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 AGFG1
Gene summary
Basic gene Info.Gene symbolAGFG1
Gene nameArfGAP with FG repeats 1
SynonymsHRB|RAB|RIP
CytomapUCSC genome browser: 2q36.3
Type of geneprotein-coding
RefGenesNM_001135187.1,
NM_001135188.1,NM_001135189.1,NM_004504.4,
DescriptionHIV-1 Rev binding proteinHIV-1 Rev-binding proteinRab, Rev/Rex activation domain-binding proteinarf-GAP domain and FG repeat-containing protein 1arf-GAP domain and FG repeats-containing protein 1hRIP, Rev interacting proteinnucleoporin-like protein
Modification date20141207
dbXrefs MIM : 600862
HGNC : HGNC
Ensembl : ENSG00000173744
HPRD : 02918
Vega : OTTHUMG00000133186
ProteinUniProt: P52594
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AGFG1
BioGPS: 3267
PathwayNCI Pathway Interaction Database: AGFG1
KEGG: AGFG1
REACTOME: AGFG1
Pathway Commons: AGFG1
ContextiHOP: AGFG1
ligand binding site mutation search in PubMed: AGFG1
UCL Cancer Institute: AGFG1
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


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Ligand binding site mutations for AGFG1
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
C29R27QCOAD1
C29R27GHNSC1
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 AGFG1
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
C29R27G-1.5407962
C29R27Q-1.4061787
(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 AGFG1 from PDB

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Differential gene expression and gene-gene network for AGFG1
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 AGFG1 and the right PPI network was created from samples without mutations in the LBS of AGFG1. 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 AGFG1
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 AGFG1
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 AGFG1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
ZNZINC(2+)2olmAC29


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Conservation information for LBS of AGFG1
Multiple alignments for P52594 in multiple species
LBSAA sequence# speciesSpecies
C29PHNRKCFDCDQ4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
C32RKCFDCDQRGP4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
C49VGSFVCTSCSG4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
C52FVCTSCSGSLR4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus


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