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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]
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 Guidance Cues and Growth Cone Motility and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include Rho guanyl-nucleotide exchange factor activity. An important paralog of this gene is SPATA13.
GeneHancer (GH) Identifier | GH Type | GH Score |
GH Sources | Gene Association Score | Total Score | TSS distance (kb) | Number of Genes Away | Size (kb) | Transcription Factor Binding Sites |
Gene Targets |
---|---|---|---|---|---|---|---|---|---|---|
GH0XJ063750 | Promoter/Enhancer | 1.8 | EPDnew Ensembl ENCODE CraniofacialAtlas | 612.1 | +56.0 | 56015 | 5.9 | SP1 CREB1 PRDM10 ZNF512 POLR2A FOS PRDM1 RELA PKNOX1 PATZ1 | ARHGEF9 HSALNG0138235 MIR1468 piR-33614-285 SPIN4 | |
GH0XJ063781 | Promoter/Enhancer | 1.5 | EPDnew Ensembl ENCODE CraniofacialAtlas | 600.3 | +25.2 | 25234 | 4.5 | POLR2A ZNF316 MAFF MAFK MAFG SIN3A TAF1 TBP | ARHGEF9 MIR1468 piR-33804-187 SPIN4 | |
GH0XJ063809 | Promoter | 0.4 | EPDnew | 600.7 | 0.0 | -11 | 0.1 | RFX5 | ARHGEF9 piR-54764-683 AMER1 | |
GH0XJ063761 | Enhancer | 0.8 | Ensembl ENCODE | 13.5 | +47.5 | 47473 | 1.2 | CTCF RAD21 IKZF2 TRIM22 EED ARID3A RELB RUNX3 BCLAF1 TCF12 | MIR1468 ARHGEF9 BTF3P8 HSALNG0138235 SPIN4 | |
GH0XJ063745 | Enhancer | 0.6 | Ensembl ENCODE | 12.3 | +63.3 | 63274 | 4.8 | RUNX3 NFIC SMARCA4 EGR2 | MIR1468 ARHGEF9 HSALNG0138235 piR-33614-285 SPIN4 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0005085 | guanyl-nucleotide exchange factor activity | IEA | -- |
GO:0005515 | protein binding | IEA | -- |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0005737 | cytoplasm | IEA | -- |
GO:0005829 | cytosol | IDA,TAS | -- |
GO:0014069 | postsynaptic density | ISS | -- |
GO:0030054 | cell junction | IEA | -- |
GO:0045202 | synapse | IEA | -- |
SuperPathway | Contained pathways | ||
---|---|---|---|
1 | p75 NTR receptor-mediated signalling |
.36
|
|
2 | GPCR Pathway |
Ras Pathway
.73
GPCR Pathway
.62
|
Pancreatic Adenocarcinoma
.59
Breast Cancer Regulation by Stathmin1
.58
|
3 | G-AlphaQ Signaling |
G-AlphaI Signaling
.47
G-AlphaQ Signaling
.47
|
Thrombin Signaling
.40
|
4 | Signaling by GPCR | ||
5 | Transmission across Chemical Synapses |
.62
|
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0007186 | G protein-coupled receptor signaling pathway | TAS | -- |
GO:0043065 | positive regulation of apoptotic process | TAS | -- |
GO:0051056 | regulation of small GTPase mediated signal transduction | TAS | -- |
GO:0099150 | regulation of postsynaptic specialization assembly | IEA | -- |
ExUns: | 1a | · | 1b | · | 1c | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10a | · | 10b |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SP1: | |||||||||||||||||||||||||
SP2: | - | - |
This gene was present in the common ancestor of chordates.
Organism | Taxonomy | Gene | Similarity | Type | Details |
---|---|---|---|---|---|
Chimpanzee (Pan troglodytes) |
Mammalia | ARHGEF9 30 31 |
|
OneToOne | |
Dog (Canis familiaris) |
Mammalia | ARHGEF9 30 31 |
|
OneToOne | |
Cow (Bos Taurus) |
Mammalia | LOC537718 30 |
|
||
ARHGEF9 31 |
|
OneToOne | |||
Platypus (Ornithorhynchus anatinus) |
Mammalia | ARHGEF9 31 |
|
OneToOne | |
Mouse (Mus musculus) |
Mammalia | Arhgef9 30 17 31 |
|
OneToOne | |
Rat (Rattus norvegicus) |
Mammalia | Arhgef9 30 |
|
||
Oppossum (Monodelphis domestica) |
Mammalia | ARHGEF9 31 |
|
OneToOne | |
Chicken (Gallus gallus) |
Aves | ARHGEF9 30 31 |
|
OneToOne | |
Lizard (Anolis carolinensis) |
Reptilia | -- 31 |
|
OneToMany | |
-- 31 |
|
OneToMany | |||
Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | arhgef9 30 |
|
||
Zebrafish (Danio rerio) |
Actinopterygii | arhgef9a 31 |
|
OneToMany | |
arhgef9b 30 31 31 |
|
OneToMany | |||
Sea Squirt (Ciona savignyi) |
Ascidiacea | CSA.7470 31 |
|
OneToMany | |
Sea Vase (Ciona intestinalis) |
Ascidiacea | Cin.3922 30 |
|
SNP ID | Clinical significance and condition | Chr 0X pos | Variation | AA Info | Type |
---|---|---|---|---|---|
644871 | Benign: Early infantile epileptic encephalopathy 8 | 63,785,117(-) | A/G | MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT | |
648941 | Likely Pathogenic: Early infantile epileptic encephalopathy 8 | 63,697,151(-) | C/T | MISSENSE_VARIANT | |
653238 | Likely Benign: Early infantile epileptic encephalopathy 8 | 63,638,135(-) | C/G | MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT | |
653302 | Uncertain Significance: Early infantile epileptic encephalopathy 8 | 63,638,167(-) | G/A | MISSENSE_VARIANT,THREE_PRIME_UTR_VARIANT | |
654805 | Uncertain Significance: Early infantile epileptic encephalopathy 8 | 63,724,666(-) | G/A | MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT |
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 |
Disorder | Aliases | PubMed IDs |
---|---|---|
epileptic encephalopathy, early infantile, 8 |
|
|
hyperekplexia |
|
|
early infantile epileptic encephalopathy |
|
|
ritscher-schinzel syndrome 2 |
|
|
epilepsy |
|
|