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Aliases for ARHGEF9 Gene

Aliases for ARHGEF9 Gene

  • Cdc42 Guanine Nucleotide Exchange Factor 9 2 3 5
  • Cdc42 Guanine Nucleotide Exchange Factor (GEF) 9 2 3
  • Rac/Cdc42 Guanine Nucleotide Exchange Factor 9 3 4
  • PEM-2 Homolog 3 4
  • Collybistin 2 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. This brain-specific protein also acts as an adaptor protein for the recruitment of gephyrin and together these proteins facilitate receceptor recruitement in GABAnergic and glycinergic synapses. Defects in this gene are the cause of startle disease with epilepsy (STHEE), also known as hyperekplexia with epilepsy, as well as several other types of cognitive disability. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

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 Hyperekplexia. Among its related pathways are p75 NTR receptor-mediated signalling and G-AlphaQ Signaling. Gene Ontology (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for ARHGEF9 Gene

Promoters and enhancers for ARHGEF9 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ063751 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 662.1 +55.2 55178 4.2 PKNOX1 SIN3A BATF IRF4 RAD21 YY1 ZNF335 GLIS2 ZNF366 ZNF350 ARHGEF9 MIR1468 BTF3P8 ARHGEF9-IT1
GH0XJ063781 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 650.3 +25.2 25234 4.5 ZNF316 MAFF POLR2A MAFG MAFK ARHGEF9 MIR1468 GC0XP063767
GH0XJ063809 Promoter 0.5 EPDnew 650.7 0.0 -11 0.1 ARHGEF9 GC0XM063831
GH0XJ063761 Enhancer 0.6 ENCODE 13.5 +47.4 47428 0.8 CTCF ZBED1 TRIM22 MEF2B RAD21 ATF2 BCL11A IKZF1 EED ETV6 MIR1468 ARHGEF9 BTF3P8 ARHGEF9-IT1
GH0XJ063745 Enhancer 0.5 Ensembl ENCODE 12.3 +62.4 62431 2.7 RUNX3 MIR1468 ARHGEF9 BTF3P8 ARHGEF9-IT1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ARHGEF9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ARHGEF9 gene promoter:
  • PPAR-gamma1
  • LCR-F1
  • PPAR-gamma2
  • Meis-1b
  • Meis-1a
  • Meis-1
  • Tal-1
  • E47
  • MyoD
  • C/EBPbeta

Genomic Locations for ARHGEF9 Gene

Genomic Locations for ARHGEF9 Gene
174,308 bases
Minus strand
150,580 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

Gene Families 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 --
GO:0005515 protein binding IEA --
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

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ARHGEF9

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ARHGEF9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA,TAS --
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:0007186 G-protein coupled receptor signaling pathway TAS --
GO:0035023 regulation of Rho protein signal transduction IEA --
GO:0043065 positive regulation of apoptotic process TAS --
GO:0051056 regulation of small GTPase mediated signal transduction TAS --
GO:0065009 regulation of molecular function IEA --
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

mRNA/cDNA for ARHGEF9 Gene

Unigene Clusters for ARHGEF9 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ARHGEF9

Clone 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 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

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 33
  • 99.68 (n)
(Canis familiaris)
Mammalia ARHGEF9 34 33
  • 95.2 (n)
(Bos Taurus)
Mammalia LOC537718 33
  • 94.61 (n)
  • 91 (a)
(Ornithorhynchus anatinus)
Mammalia ARHGEF9 34
  • 94 (a)
(Mus musculus)
Mammalia Arhgef9 16 34 33
  • 93.02 (n)
(Rattus norvegicus)
Mammalia Arhgef9 33
  • 92.97 (n)
(Monodelphis domestica)
Mammalia ARHGEF9 34
  • 41 (a)
(Gallus gallus)
Aves ARHGEF9 34 33
  • 84.15 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 85 (a)
-- 34
  • 81 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia arhgef9 33
  • 80.86 (n)
(Danio rerio)
Actinopterygii arhgef9a 34
  • 79 (a)
arhgef9b 34 34 33
  • 76.11 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7470 34
  • 29 (a)
Cin.3922 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3922 33
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)
Evolutionary constrained regions (ECRs) for ARHGEF9: view image

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 Variation AA Info Type
rs121918361 pathogenic, Early infantile epileptic encephalopathy 8, Epileptic encephalopathy, early infantile, 8 (EIEE8) [MIM:300607] 63,724,557(-) C/G 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant
rs138198839 uncertain-significance, likely-benign, not specified, Early infantile epileptic encephalopathy 8 63,706,288(-) G/A coding_sequence_variant, synonymous_variant
rs143490560 likely-benign, benign, not specified, Early infantile epileptic encephalopathy 8 63,674,044(-) G/C coding_sequence_variant, missense_variant
rs150129110 likely-benign, uncertain-significance, not specified, Early infantile epileptic encephalopathy 8 63,697,125(-) G/A coding_sequence_variant, synonymous_variant
rs373866956 likely-benign, Early infantile epileptic encephalopathy 8 63,706,309(-) C/T coding_sequence_variant, synonymous_variant

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)

Additional Variant Information 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

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

Disorder Aliases PubMed IDs
epileptic encephalopathy, early infantile, 8
  • eiee8
  • startle disease, familial
infantile epileptic encephalopathy
  • west syndrome
- 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.

Additional Disease Information for ARHGEF9

Genetic Association Database
Human Genome Epidemiology 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 RJ (The Journal of neuroscience : the official journal of the Society for Neuroscience 2004) 3 4 22 58
  2. Identification and characterization of hPEM-2, a guanine nucleotide exchange factor specific for Cdc42. (PMID: 10559246) Reid T … Collard JG (The Journal of biological chemistry 1999) 2 3 4 58
  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 research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4 58
  4. Lipid binding defects and perturbed synaptogenic activity of a Collybistin R290H mutant that causes epilepsy and intellectual disability. (PMID: 25678704) Papadopoulos T … Brose N (The Journal of biological chemistry 2015) 3 4 58
  5. Mutation of ARHGAP9 in patients with coronary spastic angina. (PMID: 19911011) Takefuji M … Kaibuchi K (Journal of human genetics 2010) 3 44 58

Products for ARHGEF9 Gene

Sources for ARHGEF9 Gene

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