RABGEF1 forms a complex with rabaptin-5 (RABPT5; MIM 603616) that is required for endocytic membrane fusion, and it serves as a specific guanine nucleotide exchange factor (GEF) for RAB5 (RAB5A; MIM 179512) (Horiuchi et al., 1997 [PubMed 9323142]).[supplied by OMIM, Mar 2010] See more...

Aliases for RABGEF1 Gene

Aliases for RABGEF1 Gene

  • RAB Guanine Nucleotide Exchange Factor 1 2 3 5
  • Rabaptin-5-Associated Exchange Factor For Rab5 3 4
  • RAB Guanine Nucleotide Exchange Factor (GEF) 1 2 3
  • Rab5 GDP/GTP Exchange Factor 3 4
  • Rabex-5 3 4
  • RABEX5 3 4
  • RAP1 3 4

External Ids for RABGEF1 Gene

Previous GeneCards Identifiers for RABGEF1 Gene

  • GC07P065544
  • GC07P065617
  • GC07P065649
  • GC07P065732
  • GC07P065843
  • GC07P066094
  • GC07P066205
  • GC07P062390
  • GC07P066148

Summaries for RABGEF1 Gene

Entrez Gene Summary for RABGEF1 Gene

  • RABGEF1 forms a complex with rabaptin-5 (RABPT5; MIM 603616) that is required for endocytic membrane fusion, and it serves as a specific guanine nucleotide exchange factor (GEF) for RAB5 (RAB5A; MIM 179512) (Horiuchi et al., 1997 [PubMed 9323142]).[supplied by OMIM, Mar 2010]

GeneCards Summary for RABGEF1 Gene

RABGEF1 (RAB Guanine Nucleotide Exchange Factor 1) is a Protein Coding gene. Diseases associated with RABGEF1 include Warburg Micro Syndrome. Among its related pathways are RAB GEFs exchange GTP for GDP on RABs and wtCFTR and delta508-CFTR traffic / Generic schema (norm and CF). Gene Ontology (GO) annotations related to this gene include ubiquitin-protein transferase activity and Rab guanyl-nucleotide exchange factor activity. An important paralog of this gene is RIN2.

UniProtKB/Swiss-Prot Summary for RABGEF1 Gene

  • Rab effector protein acting as linker between gamma-adaptin, RAB4A or RAB5A. Involved in endocytic membrane fusion and membrane trafficking of recycling endosomes. Stimulates nucleotide exchange on RAB5A. Can act as a ubiquitin ligase (By similarity).

Gene Wiki entry for RABGEF1 Gene

Additional gene information for RABGEF1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RABGEF1 Gene

Genomics for RABGEF1 Gene

GeneHancer (GH) Regulatory Elements for RABGEF1 Gene

Promoters and enhancers for RABGEF1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RABGEF1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RABGEF1

Top Transcription factor binding sites by QIAGEN in the RABGEF1 gene promoter:
  • C/EBPalpha
  • CUTL1
  • ER-alpha
  • HEN1
  • HFH-1
  • HSF1 (long)
  • HSF1short
  • MIF-1
  • MyoD
  • TGIF

Genomic Locations for RABGEF1 Gene

Genomic Locations for RABGEF1 Gene
chr7:66,682,091-66,811,464
(GRCh38/hg38)
Size:
129,374 bases
Orientation:
Plus strand
chr7:66,147,151-66,276,451
(GRCh37/hg19)
Size:
129,301 bases
Orientation:
Plus strand

Genomic View for RABGEF1 Gene

Genes around RABGEF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RABGEF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RABGEF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RABGEF1 Gene

Proteins for RABGEF1 Gene

  • Protein details for RABGEF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UJ41-RABX5_HUMAN
    Recommended name:
    Rab5 GDP/GTP exchange factor
    Protein Accession:
    Q9UJ41
    Secondary Accessions:
    • B4DZM7
    • Q3HKR2
    • Q3HKR3
    • Q53FG0

    Protein attributes for RABGEF1 Gene

    Size:
    491 amino acids
    Molecular mass:
    56891 Da
    Quaternary structure:
    • Interacts with RGS14; the interaction is GTP-dependent (By similarity). Heterodimer with RABEP1. The heterodimer binds RAB4A and RAB5A that have been activated by GTP-binding. Interacts with RAB21, and with 100-fold lower affinity also with RAB22. Binds TSC2, GGA1, GGA2, GGA3, AP1G1 and AP1G2. Interacts with ubiquitinated EGFR.
    SequenceCaution:
    • Sequence=BAC87138.1; Type=Miscellaneous discrepancy; Note=Readthrough transcript KCTD7-RABGEF1.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RABGEF1 Gene

    Alternative splice isoforms for RABGEF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RABGEF1 Gene

