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 RAB5A
Gene summary
Basic gene Info.Gene symbolRAB5A
Gene nameRAB5A, member RAS oncogene family
SynonymsRAB5
CytomapUCSC genome browser: 3p24-p22
Type of geneprotein-coding
RefGenesNM_001292048.1,
NM_004162.4,
DescriptionRAS-associated protein RAB5Aras-related protein Rab-5A
Modification date20141207
dbXrefs MIM : 179512
HGNC : HGNC
Ensembl : ENSG00000144566
HPRD : 01542
Vega : OTTHUMG00000129889
ProteinUniProt: P20339
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RAB5A
BioGPS: 5868
PathwayNCI Pathway Interaction Database: RAB5A
KEGG: RAB5A
REACTOME: RAB5A
Pathway Commons: RAB5A
ContextiHOP: RAB5A
ligand binding site mutation search in PubMed: RAB5A
UCL Cancer Institute: RAB5A
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0006184GTP catabolic process17562788
GO:0006897endocytosis15378032
GO:0036465synaptic vesicle recycling16141272
GO:0051489regulation of filopodium assembly14978216


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Ligand binding site mutations for RAB5A
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
LBSAAchange of nsSNVCancer type# samples
D136,K134A135VCOAD1
Y82,E80R81QKIRC1
G78G78RLUAD1
S34S34LUCEC1
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 RAB5A
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.
LBSAAchange of nsSNVRelative stability change
S34S34L0.42990124
Y82R81Q-1.4216287
E80R81Q-1.4216287
G78G78R-0.42799599
K134A135V-0.20863643
D136A135V-0.20863643
(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 RAB5A from PDB

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Differential gene expression and gene-gene network for RAB5A
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 RAB5A and the right PPI network was created from samples without mutations in the LBS of RAB5A. 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 RAB5A
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0151744Myocardial Ischemia1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for RAB5A
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 statusDrugBank IDNameTypeDrug structure
ExperimentalDB02467L-methionine (S)-S-oxideSmall molecule
ExperimentalDB04137Guanosine-5'-TriphosphateSmall molecule
ExperimentalDB04315Guanosine-5'-DiphosphateSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RAB5A go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
COCOBALT(2+)1tu4BE80
COCOBALT(2+)1tu4DE80
AF3ALUMINIUM TRIFLUORIDE1n6kAG78
MGMAGNESIUM(2+)1n6hAS34
MGMAGNESIUM(2+)1n6iAS34
MGMAGNESIUM(2+)1n6kAS34
MGMAGNESIUM(2+)1n6lAS34
MGMAGNESIUM(2+)1n6nAS34
MGMAGNESIUM(2+)1n6oAS34
MGMAGNESIUM(2+)1n6pAS34
MGMAGNESIUM(2+)1n6rAS34
MGMAGNESIUM(2+)1r2qAS34
MGMAGNESIUM(2+)1tu3AS34
MGMAGNESIUM(2+)1tu3BS34
MGMAGNESIUM(2+)1tu3CS34
MGMAGNESIUM(2+)1tu3DS34
MGMAGNESIUM(2+)1tu3ES34
COCOBALT(2+)1tu4BS34
COCOBALT(2+)1tu4DS34
MGMAGNESIUM(2+)3mjhAS34
MGMAGNESIUM(2+)3mjhCS34
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1n6hAS34 G78 K134 D136
GTPGTP1n6lAS34 G78 K134 D136
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1n6nAS34 G78 K134 D136
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1n6oAS34 G78 K134 D136
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1n6pAS34 G78 K134 D136
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1n6rAS34 G78 K134 D136
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1r2qAS34 G78 K134 D136
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1tu3AS34 G78 K134 D136
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1tu3BS34 G78 K134 D136
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1tu3CS34 G78 K134 D136
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1tu3DS34 G78 K134 D136
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1tu3ES34 G78 K134 D136
GTPGTP3mjhAS34 G78 K134 D136
GTPGTP3mjhCS34 G78 K134 D136
GDPGUANOSINE-5'-DIPHOSPHATE1n6iAS34 K134 D136
GDPGUANOSINE-5'-DIPHOSPHATE1n6kAS34 K134 D136
GDPGUANOSINE-5'-DIPHOSPHATE1tu4AS34 K134 D136
GDPGUANOSINE-5'-DIPHOSPHATE1tu4BS34 K134 D136
GDPGUANOSINE-5'-DIPHOSPHATE1tu4CS34 K134 D136
GDPGUANOSINE-5'-DIPHOSPHATE1tu4DS34 K134 D136
COCOBALT(2+)1tu4AY82
COCOBALT(2+)1tu4CY82


