mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

	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 RAB1A

Gene summary

Basic gene Info.	Gene symbol	RAB1A
	Gene name	RAB1A, member RAS oncogene family
	Synonyms	RAB1\|YPT1
	Cytomap	UCSC genome browser: 2p14
	Type of gene	protein-coding
	RefGenes	NM_004161.4, NM_015543.1,
	Description	GTP binding protein Rab1aRAB1, member RAS oncogene familyRab GTPase YPT1 homologYPT1-related proteinras-related protein Rab-1A
	Modification date	20141207
dbXrefs	MIM : 179508
	HGNC : HGNC
	Ensembl : ENSG00000138069
	HPRD : 01538
	Vega : OTTHUMG00000152725
Protein	UniProt: P62820 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_RAB1A
	BioGPS: 5861
Pathway	NCI Pathway Interaction Database: RAB1A
	KEGG: RAB1A
	REACTOME: RAB1A
	Pathway Commons: RAB1A
Context	iHOP: RAB1A
	ligand binding site mutation search in PubMed: RAB1A
	UCL Cancer Institute: RAB1A
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	17684057

Top

Ligand binding site mutations for RAB1A

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
G69	G69D	COAD	1
L128	T129A	KIRC	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.

Top

Protein structure related information for RAB1A

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
L128	T129A	-1.3808205
G69	G69D	-0.60257046

(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 RAB1A from PDB

Top

Differential gene expression and gene-gene network for RAB1A

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 RAB1A and the right PPI network was created from samples without mutations in the LBS of RAB1A. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.

Top

Phenotype information for RAB1A

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

Top

Pharmacological information for RAB1A

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 RAB1A go to BioLip

Ligand ID	Ligand short name	Ligand long name	PDB ID	PDB name	mutLBS
AF3		ALUMINIUM TRIFLUORIDE	4fmb	B	G69
AF3		ALUMINIUM TRIFLUORIDE	4fmb	D	G69
AF3		ALUMINIUM TRIFLUORIDE	4fmb	F	G69
AF3		ALUMINIUM TRIFLUORIDE	4fmc	B	G69
AF3		ALUMINIUM TRIFLUORIDE	4fmc	D	G69
AF3		ALUMINIUM TRIFLUORIDE	4fmd	B	G69
AF3		ALUMINIUM TRIFLUORIDE	4fmd	D	G69
AF3		ALUMINIUM TRIFLUORIDE	4fmd	F	G69
AF3		ALUMINIUM TRIFLUORIDE	4jvs	B	G69
AF3		ALUMINIUM TRIFLUORIDE	4iru	B	G69
AF3		ALUMINIUM TRIFLUORIDE	4iru	D	G69
GTP		GTP	3tkl	A	G69 L128
GDP		GUANOSINE-5'-DIPHOSPHATE	3sfv	A	L128
GDP		GUANOSINE-5'-DIPHOSPHATE	4fmb	B	L128
GDP		GUANOSINE-5'-DIPHOSPHATE	4fmb	D	L128
GDP		GUANOSINE-5'-DIPHOSPHATE	4fmb	F	L128
GDP		GUANOSINE-5'-DIPHOSPHATE	4fmd	D	L128
GDP		GUANOSINE-5'-DIPHOSPHATE	4fme	B	L128
GDP		GUANOSINE-5'-DIPHOSPHATE	4fme	E	L128
GDP		GUANOSINE-5'-DIPHOSPHATE	4jvs	B	L128
GDP		GUANOSINE-5'-DIPHOSPHATE	4iru	B	L128
GDP		GUANOSINE-5'-DIPHOSPHATE	4iru	D	L128
GDP		GUANOSINE-5'-DIPHOSPHATE	4iru	F	L128

