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 RAB8A

Gene summary

Basic gene Info.	Gene symbol	RAB8A
	Gene name	RAB8A, member RAS oncogene family
	Synonyms	MEL\|RAB8
	Cytomap	UCSC genome browser: 19p13.1
	Type of gene	protein-coding
	RefGenes	NM_005370.4,
	Description	mel transforming oncogene (RAB8 homolog)mel transforming oncogene (derived from cell line NK14)mel transforming oncogene (derived from cell line NK14)- RAB8 homologoncogene c-melras-associated protein RAB8ras-related protein Rab-8A
	Modification date	20141207
dbXrefs	MIM : 165040
	HGNC : HGNC
	HPRD : 01296
Protein	UniProt: P61006 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RAB8A
	BioGPS: 4218
Pathway	NCI Pathway Interaction Database: RAB8A
	KEGG: RAB8A
	REACTOME: RAB8A
	Pathway Commons: RAB8A
Context	iHOP: RAB8A
	ligand binding site mutation search in PubMed: RAB8A
	UCL Cancer Institute: RAB8A
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	17646400
GO:0006904	vesicle docking involved in exocytosis	17574030
GO:0042384	cilium assembly	17574030
GO:0048210	Golgi vesicle fusion to target membrane	17574030

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Ligand binding site mutations for RAB8A

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
G20	G20W	LUAD	1
A152	A152V	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 RAB8A

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
G20	G20W	0.098209591
A152	A152V	-0.86440217

(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 RAB8A from PDB

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Differential gene expression and gene-gene network for RAB8A

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 RAB8A and the right PPI network was created from samples without mutations in the LBS of RAB8A. 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 RAB8A

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0003873	Arthritis, Rheumatoid	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for RAB8A

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 RAB8A go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3qbt	A	G20 A152
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3qbt	C	G20 A152
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3qbt	E	G20 A152
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3qbt	G	G20 A152
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	3tnf	A	G20 A152
GDP		GUANOSINE-5'-DIPHOSPHATE	4lhv	A	G20 A152
GDP		GUANOSINE-5'-DIPHOSPHATE	4lhv	B	G20 A152
GDP		GUANOSINE-5'-DIPHOSPHATE	4lhv	C	G20 A152
GDP		GUANOSINE-5'-DIPHOSPHATE	4lhv	D	G20 A152
GDP		GUANOSINE-5'-DIPHOSPHATE	4lhv	E	G20 A152
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	4lhw	A	G20 A152
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	4lhw	B	G20 A152
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	4lhw	C	G20 A152
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	4lhw	D	G20 A152
GNP		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	4lhw	E	G20 A152
GDP		GUANOSINE-5'-DIPHOSPHATE	4lhy	A	G20 A152
GDP		GUANOSINE-5'-DIPHOSPHATE	4lhy	B	G20 A152
GTP		GTP	4lhz	A	G20 A152
GTP		GTP	4lhz	B	G20 A152
GDP		GUANOSINE-5'-DIPHOSPHATE	4li0	A	G20 A152
GDP		GUANOSINE-5'-DIPHOSPHATE	4li0	B	G20 A152

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Conservation information for LBS of RAB8A

