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Aliases for ARHGEF9 Gene

Aliases for ARHGEF9 Gene

  • Cdc42 Guanine Nucleotide Exchange Factor 9 2 3 5
  • Collybistin 2 3 4
  • Cdc42 Guanine Nucleotide Exchange Factor (GEF) 9 2 3
  • Rac/Cdc42 Guanine Nucleotide Exchange Factor 9 3 4
  • PEM-2 Homolog 3 4
  • Rho Guanine Nucleotide Exchange Factor 9 3
  • HPEM-2 Collybistin 3
  • KIAA0424 4
  • HPEM-2 3
  • ARHDH9 4
  • EIEE8 3
  • PEM-2 3
  • PEM2 3

External Ids for ARHGEF9 Gene

Previous GeneCards Identifiers for ARHGEF9 Gene

  • GC0XM059065
  • GC0XM060320
  • GC0XM061088
  • GC0XM061722
  • GC0XM061723
  • GC0XM062637
  • GC0XM062771
  • GC0XM056681

Summaries for ARHGEF9 Gene

Entrez Gene Summary for ARHGEF9 Gene

  • The protein encoded by this gene is a Rho-like GTPase that switches between the active (GTP-bound) state and inactive (GDP-bound) state to regulate CDC42 and other genes. Defects in this gene are a cause of startle disease with epilepsy (STHEE), also known as hyperekplexia with epilepsy. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2010]

GeneCards Summary for ARHGEF9 Gene

ARHGEF9 (Cdc42 Guanine Nucleotide Exchange Factor 9) is a Protein Coding gene. Diseases associated with ARHGEF9 include Epileptic Encephalopathy, Early Infantile, 8 and Arhgef9-Related Hyperekplexia. Among its related pathways are GPCR Pathway and Ligand-gated ion channel transport. GO annotations related to this gene include Rho guanyl-nucleotide exchange factor activity. An important paralog of this gene is SPATA13.

UniProtKB/Swiss-Prot for ARHGEF9 Gene

  • Acts as guanine nucleotide exchange factor (GEF) for CDC42. Promotes formation of GPHN clusters.

Gene Wiki entry for ARHGEF9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ARHGEF9 Gene

Genomics for ARHGEF9 Gene

Regulatory Elements for ARHGEF9 Gene

Enhancers for ARHGEF9 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XG063751 0.9 ENCODE 12.1 +55.2 55178 4.2 TBP PKNOX1 ATF1 ZNF76 RAD21 YY1 GLIS2 GATA2 ZNF366 ZNF350 MIR1468 ARHGEF9 BTF3P8 ARHGEF9-IT1
GH0XG063745 0.7 Ensembl ENCODE 12.3 +62.4 62431 2.7 GATA2 SMARCA4 PRDM1 MIR1468 ARHGEF9 BTF3P8 ARHGEF9-IT1
GH0XG063750 0.2 ENCODE 12 +58.5 58520 0.9 MIR1468 ARHGEF9 BTF3P8 ARHGEF9-IT1
GH0XG063752 0.2 ENCODE 12 +57.6 57559 0.2 MIR1468 ARHGEF9 BTF3P8 ARHGEF9-IT1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ARHGEF9 on UCSC Golden Path with GeneCards custom track

Genomic Location for ARHGEF9 Gene

63,634,967 bp from pter
63,809,274 bp from pter
174,308 bases
Minus strand

Genomic View for ARHGEF9 Gene

Genes around ARHGEF9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ARHGEF9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ARHGEF9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ARHGEF9 Gene

Proteins for ARHGEF9 Gene

  • Protein details for ARHGEF9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Rho guanine nucleotide exchange factor 9
    Protein Accession:
    Secondary Accessions:
    • A8K1S8
    • B4DHC7
    • F8W7P8
    • Q5JSL6

    Protein attributes for ARHGEF9 Gene

    516 amino acids
    Molecular mass:
    60982 Da
    Quaternary structure:
    • Interacts with GPHN.
    • Sequence=BAA24854.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ARHGEF9 Gene