Post-translational modifications for RABGEF1 Gene

  • Monoubiquitinated.
  • Ubiquitination at Lys263, Lys281, Lys299, Lys318, Lys325, Lys329, Lys348, Lys423, Lys520, and Lys629
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RABGEF1 Gene

Domains & Families for RABGEF1 Gene

Gene Families for RABGEF1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transporters

Protein Domains for RABGEF1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RABGEF1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ55772, highly similar to Rab5 GDP/GTP exchange factor (B4DZM7_HUMAN)
  • Rabex-5 (RABX5_HUMAN)
genes like me logo Genes that share domains with RABGEF1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RABGEF1 Gene

Function for RABGEF1 Gene

Molecular function for RABGEF1 Gene

UniProtKB/Swiss-Prot Function:
Rab effector protein acting as linker between gamma-adaptin, RAB4A or RAB5A. Involved in endocytic membrane fusion and membrane trafficking of recycling endosomes. Stimulates nucleotide exchange on RAB5A. Can act as a ubiquitin ligase (By similarity).

Phenotypes From GWAS Catalog for RABGEF1 Gene

Gene Ontology (GO) - Molecular Function for RABGEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 16189514
GO:0008270 zinc ion binding IEA --
GO:0017112 Rab guanyl-nucleotide exchange factor activity IMP 23382462
GO:0017137 Rab GTPase binding IPI 23382462
genes like me logo Genes that share ontologies with RABGEF1: view
genes like me logo Genes that share phenotypes with RABGEF1: view

Animal Models for RABGEF1 Gene

MGI Knock Outs for RABGEF1:

Animal Model Products

CRISPR Products

miRNA for RABGEF1 Gene

miRTarBase miRNAs that target RABGEF1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RABGEF1 Gene

Localization for RABGEF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RABGEF1 Gene

Cytoplasm. Early endosome. Recycling endosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RABGEF1 gene
Compartment Confidence
endosome 5
nucleus 4
cytosol 4
plasma membrane 2
cytoskeleton 2
lysosome 2
golgi apparatus 2
extracellular 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoli (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RABGEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005730 nucleolus IDA --
GO:0005737 cytoplasm IEA --
GO:0005768 endosome IEA --
GO:0005769 early endosome IMP 23382462
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with RABGEF1: view

Pathways & Interactions for RABGEF1 Gene

PathCards logo

SuperPathways for RABGEF1 Gene

SuperPathway Contained pathways
1 Vesicle-mediated transport
2 Delta508-CFTR traffic / Sorting endosome formation in CF
.01
-
3 NF-kappaB Signaling
4 RAB GEFs exchange GTP for GDP on RABs
5 TBC/RABGAPs
genes like me logo Genes that share pathways with RABGEF1: view

Pathways by source for RABGEF1 Gene

3 GeneGo (Thomson Reuters) pathways for RABGEF1 Gene
  • Delta508-CFTR traffic / Sorting endosome formation in CF
  • Normal wtCFTR traffic / Sorting endosome formation
  • Transport Clathrin-coated vesicle cycle
1 Cell Signaling Technology pathway for RABGEF1 Gene

SIGNOR curated interactions for RABGEF1 Gene

Activates:
Is activated by:

Gene Ontology (GO) - Biological Process for RABGEF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006612 protein targeting to membrane IMP 23382462
GO:0006897 endocytosis IEA --
GO:0015031 protein transport IEA --
GO:0016567 protein ubiquitination IEA --
genes like me logo Genes that share ontologies with RABGEF1: view

Drugs & Compounds for RABGEF1 Gene

(1) Drugs for RABGEF1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine triphosphate Experimental Pharma 0

(2) Additional Compounds for RABGEF1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RABGEF1: view

Transcripts for RABGEF1 Gene

mRNA/cDNA for RABGEF1 Gene

39 REFSEQ mRNAs :
23 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RABGEF1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d · 6e ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c ^ 10a · 10b · 10c ^ 11 ^ 12a ·
SP1: - - - - - -
SP2: - - - - - - - - -
SP3:
SP4: - - - - - - - - -
SP5: - - - - - - -
SP6: - - - - - -
SP7: - - -
SP8: - - -
SP9: - - - - -
SP10: - - -
SP11: - - - - -
SP12:
SP13: -

ExUns: 12b ^ 13 ^ 14 ^ 15a · 15b · 15c
SP1: -
SP2: -
SP3: -
SP4:
SP5: -
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for RABGEF1 Gene

GeneLoc Exon Structure for
RABGEF1

Expression for RABGEF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RABGEF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RABGEF1 Gene

This gene is overexpressed in Whole Blood (x4.7).

