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Relevance to Autism

Bereshneh et al., 2026 identified five unrelated individuals carrying de novo heterozygous variants (three missense variants, a frameshift variant, and a nonsense variant) in the RAPGEF2 gene presenting with a neurodevelopmental disorder characterized by developmental delay, intellectual disability, behavioral abnormalities (including autism in two individuals), seizures, and dysmorphic features; functional assessment of the three missense variants and the nonsense variant in PDZ-GEF mutant Drosophila found that, while wild-type RAPGEF2 was able to rescue phenotypes associated with loss of PDZ (lethality, severe locomotion defects, aberrant microtubular stability in motor neurons axons, and synaptic overgrowth at neuromuscular junctions in third instar larvae), mutant RAPGEF2 with these variants failed to do so, indicating a loss-of-function effect. De novo missense variants in the RAPGEF2 gene have been previously reported in ASD probands from the Autism Sequencing Consortium, the MSSNG cohort, and the SPARK cohort (De Rubeis et al., 2014; Yuen et al., 2017; Zhou et al., 2022).

Molecular Function

Members of the RAS subfamily of GTPases function in signal transduction as GTP/GDP-regulated switches that cycle between inactive GDP- and active GTP-bound states. Guanine nucleotide exchange factors (GEFs), such as RAPGEF2, serve as RAS activators by promoting acquisition of GTP to maintain the active GTP-bound state and are the key link between cell surface receptors and RAS activation.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Rare heterozygous de novo variants in RAPGEF2 are associated with a neurodevelopmental disorder
DD, ID
ASD, ADHD, epilepsy/seizures
Support
Integrating de novo and inherited variants in 42
ASD
Support
DSCAM regulates delamination of neurons in the developing midbrain
Support
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
ASD
Support
Synaptic, transcriptional and chromatin genes disrupted in autism.
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1534R001 
 stop_gained 
 c.3634C>T 
 p.Arg1212Ter 
 De novo 
  
  
 GEN1534R002 
 missense_variant 
 c.433C>G 
 p.Arg145Gly 
 De novo 
  
  
 GEN1534R003 
 missense_variant 
 c.454_455delinsAG 
 p.Val152Arg 
 De novo 
  
  
 GEN1534R004 
 missense_variant 
 c.758T>C 
 p.Met253Thr 
 De novo 
  
  
 GEN1534R005 
 frameshift_variant 
 c.1769dup 
 p.Leu590PhefsTer15 
 De novo 
  
 Simplex 
 GEN1534R006 
 missense_variant 
 c.3154C>G 
 p.Leu1052Val 
 De novo 
  
  
 GEN1534R007 
 missense_variant 
 c.3305C>G 
 p.Ala1102Gly 
 De novo 
  
 Multiplex 
 GEN1534R008 
 missense_variant 
 c.3332G>T 
 p.Gly1111Val 
 De novo 
  
 Simplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
4
Duplication
 1
 
4
Duplication
 1
 
4
Duplication
 1
 
4
Duplication
 1
 
4
Duplication
 1
 
4
Duplication
 3
 
4
Deletion
 1
 
4
Deletion-Duplication
 17
 
4
Duplication
 1
 
4
Deletion
 1
 

No Animal Model Data Available

No PIN Data Available
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