    Alternative splice isoforms for ARHGEF9 Gene


neXtProt entry for ARHGEF9 Gene

Post-translational modifications for ARHGEF9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ARHGEF9 Gene

Domains & Families for ARHGEF9 Gene

Protein Domains for ARHGEF9 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ARHGEF9: view

No data available for UniProtKB/Swiss-Prot for ARHGEF9 Gene

Function for ARHGEF9 Gene

Molecular function for ARHGEF9 Gene

UniProtKB/Swiss-Prot Function:
Acts as guanine nucleotide exchange factor (GEF) for CDC42. Promotes formation of GPHN clusters.

Gene Ontology (GO) - Molecular Function for ARHGEF9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity TAS --
GO:0005089 Rho guanyl-nucleotide exchange factor activity IEA,TAS --
genes like me logo Genes that share ontologies with ARHGEF9: view
genes like me logo Genes that share phenotypes with ARHGEF9: view

Human Phenotype Ontology for ARHGEF9 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ARHGEF9 Gene

MGI Knock Outs for ARHGEF9:

Animal Model Products

CRISPR Products

miRNA for ARHGEF9 Gene

miRTarBase miRNAs that target ARHGEF9

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for ARHGEF9 Gene

Localization for ARHGEF9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ARHGEF9 Gene


Subcellular locations from

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 ARHGEF9 gene
Compartment Confidence
cytosol 5
plasma membrane 2
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for ARHGEF9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS,IDA --
genes like me logo Genes that share ontologies with ARHGEF9: view

Pathways & Interactions for ARHGEF9 Gene

genes like me logo Genes that share pathways with ARHGEF9: view

Gene Ontology (GO) - Biological Process for ARHGEF9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0034220 ion transmembrane transport TAS --
GO:0035023 regulation of Rho protein signal transduction IEA --
GO:0043065 positive regulation of apoptotic process TAS --
GO:0043547 positive regulation of GTPase activity IEA --
GO:0051056 regulation of small GTPase mediated signal transduction TAS --
genes like me logo Genes that share ontologies with ARHGEF9: view

No data available for SIGNOR curated interactions for ARHGEF9 Gene

Drugs & Compounds for ARHGEF9 Gene

(3) Drugs for ARHGEF9 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with ARHGEF9: view

Transcripts for ARHGEF9 Gene

Unigene Clusters for ARHGEF9 Gene

Cdc42 guanine nucleotide exchange factor (GEF) 9:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for ARHGEF9 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b
SP2: - -

Relevant External Links for ARHGEF9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ARHGEF9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ARHGEF9 Gene

Protein differential expression in normal tissues from HIPED for ARHGEF9 Gene

This gene is overexpressed in Blymphocyte (36.3) and Platelet (25.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ARHGEF9 Gene

Protein tissue co-expression partners for ARHGEF9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ARHGEF9 Gene:


SOURCE GeneReport for Unigene cluster for ARHGEF9 Gene:


mRNA Expression by UniProt/SwissProt for ARHGEF9 Gene:

Tissue specificity: Detected in brain. Detected at low levels in heart.

Evidence on tissue expression from TISSUES for ARHGEF9 Gene

  • Nervous system(4.9)
  • Eye(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ARHGEF9 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
Head and neck:
  • brain
  • head
  • spinal cord
genes like me logo Genes that share expression patterns with ARHGEF9: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for ARHGEF9 Gene

Orthologs for ARHGEF9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ARHGEF9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ARHGEF9 34 35
  • 99.68 (n)
(Canis familiaris)
Mammalia ARHGEF9 34 35
  • 95.2 (n)
(Bos Taurus)
Mammalia LOC537718 34
  • 94.61 (n)
  • 91 (a)
(Ornithorhynchus anatinus)
Mammalia ARHGEF9 35
  • 94 (a)
(Mus musculus)
Mammalia Arhgef9 34 16 35
  • 93.02 (n)
(Rattus norvegicus)
Mammalia Arhgef9 34
  • 92.97 (n)
(Monodelphis domestica)
Mammalia ARHGEF9 35
  • 41 (a)
(Gallus gallus)
Aves ARHGEF9 34 35
  • 84.15 (n)
(Anolis carolinensis)
Reptilia -- 35
  • 85 (a)
-- 35
  • 81 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia arhgef9 34
  • 80.86 (n)
(Danio rerio)
Actinopterygii arhgef9a 35
  • 79 (a)
arhgef9b 34 35 35
  • 76.11 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7470 35
  • 29 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3922 34
Species where no ortholog for ARHGEF9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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 (Oryza sativa)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ARHGEF9 Gene

