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 ARFGEF1
Gene summary
Basic gene Info.Gene symbolARFGEF1
Gene nameADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)
CytomapUCSC genome browser: 8q13
Type of geneprotein-coding
Descriptionbrefeldin A-inhibited guanine nucleotide-exchange protein 1p200 ARF guanine nucleotide exchange factor
Modification date20141207
dbXrefs MIM : 604141
Ensembl : ENSG00000066777
HPRD : 09163
Vega : OTTHUMG00000164626
ProteinUniProt: Q9Y6D6
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ARFGEF1
BioGPS: 10565
PathwayNCI Pathway Interaction Database: ARFGEF1
Pathway Commons: ARFGEF1
ContextiHOP: ARFGEF1
ligand binding site mutation search in PubMed: ARFGEF1
UCL Cancer Institute: ARFGEF1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0034259negative regulation of Rho GTPase activity15644318
GO:0043547positive regulation of GTPase activity15644318

Ligand binding site mutations for ARFGEF1

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for ARFGEF1
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
(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 ARFGEF1 from PDB

Differential gene expression and gene-gene network for ARFGEF1
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 ARFGEF1 and the right PPI network was created from samples without mutations in the LBS of ARFGEF1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for ARFGEF1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0017661Glomerulonephritis, IGA1Biomarker

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

Pharmacological information for ARFGEF1
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 ARFGEF1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of ARFGEF1
Multiple alignments for Q9Y6D6 in multiple species
LBSAA sequence# speciesSpecies
F784SALRMFLEGFR2Homo sapiens, Bos taurus
F784SALRLFLEGFR2Mus musculus, Rattus norvegicus
F784EAIRTFLEGFR1Arabidopsis thaliana
F784EAIRAFLRGFR1Arabidopsis thaliana
F784DALRRLLQCFR1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F784DALRSFLQSFR1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
F788MFLEGFRLPGE2Homo sapiens, Bos taurus
F788LFLEGFRLPGE2Mus musculus, Rattus norvegicus
F788TFLEGFRLPGE1Arabidopsis thaliana
F788AFLRGFRLPGE1Arabidopsis thaliana
F788RLLQCFRLPGE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
F788SFLQSFRLPGE1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G787RMFLEGFRLPG2Homo sapiens, Bos taurus
G787RLFLEGFRLPG2Mus musculus, Rattus norvegicus
G787RTFLEGFRLPG1Arabidopsis thaliana
G787RAFLRGFRLPG1Arabidopsis thaliana
G787RRLLQCFRLPG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G787RSFLQSFRLPG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
H770AYVDQHDFSGK4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
H770AYVDSFDFRGM1Arabidopsis thaliana
H770AYVDSFEFQGM1Arabidopsis thaliana
H770EFIDCLSFINL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
H770AFVDEFDFTGM1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L785ALRMFLEGFRL2Homo sapiens, Bos taurus
L785ALRLFLEGFRL2Mus musculus, Rattus norvegicus
L785AIRTFLEGFRL1Arabidopsis thaliana
L785AIRAFLRGFRL1Arabidopsis thaliana
L785ALRRLLQCFRL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L785ALRSFLQSFRL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L790LEGFRLPGEAQ5Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Arabidopsis thaliana
L790LRGFRLPGEAQ1Arabidopsis thaliana
L790LQCFRLPGEAQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L790LQSFRLPGEGQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M435LCKLSMK-PLS4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
M435LCKLSMKAPPK1Arabidopsis thaliana
M435LCKLSMKTPPK1Arabidopsis thaliana
M435MCRLAVRQTSP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M435MAKICAK-PL-1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
M783VSALRMFLEGF2Homo sapiens, Bos taurus
M783VSALRLFLEGF2Mus musculus, Rattus norvegicus
M783DEAIRTFLEGF1Arabidopsis thaliana
M783DEAIRAFLRGF1Arabidopsis thaliana
M783VDALRRLLQCF1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
M783VDALRSFLQSF1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R789FLEGFRLPGEA5Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Arabidopsis thaliana
R789FLRGFRLPGEA1Arabidopsis thaliana
R789LLQCFRLPGEA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R789FLQSFRLPGEG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y766EVMYAYVDQHD4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Y766KVMHAYVDSFD1Arabidopsis thaliana
Y766KVMHAYVDSFE1Arabidopsis thaliana
Y766SVMHEFIDCLS1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y766AIMHAFVDEFD1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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