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Relevance to Autism

A de novo deletion encompassing the ARHGEF9 gene was identified in a male patient presenting with mild-to-moderate autism, severe intellectual disability, and epilepsy; iPSC-derived neural progenitor cells from this patient showed a complete loss of CB expression and hyperactivation of mTORC1 signaling under basal conditions (Machado et al., 2016). A second de novo deletion involving the ARHGEF9 gene was identified in an 8-year-old female patient diagnosed with ASD and ADHD and presenting with mild intellectual disability, global developmental delay, and severe speech impairment (Bhat et al., 2016). A phenotypic review of 18 patients with ARHGEF9 variants (10 previously published, 8 novel; 13 males, 5 females with highly skewed X-chromosome inactivation) demonstrated that the majority of patients presented with intellectual disability, epilepsy, and dysmorphic facial features; 4 of the 18 patients described in this report presented with autistic features (Alber et al., 2017).

Molecular Function

The protein encoded by this gene is a Rho-like GTPase that acts as a guanine nucleotide exchange factor (GEF) for CDC42 and other genes and promotes the formation of GPHN clusters. Variants in this gene are associated with a form of early infantile epileptic encephalopathy (EIEE8, OMIM 300607).

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Collybistin binds and inhibits mTORC1 signaling: a potential novel mechanism contributing to intellectual disability and autism.
ASD, ID, epilepsy/seizures
Support
Using medical exome sequencing to identify the causes of neurodevelopmental disorders: experience of two clinical units and 216 patients.
ID
Macrocephaly
Support
Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder
ASD
Support
Developmental and epileptic encephalopathy 8, DD
Support
Xq11.1-11.2 deletion involving ARHGEF9 in a girl with autism spectrum disorder.
ASD, ADHD, ID, DD
Support
A recurrent PJA1 variant in trigonocephaly and neurodevelopmental disorders
DD, epilepsy/seizures
Support
Integrating de novo and inherited variants in 42
ASD
Support
Missense Mutation R338W in ARHGEF9 in a Family with X-linked Intellectual Disability with Variable Macrocephaly and Macro-Orchidism.
ID
Support
Increased diagnostic and new genes identification outcome using research reanalysis of singleton exome sequencing.
Epilepsy/seizures
Support
ARHGEF9 gene variant leads to developmental and epileptic encephalopathy: Genotypic phenotype analysis and treatment exploration
DD, epilepsy/seizures
Support
The GDP-GTP exchange factor collybistin: an essential determinant of neuronal gephyrin clustering.
Epilepsy/seizures
Hyperekplexia
Support
Neurological Diseases With Autism Spectrum Disorder: Role of ASD Risk Genes.
ASD
ID, epilepsy/seizures
Support
Human ARHGEF9 intellectual disability syndrome is phenocopied by a mutation that disrupts collybistin binding to the GABA A receptor α2 subunit
ASD, DD, ID, epilepsy/seizures
ADHD
Support
Autism spectrum disorder in females with ARHGEF9 alterations and a random pattern of X chromosome inactivation.
ASD, DD/ID
Support
A novel de novo hemizygous ARHGEF9 mutation associated with severe intellectual disability and epilepsy: a case report
DD, ID, epilepsy/seizures
Support
ARHGEF9 mutations in epileptic encephalopathy/intellectual disability: toward understanding the mechanism underlying phenotypic variation.
ID, epilepsy/seizures
Support
Autism spectrum disorder and comorbid neurodevelopmental disorders (ASD-NDDs): Clinical and genetic profile of a pediatric cohort
ASD
Epilepsy/seizures
Recent Recommendation
ARHGEF9 disease: Phenotype clarification and genotype-phenotype correlation.
ID, epilepsy/seizures
Autistic features

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN715R001 
 copy_number_loss 
  
  
 De novo 
  
 Simplex 
 GEN715R002 
 missense_variant 
 c.164G>C 
 p.Gly55Ala 
 De novo 
  
  
 GEN715R003 
 missense_variant 
 c.1012C>T 
 p.Arg338Trp 
 Familial 
 Maternal 
 Multi-generational 
 GEN715R004 
 copy_number_loss 
  
  
 De novo 
  
  
 GEN715R005 
 translocation 
  
  
 De novo 
  
  
 GEN715R006 
 translocation 
  
  
 De novo 
  
  
 GEN715R007 
 copy_number_loss 
  
  
 De novo 
  
  
 GEN715R008 
 copy_number_loss 
  
  
 De novo 
  
  
 GEN715R009 
 inversion 
  
  
 De novo 
  
  
 GEN715R010 
 copy_number_loss 
  
  
 De novo 
  
  
 GEN715R011 
 copy_number_loss 
  
  
 De novo 
  
  
 GEN715R012 
 stop_gained 
 c.4C>T 
 p.Gln2Ter 
 Familial 
 Maternal 
  
 GEN715R013 
 missense_variant 
 c.950C>G 
 p.Ser317Trp 
 Familial 
 Maternal 
 Multiplex 
 GEN715R014 
 missense_variant 
 c.530T>C 
 p.Leu177Pro 
 De novo 
  