Gene Tree for ARHGEF9 (if available)
Gene Tree for ARHGEF9 (if available)

Paralogs for ARHGEF9 Gene

(6) SIMAP similar genes for ARHGEF9 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with ARHGEF9: view

Variants for ARHGEF9 Gene

Sequence variations from dbSNP and Humsavar for ARHGEF9 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs121918361 Pathogenic, Epileptic encephalopathy, early infantile, 8 (EIEE8) [MIM:300607] 63,724,557(-) GGAGG(C/G)ATGGT intron-variant, reference, missense, utr-variant-5-prime
VAR_072742 Epileptic encephalopathy, early infantile, 8 (EIEE8) [MIM:300607]
rs397514460 Pathogenic 63,785,142(-) CCATG(C/T)AGTGG reference, stop-gained, utr-variant-5-prime
rs869312941 Likely pathogenic 63,665,930(-) AGCAG(C/T)GGGTC intron-variant, reference, missense
rs140777637 Uncertain significance 63,678,480(+) AAGTG(C/T)TGGTA reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for ARHGEF9 Gene

Variant ID Type Subtype PubMed ID
esv1584074 OTHER inversion 17803354
esv3558915 CNV deletion 23714750
esv3574010 CNV loss 25503493
esv3576915 CNV gain 25503493
nsv474047 CNV novel sequence insertion 20440878

Variation tolerance for ARHGEF9 Gene

Residual Variation Intolerance Score: 70.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.42; 9.31% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ARHGEF9 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ARHGEF9 Gene

Disorders for ARHGEF9 Gene

MalaCards: The human disease database

(4) MalaCards diseases for ARHGEF9 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards


  • Epileptic encephalopathy, early infantile, 8 (EIEE8) [MIM:300607]: A disorder characterized by hyperekplexia and early infantile epileptic encephalopathy. Neurologic features include exaggerated startle response, seizures, impaired psychomotor development, and mental retardation. Seizures can be provoked by tactile stimulation or extreme emotion. {ECO:0000269 PubMed:15215304, ECO:0000269 PubMed:22612257, ECO:0000269 PubMed:25678704}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for ARHGEF9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with ARHGEF9: view

No data available for Genatlas for ARHGEF9 Gene

Publications for ARHGEF9 Gene

  1. The GDP-GTP exchange factor collybistin: an essential determinant of neuronal gephyrin clustering. (PMID: 15215304) Harvey K. … Harvey R.J. (J. Neurosci. 2004) 3 4 22 64
  2. Identification and characterization of hPEM-2, a guanine nucleotide exchange factor specific for Cdc42. (PMID: 10559246) Reid T. … Collard J.G. (J. Biol. Chem. 1999) 2 3 4 64
  3. Prediction of the coding sequences of unidentified human genes. VIII. 78 new cDNA clones from brain which code for large proteins in vitro. (PMID: 9455477) Ishikawa K. … Ohara O. (DNA Res. 1997) 2 3 4 64
  4. Lipid binding defects and perturbed synaptogenic activity of a collybistinR290H mutant that causes epilepsy and intellectual disability. (PMID: 25678704) Papadopoulos T. … Brose N. (J. Biol. Chem. 2015) 3 4 64
  5. Mutation of ARHGAP9 in patients with coronary spastic angina. (PMID: 19911011) Takefuji M. … Kaibuchi K. (J. Hum. Genet. 2010) 3 46 64

Products for ARHGEF9 Gene

Sources for ARHGEF9 Gene

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