Protein differential expression in normal tissues from HIPED for RABGEF1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (18.2) and Fetal Brain (13.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RABGEF1 Gene



Protein tissue co-expression partners for RABGEF1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RABGEF1

SOURCE GeneReport for Unigene cluster for RABGEF1 Gene:

Hs.530053

Evidence on tissue expression from TISSUES for RABGEF1 Gene

  • Nervous system(4.1)
  • Blood(4)
  • Liver(4)
genes like me logo Genes that share expression patterns with RABGEF1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RABGEF1 Gene

Orthologs for RABGEF1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RABGEF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RABGEF1 31 30
  • 99.47 (n)
OneToMany
cow
(Bos Taurus)
Mammalia RABGEF1 31 30
  • 92.74 (n)
OneToMany
dog
(Canis familiaris)
Mammalia RABGEF1 30
  • 92.58 (n)
-- 31
  • 63 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 92 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 89 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Rabgef1 17 31 30
  • 88.53 (n)
rat
(Rattus norvegicus)
Mammalia Rabgef1 30
  • 87.37 (n)
chicken
(Gallus gallus)
Aves -- 31
  • 89 (a)
OneToMany
zebrafish
(Danio rerio)
Actinopterygii rabgef1 31 30
  • 70.97 (n)
ManyToMany
rabgef1l 31
  • 53 (a)
ManyToMany
zgc65944 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005551 30
  • 48.7 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rabex-5 31 30
  • 48.37 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rabx-5 31 30
  • 48.83 (n)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS9 33 31
  • 19 (a)
rice
(Oryza sativa)
Liliopsida Os03g0842700 30
  • 50.21 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1840 31
  • 34 (a)
OneToMany
Species where no ortholog for RABGEF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for RABGEF1 Gene

ENSEMBL:
Gene Tree for RABGEF1 (if available)
TreeFam:
Gene Tree for RABGEF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RABGEF1: view image

Paralogs for RABGEF1 Gene

Paralogs for RABGEF1 Gene

(7) SIMAP similar genes for RABGEF1 Gene using alignment to 5 proteins:

  • RABX5_HUMAN
  • B4DZM7_HUMAN
  • C9JDA2_HUMAN
  • E9PFK9_HUMAN
  • V9GYI8_HUMAN

Pseudogenes.org Pseudogenes for RABGEF1 Gene

genes like me logo Genes that share paralogs with RABGEF1: view

Variants for RABGEF1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RABGEF1 Gene

SNP ID Clinical significance and condition Chr 07 pos Variation AA Info Type
732649 Likely Benign: not provided 66,805,218(+) A/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
748400 Likely Benign: not provided 66,805,336(+) G/C NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
753145 Likely Benign: not provided 66,772,073(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for RABGEF1 Gene

Structural Variations from Database of Genomic Variants (DGV) for RABGEF1 Gene

Variant ID Type Subtype PubMed ID
esv2668786 CNV deletion 23128226
esv2671700 CNV deletion 23128226
esv3541805 CNV deletion 23714750
esv3541806 CNV deletion 23714750
esv3571891 CNV loss 25503493
esv3613520 CNV gain 21293372
esv3613521 CNV gain 21293372
esv3891135 CNV gain 25118596
esv3891136 CNV gain 25118596
nsv1117731 CNV deletion 24896259
nsv507396 OTHER sequence alteration 20534489
nsv5773 CNV insertion 18451855
nsv958410 CNV deletion 24416366
nsv966835 CNV duplication 23825009
nsv970870 CNV duplication 23825009
nsv970871 CNV duplication 23825009
nsv981512 CNV duplication 23825009

Variation tolerance for RABGEF1 Gene

Residual Variation Intolerance Score: 21.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.01; 0.27% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RABGEF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RABGEF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RABGEF1 Gene

Disorders for RABGEF1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RABGEF1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
warburg micro syndrome
  • micro syndrome
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for RABGEF1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with RABGEF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RABGEF1 Gene

Publications for RABGEF1 Gene

  1. Divalent interaction of the GGAs with the Rabaptin-5-Rabex-5 complex. (PMID: 12505986) Mattera R … Bonifacino JS (The EMBO journal 2003) 2 3 4 54
  2. Functional synergy between Rab5 effector Rabaptin-5 and exchange factor Rabex-5 when physically associated in a complex. (PMID: 11452015) Lippé R … Zerial M (Molecular biology of the cell 2001) 3 4 23 54
  3. Seven genes that are differentially transcribed in colorectal tumor cell lines. (PMID: 11098082) Nimmrich I … Müller O (Cancer letters 2000) 2 3 4 54
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41 54
  5. Roles of RabGEF1/Rabex-5 domains in regulating Fc epsilon RI surface expression and Fc epsilon RI-dependent responses in mast cells. (PMID: 17341663) Kalesnikoff J … Galli SJ (Blood 2007) 3 23 54

Products for RABGEF1 Gene

Sources for RABGEF1 Gene