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Relevance to Autism

Mah-som et al., 2023 identified 13 unrelated individuals harboring heterozygous variants in the VCP gene associated with a childhood-onset order characterized by developmental delay, intellectual disability, hypotonia, and macrocephaly; three of the individuals in this study were formally diagnosed with autism (one of whom was enrolled in the SPARK study), while several additional individuals presented with autistic features and/or motor stereotypy. Furthermore, all disease-associated VCP missense and in-frame deletion variants reported in Mah-som et al., 2023 were experimentally shown to cause either a statistically significant increase or decrease in ATPase function compared to wild-type VCP, consistent with a gain-of-function or loss-of-function effect, respectively. A de novo loss-of-function variant and additional de novo missense variants in the VCP gene had previously been reported in ASD probands from the Simons Simplex Collection, the SPARK cohort, and the Autism Simplex Collection (O'Roak et al., 2014; Trost et al., 2022). Huang et al., 2020 observed that knock-in mice with a p.Arg95Gly mutation, which was originally identiifed in patients with IBMPFD and had been found to reduce the protein synthesis efficiency of neurons, displayed social deficits and reduced vocal communications.

Molecular Function

This gene encodes a member of the AAA ATPase family of proteins. The encoded protein plays a role in protein degradation, intracellular membrane fusion, DNA repair and replication, regulation of the cell cycle, and activation of the NF-kappa B pathway. This protein forms a homohexameric complex that interacts with a variety of cofactors and extracts ubiquitinated proteins from lipid membranes or protein complexes. Mutations in this gene cause IBMPFD (inclusion body myopathy with paget disease of bone and frontotemporal dementia), ALS (amyotrophic lateral sclerosis) and Charcot-Marie-Tooth disease in human patients.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
An autosomal-dominant childhood-onset disorder associated with pathogenic variants in VCP
DD, ID
ASD or autistic features, ADHD, epilepsy/seizures,
Support
VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy
Support
Recurrent de novo mutations implicate novel genes underlying simplex autism risk.
ASD
Support
Shared and divergent alteration of whole-brain connectivity and sensory deficits in multiple autism mouse models
ASD
Support
Burden re-analysis of neurodevelopmental disorder cohorts for prioritization of candidate genes
ASD, ID
Support
Genomic architecture of autism from comprehensive whole-genome sequence annotation
ASD
Support
Social behaviors and contextual memory of Vcp mutant mice are sensitive to nutrition and can be ameliorated by amino acid supplementation
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1418R001 
 frameshift_variant 
 c.265del 
 p.Arg89GlyfsTer8 
 De novo 
  
  
 GEN1418R002 
 missense_variant 
 c.685C>T 
 p.Leu229Phe 
 De novo 
  
 Multiplex 
 GEN1418R003 
 splice_site_variant 
 c.709-2A>G 
  
 De novo 
  
  
 GEN1418R004 
 missense_variant 
 c.753G>T 
 p.Lys251Asn 
 De novo 
  
 Simplex 
 GEN1418R005 
 missense_variant 
 c.766C>G 
 p.Arg256Gly 
 De novo 
  
  
 GEN1418R006 
 inframe_deletion 
 c.801_803del 
 p.Phe267del 
 De novo 
  
 Simplex 
 GEN1418R007 
 missense_variant 
 c.812G>A 
 p.Gly271Asp 
 De novo 
  
 Simplex 
 GEN1418R008 
 inframe_deletion 
 c.901_903del 
 p.Ile301del 
 De novo 
  
 Simplex 
 GEN1418R009 
 missense_variant 
 c.1084C>T 
 p.Arg362Cys 
 De novo 
  
  
 GEN1418R010 
 missense_variant 
 c.1622C>A 
 p.Ser541Tyr 
 De novo 
  
 Simplex 
 GEN1418R011 
 missense_variant 
 c.1874G>C 
 p.Arg625Pro 
 De novo 
  
  
 GEN1418R012 
 missense_variant 
 c.2257C>T 
 p.Arg753Trp 
 Familial 
 Paternal 
  
 GEN1418R013 
 missense_variant 
 c.892C>T 
 p.Pro298Ser 
 De novo 
  
 Simplex 
 GEN1418R014 
 frameshift_variant 
 c.1545_1549del 
 p.Phe516TrpfsTer16 
 De novo 
  
 Simplex 
 GEN1418R015 
 missense_variant 
 c.1153A>C 
 p.Thr385Pro 
 De novo 
  
 Simplex 
 GEN1418R016 
 missense_variant 
 c.250A>G 
 p.Met84Val 
 De novo 
  
  
 GEN1418R017 
 inframe_deletion 
 c.801_803del 
 p.Phe267del 
 De novo 
  
 Simplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
9
Deletion-Duplication
 12
 
9
Deletion
 2
 
9
Duplication
 1
 
9
Duplication
 2
 
9
N/A
 1
 
9
Duplication
 8
 
9
Duplication
 3
 
9
Duplication
 1