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Relevance to Autism

Thomas et al., 2021 identified 13 individuals with both de novo and inherited likely pathogenic heterozygous variants in the ARFGEF1 gene; affected individuals typically presented with developmental delay, intellectual disability, and behavioral problems (including autism spectrum disorder in three individuals), with approximately half of this cohort also presenting with neurological features, abnormal brain MRI findings, and epilepsy. Private likely gene-disruptive (LGD) variants that were exclusively transmitted to ASD probands in two independent families were observed in this highly constrained (pLI 0.99) gene in Wilfert et al., 2021; one of these families consisted of a multiplex family from the iHART cohort originally described in Ruzzo et al., 2019 in which a maternally-inherited frameshift variant in ARFGEF1 was transmitted to both ASD-affected siblings.

Molecular Function

ADP-ribosylation factors (ARFs) play an important role in intracellular vesicular trafficking. The protein encoded by this gene is involved in the activation of ARFs by accelerating replacement of bound GDP with GTP. It contains a Sec7 domain, which may be responsible for guanine-nucleotide exchange activity and also brefeldin A inhibition.

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References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Haploinsufficiency of ARFGEF1 is associated with developmental delay, intellectual disability, and epilepsy with variable expressivity
DD, ID
ASD, ADHD, epilepsy/seizures
Support
Integrating de novo and inherited variants in 42
ASD
Support
Expanding the Phenotypic and Genotypic Spectrum of ARFGEF1-Related Neurodevelopmental Disorder
DD, ID, epilepsy/seizures
ASD
Support
Recent ultra-rare inherited variants implicate new autism candidate risk genes
ASD
Support
Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1261R001 
 missense_variant 
 c.2392G>A 
 p.Asp798Asn 
 De novo 
  
 Simplex 
 GEN1261R002 
 stop_gained 
 c.5320C>T 
 p.Arg1774Ter 
 De novo 
  
 Simplex 
 GEN1261R003 
 splice_site_variant 
 c.3592-2A>G 
  
 De novo 
  
 Simplex 
 GEN1261R004 
 frameshift_variant 
 c.2158del 
 p.Leu720SerfsTer24 
 De novo 
  
 Simplex 
 GEN1261R005 
 stop_gained 
 c.2524C>T 
 p.Gln842Ter 
 De novo 
  
 Simplex 
 GEN1261R006 
 frameshift_variant 
 c.2923_2924insCT 
 p.Leu975ProfsTer7 
 De novo 
  
  
 GEN1261R007 
 frameshift_variant 
 c.1006del 
 p.Met336TrpfsTer2 
 Familial 
 Paternal 
 Simplex 
 GEN1261R008 
 stop_gained 
 c.1942C>T 
 p.Gln648Ter 
 Familial 
 Paternal 
 Extended multiplex 
 GEN1261R009 
 stop_gained 
 c.3697C>T 
 p.Gln1233Ter 
 Familial 
 Paternal 
 Multiplex 
 GEN1261R010 
 stop_gained 
 c.4033C>T 
 p.Arg1345Ter 
 Unknown 
  
 Simplex 
 GEN1261R011 
 stop_gained 
 c.2395C>T 
 p.Arg799Ter 
 Unknown 
 Not maternal 
 Multiplex 
 GEN1261R012 
 frameshift_variant 
 c.212del 
 p.Lys71ArgfsTer25 
 Familial 
 Maternal 
 Multiplex 
 GEN1261R013 
 stop_gained 
 c.4627C>T 
 p.Arg1543Ter 
 Familial 
  
 Simplex 
 GEN1261R014 
 splice_site_variant 
 c.2850+2T>A 
  
 De novo 
  
 Simplex 
 GEN1261R015 
 frameshift_variant 
 c.4951del 
 p.Ala1651GlnfsTer24 
 De novo 
  
 Simplex 
 GEN1261R016 
 splice_site_variant 
 c.917-1G>T 
  
 Familial 
 Maternal 
  
 GEN1261R017 
 missense_variant 
 c.3539T>G 
 p.Ile1180Arg 
 De novo 
  
 Simplex 
 GEN1261R018 
 frameshift_variant 
 c.2923_2924del 
 p.Cys976ProfsTer41 
 De novo 
  
 Simplex 
 GEN1261R019 
 synonymous_variant 
 c.3903C>T 
 p.Thr1301%3D 
 De novo 
  
  
 GEN1261R020 
 synonymous_variant 
 c.747G>A 
 p.Leu249%3D 
 De novo 
  
  
 GEN1261R021 
 synonymous_variant 
 c.945C>T 
 p.Asp315%3D 
 De novo 
  
 Multiplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
8
Duplication
 1
 
8
Duplication
 1
 
8
Deletion
 2
 
8
Deletion
 2
 
8
Deletion
 1
 
8
Duplication
 1
 
8
Deletion-Duplication
 10
 

No Animal Model Data Available

No PIN Data Available
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