  
 GEN715R015 
 missense_variant 
 c.311G>A 
 p.Arg104Gln 
 De novo 
  
  
 GEN715R016 
 missense_variant 
 c.869G>A 
 p.Arg290His 
 De novo 
  
 Multiplex 
 GEN715R017 
 missense_variant 
 c.1198G>A 
 p.Glu400Lys 
 De novo 
  
  
 GEN715R018 
 splice_site_variant 
 c.1141+2T>C 
  
 De novo 
  
  
 GEN715R019 
 missense_variant 
 c.1067G>A 
 p.Arg356Gln 
 Familial 
 Maternal 
  
 GEN715R020 
 stop_gained 
 c.865C>T 
 p.Arg289Ter 
 Familial 
 Paternal 
  
 GEN715R021 
 missense_variant 
 c.868C>T 
 p.Arg290Cys 
 Familial 
 Maternal 
 Multiplex 
 GEN715R022 
 copy_number_loss 
  
  
 De novo 
  
  
 GEN715R023 
 copy_number_loss 
  
  
 De novo 
  
  
 GEN715R024 
 stop_gained 
 c.417G>A 
 p.Met139Ile 
 Familial 
 Maternal 
  
 GEN715R025 
 stop_gained 
 c.510T>A 
 p.Tyr170Ter 
 Familial 
 Maternal 
  
 GEN715R026 
 missense_variant 
 c.950C>T 
 p.Ser317Leu 
 Familial 
 Maternal 
  
 GEN715R027 
 inframe_insertion 
 c.882_883insATT 
 p.Thr294_Gln295insIle 
 Familial 
 Maternal 
 Simplex 
 GEN715R028 
 stop_gained 
 c.940C>T 
 p.Gln314Ter 
 Unknown 
  
  
 GEN715R029 
 frameshift_variant 
 c.477_490del 
 p.Met159IlefsTer6 
 De novo 
  
 Simplex 
 GEN715R030 
 stop_gained 
 c.417G>A 
 p.Gln139%3D 
 Familial 
 Maternal 
  
 GEN715R031 
 stop_gained 
 c.510T>A 
 p.Tyr170Ter 
 Familial 
 Maternal 
  
 GEN715R032 
 stop_gained 
 c.194G>A 
 p.Trp65Ter 
 De novo 
  
  
 GEN715R033 
 frameshift_variant 
 c.1105del 
 p.Glu369LysfsTer26 
 De novo 
  
  
 GEN715R034 
 missense_variant 
 c.1094G>A 
 p.Arg365His 
 Familial 
 Maternal 
  
 GEN715R035 
 missense_variant 
 c.1162A>G 
 p.Met388Val 
 Familial 
 Maternal 
  
 GEN715R036 
 missense_variant 
 c.639C>G 
 p.Asn213Lys 
 Familial 
 Maternal 
  
 GEN715R037 
 missense_variant 
 c.188G>A 
 p.Arg63Lys 
 De novo 
  
  
 GEN715R038 
 missense_variant 
 c.1094G>A 
 p.Arg365His 
 De novo 
  
  
 GEN715R039 
 splice_site_variant 
 c.925-1G>T 
  
 De novo 
  
  
 GEN715R040 
 missense_variant 
 c.311G>A 
 p.Arg104Gln 
 De novo 
  
  
 GEN715R041 
 stop_gained 
 c.138G>A 
 p.Trp46Ter 
 De novo 
  
  
 GEN715R042 
 missense_variant 
 c.924G>T 
 p.Glu308Asp 
 De novo 
  
  
 GEN715R043 
 stop_gained 
 c.741C>A 
 p.Cys247Ter 
 De novo 
  
  
 GEN715R044 
 stop_gained 
 c.682C>T 
 p.Gln228Ter 
 De novo 
  
 Simplex 
 GEN715R045 
 splice_site_variant 
 c.1370-2A>G 
  
 De novo 
  
  
 GEN715R046 
 missense_variant 
 c.347G>A 
 p.Arg116His 
 Familial 
 Maternal 
 Simplex 
  et al.  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
X
Deletion
 1
 
X
Duplication
 1
 
X
Duplication
 1
 
X
Deletion
 1
 
X
Deletion-Duplication
 21
 
X
Deletion-Duplication
 8
 
X
Deletion
 2
 
X
Duplication
 2
 
X
Deletion
 2
 
X
Duplication
 1
 

No Animal Model Data Available


Interactor Symbol Interactor Name Interactor Organism Entrez ID Uniprot ID Interaction Type Evidence Reference
GPHN gephyrin 10243 Q9NQX3 IP/WB; Y2H
Kins S , et al. 1999
GPHN gephyrin 10243 Q9NQX3 Y2H
Um JW , et al. 2016
MTOR mechanistic target of rapamycin (serine/threonine kinase) 2475 P42345 IP/WB
Machado CO , et al. 2015

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