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Conservation information for LBS of RAB5A
Multiple alignments for P20339 in multiple species
LBSAA sequence# speciesSpecies
A164FMETSAKTSMN4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
A164FMETSAKTATN2Arabidopsis thaliana, Arabidopsis thaliana
A164FMETSAKTPMN1Rattus norvegicus
A30LLGESAVGKSS5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
A30LLGDVGAGKSS2Arabidopsis thaliana, Arabidopsis thaliana
D136SGNKADLANKR5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
D136AGNKSDLLDAR1Arabidopsis thaliana
D136AGNKADLLDAR1Arabidopsis thaliana
D75KFEIWDTAGQE7Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana
E47KGQFHEFQEST5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
E47KDQFVEFQEST2Arabidopsis thaliana, Arabidopsis thaliana
E50FHEFQESTIGA5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
E50FVEFQESTIGA2Arabidopsis thaliana, Arabidopsis thaliana
E80DTAGQERYHSL7Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana
F45FVKGQFHEFQE5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
F45FVKDQFVEFQE2Arabidopsis thaliana, Arabidopsis thaliana
F48GQFHEFQESTI5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
F48DQFVEFQESTI2Arabidopsis thaliana, Arabidopsis thaliana
G32GESAVGKSSLV5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
G32GDVGAGKSSLV2Arabidopsis thaliana, Arabidopsis thaliana
G78IWDTAGQERYH7Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana
H46VKGQFHEFQES5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
H46VKDQFVEFQES2Arabidopsis thaliana, Arabidopsis thaliana
H83GQERYHSLAPM7Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana
K134ALSGNKADLAN5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
K134ALAGNKSDLLD1Arabidopsis thaliana
K134ALAGNKADLLD1Arabidopsis thaliana
K165METSAKTSMNV4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
K165METSAKTATNV2Arabidopsis thaliana, Arabidopsis thaliana
K165METSAKTPMNV1Rattus norvegicus
K33ESAVGKSSLVL5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
K33DVGAGKSSLVL2Arabidopsis thaliana, Arabidopsis thaliana
L137GNKADLANKRA5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
L137GNKSDLLDARK1Arabidopsis thaliana
L137GNKADLLDARK1Arabidopsis thaliana
N133IALSGNKADLA5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
N133MALAGNKSDLL1Arabidopsis thaliana
N133MALAGNKADLL1Arabidopsis thaliana
Q49QFHEFQESTIG5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
Q49QFVEFQESTIG2Arabidopsis thaliana, Arabidopsis thaliana
S163LFMETSAKTSM4Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus
S163FFMETSAKTAT2Arabidopsis thaliana, Arabidopsis thaliana
S163LFMETSAKTPM1Rattus norvegicus
S29VLLGESAVGKS5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
S29VLLGDVGAGKS2Arabidopsis thaliana, Arabidopsis thaliana
S34SAVGKSSLVLR5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
S34VGAGKSSLVLR2Arabidopsis thaliana, Arabidopsis thaliana
S35AVGKSSLVLRF5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
S35GAGKSSLVLRF2Arabidopsis thaliana, Arabidopsis thaliana
S51HEFQESTIGAA5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
S51VEFQESTIGAA2Arabidopsis thaliana, Arabidopsis thaliana
T52EFQESTIGAAF7Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana
V31LGESAVGKSSL5Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus
V31LGDVGAGKSSL2Arabidopsis thaliana, Arabidopsis thaliana
Y82AGQERYHSLAP7Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana


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