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 RAP1B
Gene summary
Basic gene Info.Gene symbolRAP1B
Gene nameRAP1B, member of RAS oncogene family
SynonymsK-REV|RAL1B
CytomapUCSC genome browser: 12q14
Type of geneprotein-coding
RefGenesNM_001010942.2,
NM_001251917.1,NM_001251918.1,NM_001251921.1,NM_001251922.1,
NM_015646.5,
DescriptionGTP-binding protein smg p21BRAS-related protein RAP1BRas family small GTP binding protein RAP1Bras-related protein Rap-1bsmall GTP binding protein
Modification date20141207
dbXrefs MIM : 179530
HGNC : HGNC
Ensembl : ENSG00000127314
HPRD : 01546
Vega : OTTHUMG00000133660
ProteinUniProt: P61224
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RAP1B
BioGPS: 5908
PathwayNCI Pathway Interaction Database: RAP1B
KEGG: RAP1B
REACTOME: RAP1B
Pathway Commons: RAP1B
ContextiHOP: RAP1B
ligand binding site mutation search in PubMed: RAP1B
UCL Cancer Institute: RAP1B
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:0071320cellular response to cAMP21840392


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Ligand binding site mutations for RAP1B
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
T35E37QBLCA1
T35T35MCOAD1
G12G12EHNSC1
N116G115CKIRC1
G13G13DKIRC1
G12G12ELAML1
G12G12ESTAD1
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 RAP1B
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
G12G12E0.15304459
T35E37Q-1.1841367
G13G13D-0.82569764
T35T35M-0.80499384
N116G115C-0.45782386
(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 RAP1B from PDB

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Differential gene expression and gene-gene network for RAP1B
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 RAP1B and the right PPI network was created from samples without mutations in the LBS of RAP1B. 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 RAP1B
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for RAP1B
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 statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of RAP1B go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
BEFTRIFLUOROBERYLLATE(1-)3brwDG12 G13 T35
AF3ALUMINIUM TRIFLUORIDE4m8nEG12 G13 T35
AF3ALUMINIUM TRIFLUORIDE4m8nHG12 G13 T35
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER4hdqBG12 G13 T35 N116
AF3ALUMINIUM TRIFLUORIDE4m8nFG12 T35
AF3ALUMINIUM TRIFLUORIDE4m8nGG12 T35
GDPGUANOSINE-5'-DIPHOSPHATE3brwDG13 N116
GDPGUANOSINE-5'-DIPHOSPHATE4m8nEG13 N116
GDPGUANOSINE-5'-DIPHOSPHATE4m8nGG13 N116
GDPGUANOSINE-5'-DIPHOSPHATE4m8nHG13 T35
GSPGUANOSINE 5'-[GAMMA-THIO]TRIPHOSPHATE4dxaAG13 T35 N116
GNPPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER4hdoBG13 T35 N116
GDPGUANOSINE-5'-DIPHOSPHATE4m8nFG13 T35 N116
MGMAGNESIUM(2+)3brwDT35
MGMAGNESIUM(2+)4dxaAT35
MGMAGNESIUM(2+)4hdoBT35
MGMAGNESIUM(2+)4hdqBT35
MGMAGNESIUM(2+)4m8nET35
MGMAGNESIUM(2+)4m8nFT35
MGMAGNESIUM(2+)4m8nGT35
MGMAGNESIUM(2+)4m8nHT35


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Conservation information for LBS of RAP1B
Multiple alignments for P61224 in multiple species
LBSAA sequence# speciesSpecies
A148FLESSAKSKIN8Homo sapiens, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
A148FYETSALLRSN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A148FLETSAKAKIN1Caenorhabditis elegans
A18GVGKSALTVQF9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
A18GVGKSCLTVQF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A59EILDTAGTEQF9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
A59EILDTAGIAQF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D119VGNKCDLEDER9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
D119IGNKADLINER1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D57MLEILDTAGTE9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
D57DLEILDTAGIA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
E30QGIFVEKYDPT9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
E30QGVYLDTYDPT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F28FVQGIFVEKYD9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
F28FVQGVYLDTYD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G12VVLGSGGVGKS9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
G12VVLGAGGVGKS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G13VLGSGGVGKSA9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
G13VLGAGGVGKSC1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G15GSGGVGKSALT9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
G15GAGGVGKSCLT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G60ILDTAGTEQFT9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
G60ILDTAGIAQFT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K117ILVGNKCDLED9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
K117VLIGNKADLIN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K149LESSAKSKINV8Homo sapiens, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
K149YETSALLRSNV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K149LETSAKAKINV1Caenorhabditis elegans
K16SGGVGKSALTV9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
K16AGGVGKSCLTV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K31GIFVEKYDPTI9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
K31GVYLDTYDPTI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L120GNKCDLEDERV9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
L120GNKADLINERV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N116MILVGNKCDLE9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
N116MVLIGNKADLI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P34VEKYDPTIEDS9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
P34LDTYDPTIEDS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q63TAGTEQFTAMR9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
Q63TAGIAQFTAMR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S11LVVLGSGGVGK8Homo sapiens, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
S11LVVLGAGGVGK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S11IVVLGSGGVGK1Caenorhabditis elegans
S147AFLESSAKSKI8Homo sapiens, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
S147PFYETSALLRS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S147AFLETSAKAKI1Caenorhabditis elegans
S17GGVGKSALTVQ9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
S17GGVGKSCLTVQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T35EKYDPTIEDSY9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
T35DTYDPTIEDSY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T58LEILDTAGTEQ9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
T58LEILDTAGIAQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V14LGSGGVGKSAL9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
V14LGAGGVGKSCL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
V29VQGIFVEKYDP9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
V29VQGVYLDTYDP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y32IFVEKYDPTIE9Homo sapiens, Caenorhabditis elegans, Danio rerio, Xenopus tropicalis, Pan troglodytes, Bos taurus, Mus musculus, Gallus gallus, Rattus norvegicus
Y32VYLDTYDPTIE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)


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