Multiple alignments for P61006 in multiple species

LBS	AA sequence	# species	Species
A152	FMETSAKANIN	6	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
A152	FFETSAKTNLN	2	Arabidopsis thaliana, Arabidopsis thaliana
A152	FIESSAKNDDN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A152	FLEASAKTNVN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A65	QIWDTAGQERF	9	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A65	QLWDTAGQERF	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
C23	GVGKTCVLFRF	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
C23	GVGKSCLLLRF	3	Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
C23	GVGKSCLLVRF	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
C23	GVGKTCALFRF	1	Gallus gallus
D124	LGNKCDVND-K	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
D124	VGNKADMDESK	2	Arabidopsis thaliana, Arabidopsis thaliana
D124	VGNKSDME--T	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D124	LGNKCDAND-K	1	Gallus gallus
D124	IGNKCDCED-Q	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D16	LLLIGDSGVGK	9	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D16	ILLIGDSGVGK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D63	KLQIWDTAGQE	9	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D63	KLQLWDTAGQE	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F33	FSEDAFNSTFI	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
F33	FSDGSFTTSFI	2	Arabidopsis thaliana, Arabidopsis thaliana
F33	FVEDKFNPSFI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F33	FSEDAFNATFI	1	Gallus gallus
F33	FSEDSFTPSFI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F37	AFNSTFISTIG	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
F37	SFTTSFITTIG	2	Arabidopsis thaliana, Arabidopsis thaliana
F37	KFNPSFITTIG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F37	AFNATFISTIG	1	Gallus gallus
F37	SFTPSFITTIG	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G18	LIGDSGVGKTC	6	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
G18	LIGDSGVGKSC	4	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G20	GDSGVGKTCVL	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
G20	GDSGVGKSCLL	4	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G20	GDSGVGKTCAL	1	Gallus gallus
G66	IWDTAGQERFR	9	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G66	LWDTAGQERFR	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K122	MILGNKCDVND	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
K122	ILVGNKADMDE	2	Arabidopsis thaliana, Arabidopsis thaliana
K122	LLVGNKSDME-	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K122	MILGNKCDAND	1	Gallus gallus
K122	ILIGNKCDCED	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K153	METSAKANINV	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
K153	FETSAKTNLNV	2	Arabidopsis thaliana, Arabidopsis thaliana
K153	IESSAKNDDNV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K153	METSAKANINI	1	Gallus gallus
K153	LEASAKTNVNV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K21	DSGVGKTCVLF	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
K21	DSGVGKSCLLL	3	Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K21	DSGVGKSCLLV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K21	DSGVGKTCALF	1	Gallus gallus
N121	KMILGNKCDVN	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
N121	KILVGNKADMD	2	Arabidopsis thaliana, Arabidopsis thaliana
N121	LLLVGNKSDME	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N121	KMILGNKCDAN	1	Gallus gallus
N121	KILIGNKCDCE	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N34	SEDAFNSTFIS	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
N34	SDGSFTTSFIT	2	Arabidopsis thaliana, Arabidopsis thaliana
N34	VEDKFNPSFIT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N34	SEDAFNATFIS	1	Gallus gallus
N34	SEDSFTPSFIT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S151	KFMETSAKANI	6	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
S151	KFFETSAKTNL	2	Arabidopsis thaliana, Arabidopsis thaliana
S151	PFIESSAKNDD	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S151	KFLEASAKTNV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S17	LLIGDSGVGKT	6	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
S17	LLIGDSGVGKS	4	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S35	EDAFNSTFIST	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
S35	DGSFTTSFITT	2	Arabidopsis thaliana, Arabidopsis thaliana
S35	EDKFNPSFITT	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S35	EDAFNATFIST	1	Gallus gallus
S35	EDSFTPSFITT	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S39	NSTFISTIGID	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
S39	TTSFITTIGID	2	Arabidopsis thaliana, Arabidopsis thaliana
S39	NPSFITTIGID	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S39	NATFISTIGID	1	Gallus gallus
S39	TPSFITTIGID	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T22	SGVGKTCVLFR	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
T22	SGVGKSCLLLR	3	Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T22	SGVGKSCLLVR	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T22	SGVGKTCALFR	1	Gallus gallus
T36	DAFNSTFISTI	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
T36	GSFTTSFITTI	2	Arabidopsis thaliana, Arabidopsis thaliana
T36	DKFNPSFITTI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T36	DAFNATFISTI	1	Gallus gallus
T36	DSFTPSFITTI	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T40	STFISTIGIDF	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
T40	PSFITTIGIDF	2	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T40	TSFITTIGIDF	2	Arabidopsis thaliana, Arabidopsis thaliana
T40	ATFISTIGIDF	1	Gallus gallus
T64	LQIWDTAGQER	9	Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T64	LQLWDTAGQER	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V125	GNKCDVND-KR	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
V125	GNKADMDESKR	2	Arabidopsis thaliana, Arabidopsis thaliana
V125	GNKSDME--TR	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V125	GNKCDAND-KR	1	Gallus gallus
V125	GNKCDCED-QR	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V19	IGDSGVGKTCV	5	Homo sapiens, Mus musculus, Rattus norvegicus, Canis lupus familiaris, Bos taurus
V19	IGDSGVGKSCL	4	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Arabidopsis thaliana, Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V19	IGDSGVGKTCA	1	Gallus gallus