157	FETSAKVGTNV	1	Arabidopsis thaliana
K157	YETSAKVGTNV	1	Arabidopsis thaliana
K21	DSGVGKTSLMN	8	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
K21	DSGVGKTSLMH	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K21	ESGVGKTSIMN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L129	GNKIDLEN---	5	Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
L129	GNKIDAEE-SK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L129	GNKVDVDDGNS	1	Arabidopsis thaliana
L129	GNKIDVDGGSS	1	Arabidopsis thaliana
L129	GNKVDVEE-QK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L129	GNKIDMEE-SK	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
N125	FVVLGNKIDLE	5	Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
N125	FVILGNKIDAE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N125	FVLIGNKVDVD	1	Arabidopsis thaliana
N125	FVVIGNKIDVD	1	Arabidopsis thaliana
N125	FILLGNKVDVE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N125	FVVLGNKIDME	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
N35	NKKFSNQYKAT	7	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
N35	NDKYSQQYKAT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N35	NRKFSKDYKAT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N35	NKKFSASYKAT	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
S155	PYFETSAKEAI	7	Homo sapiens, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
S155	PLFLTSAKNAI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S155	PYFETSAKVGT	1	Arabidopsis thaliana
S155	PYYETSAKVGT	1	Arabidopsis thaliana
S17	IILGDSGVGKT	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257
S17	IILGESGVGKT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S23	GVGKTSLMNQY	8	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
S23	GVGKTSLMHRY	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S23	GVGKTSIMNQY	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S34	VNKKFSNQYKA	7	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
S34	VNDKYSQQYKA	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S34	VNRKFSKDYKA	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S34	VNKKFSASYKA	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
T22	SGVGKTSLMNQ	8	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
T22	SGVGKTSLMHR	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T22	SGVGKTSIMNQ	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T40	NQYKATIGADF	7	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
T40	QQYKATIGADF	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T40	KDYKATIGADF	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T40	ASYKATIGADF	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
T64	MQIWDTAGQER	5	Homo sapiens, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
T64	LQIWDTAGQER	2	Arabidopsis thaliana, Arabidopsis thaliana
T64	MQVWDTAGQER	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T64	LQLWDTAGQER	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T64	MQLWDTAGQER	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
V19	LGDSGVGKTSL	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257
V19	LGESGVGKTSI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y37	KFSNQYKATIG	7	Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Bos taurus, Rattus norvegicus, Mus musculus, Canis lupus familiaris
Y37	KYSQQYKATIG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y37	KFSKDYKATIG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y37	KFSASYKATIG	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)