Top

Conservation information for LBS of RAB1A

Multiple alignments for P62820 in multiple species

LBS	AA sequence	# species	Species
A155	FLETSAKNATN	4	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus
A155	FLETSALDSTN	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A155	FMETSAKDATN	1	Arabidopsis thaliana
A155	FLETSAKDATN	1	Oryza sativa subsp. japonica
A155	FLETSAKDSTN	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A155	FLETSAKNASN	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
C26	GVGKSCLLLRF	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strai
D127	VGNKCDLTTKK	4	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus
D127	VGNKCDLKDKR	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D127	VGNKSDLTENR	1	Arabidopsis thaliana
D127	VGNKCDLAENR	1	Oryza sativa subsp. japonica
D127	VGNKSDMVDKK	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D127	VGNKSDMTDKK	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
D19	LLLIGDSGVGK	8	Homo sapiens, Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGS
D19	LLLIGNSGVGK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D66	KLQIWDTAGQE	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strai
E38	DDTYTESYIST	6	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
E38	DDTYTNDYIST	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E38	DDSYVESYIST	1	Arabidopsis thaliana
E38	DDSYLESYIST	1	Oryza sativa subsp. japonica
G21	LIGDSGVGKSC	8	Homo sapiens, Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGS
G21	LIGNSGVGKSC	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G23	GDSGVGKSCLL	8	Homo sapiens, Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGS
G23	GNSGVGKSCLL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G69	IWDTAGQERFR	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strai
I41	YTESYISTIGV	6	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
I41	YTNDYISTIGV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I41	YVESYISTIGV	1	Arabidopsis thaliana
I41	YLESYISTIGV	1	Oryza sativa subsp. japonica
K125	LLVGNKCDLTT	4	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus
K125	LLVGNKCDLKD	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K125	LLVGNKSDLTE	1	Arabidopsis thaliana
K125	LLVGNKCDLAE	1	Oryza sativa subsp. japonica
K125	LLVGNKSDMVD	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K125	LLVGNKSDMTD	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
K156	LETSAKNATNV	4	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus
K156	LETSALDSTNV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K156	METSAKDATNV	1	Arabidopsis thaliana
K156	LETSAKDATNV	1	Oryza sativa subsp. japonica
K156	LETSAKDSTNV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K156	LETSAKNASNV	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
K24	DSGVGKSCLLL	8	Homo sapiens, Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGS
K24	NSGVGKSCLLL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L128	GNKCDLTTKKV	4	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus
L128	GNKCDLKDKRV	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L128	GNKSDLTENRA	1	Arabidopsis thaliana
L128	GNKCDLAENRV	1	Oryza sativa subsp. japonica
L128	GNKSDMVDKKV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L128	GNKSDMTDKKV	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
N124	KLLVGNKCDLT	4	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus
N124	KLLVGNKCDLK	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N124	KLLVGNKSDLT	1	Arabidopsis thaliana
N124	KLLVGNKCDLA	1	Oryza sativa subsp. japonica
N124	RLLVGNKSDMV	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N124	KLLVGNKSDMT	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Q70	WDTAGQERFRT	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strai
S154	PFLETSAKNAT	4	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus
S154	PFLETSALDST	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S154	PFMETSAKDAT	1	Arabidopsis thaliana
S154	PFLETSAKDAT	1	Oryza sativa subsp. japonica
S154	PFLETSAKDST	1	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S154	PFLETSAKNAS	1	Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
S20	LLIGDSGVGKS	8	Homo sapiens, Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGS
S20	LLIGNSGVGKS	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S25	SGVGKSCLLLR	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strai
S42	TESYISTIGVD	6	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
S42	TNDYISTIGVD	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S42	VESYISTIGVD	1	Arabidopsis thaliana
S42	LESYISTIGVD	1	Oryza sativa subsp. japonica
T37	ADDTYTESYIS	6	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
T37	SDDTYTNDYIS	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T37	SDDSYVESYIS	1	Arabidopsis thaliana
T37	ADDSYLESYIS	1	Oryza sativa subsp. japonica
T43	ESYISTIGVDF	8	Homo sapiens, Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGS
T43	NDYISTIGVDF	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T67	LQIWDTAGQER	9	Homo sapiens, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strai
V22	IGDSGVGKSCL	8	Homo sapiens, Arabidopsis thaliana, Oryza sativa subsp. japonica, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGS
V22	IGNSGVGKSCL	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y36	FADDTYTESYI	6	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Y36	FSDDTYTNDYI	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y36	FSDDSYVESYI	1	Arabidopsis thaliana
Y36	FADDSYLESYI	1	Oryza sativa subsp. japonica
Y40	TYTESYISTIG	6	Homo sapiens, Canis lupus familiaris, Mus musculus, Rattus norvegicus, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987)
Y40	TYTNDYISTIG	1	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y40	SYVESYISTIG	1	Arabidopsis thaliana
Y40	SYLESYISTIG	1	Oryza sativa subsp. japonica