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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.

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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
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
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

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
 

M_VCP_1_KI_HM_LEUCINE

Rescue Type: RESCUE-Dietary
Rescue Paradigm: Mice were provided with leucine-supplemented water (1.8%) for 7 days prior to testing and then continuously for the duration of the entire behavioral task. Leucine solutions were replaced daily throughout the entire assay period. Leucine uptake was estimated to be 1.8g leucine/100 mL x 5 mL water/25 g body weight = 3.6 mg/g mouse body weight/day.

M_VCP_1_KI_HM_LEUCINE

Category
Entity
Effect on phenotype Qualification
Restored Treatment improves measured phenotype significantly
Refractory Treatment does not improve measured phenotype (was expected to do so)
Ameliorated Treatment provides partial correction or improvement of measured phenotype
No adverse effect Treatment does not affect the parameter adversely
Sustained effect Treatment has long term effect of restoration or amelioration, tested AFTER stopping administration (not applied for continuing long-term treatment) . Will be applied only where treatment has had restorative effects during administration or in the first battery of tests conducted.
No sustained effect Treatment has no long term of restoration or amelioration detectable, after stopping administration. Will be applied only where treatment has had restorative effects during administration or in the first battery of tests conducted.
Unexpected results Treats an unexpected phenotype
Side effect Exaggerates an unexpected phenotype
Experimental Paradigm
Age at Testing
General locomotor activity1
Side effect
Description: Vcp mutant mice fed 19% protein chow and treated with leucine exhibited a slight decrease in total distance traveled compared to untreated mutant mice.
 Open field test
 8 weeks
Dendritic architecture: spine density1
Restored
Description: Vcp mutant mice fed 19% protein chow and treated with leucine exhibited increased dendritic spine density to a level comparable to wildtype controls.
 Fluorescence microscopy
 9 weeks
Social interaction1
Restored
Description: Vcp mutant mice fed 19% protein chow and treated with leucine exhibited an increase in time spent interacting with stranger mice, to a level comparable to that of wildtype controls.
 Reciprocal social interaction test
 9 weeks
 Not Reported:

M_VCP_1_KI_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
 Grip strength1
 Decreased
Description: Vcp mutant mice fed 19% protein chow exhibited decreased muscle strength at 18 months compared to wildtype controls.
Exp Paradigm: Force gauge
 Grip strength test
 18 months
 Dendritic architecture: spine density1
 Decreased
Description: Vcp mutant mice fed 19% protein chow exhibited a significant decrease in dendritic spine density compared to wildtype controls.
 Fluorescence microscopy
 9 weeks
 Social interaction1
 Decreased
Description: Vcp mutant mice fed 19% protein chow spent less time interacting with stranger mice compared to wildtype controls.
 Reciprocal social interaction test
 10 weeks
 Social approach1
 Decreased
Description: Vcp mutant mice fed 19% protein chow spent significantly less time interacting with stranger 1, as demonstrated by the preference index, compared to wildtype controls.
Exp Paradigm: stranger mouse in chamber 1 (s1), object in chamber 2
 Three-chamber social approach test
 9-10 weeks
 Ultrasonic vocalization1
 Decreased
Description: Vcp mutant mice fed 19% protein chow exhibited reduced ultrasonic vocalization production compared to wildtype mice, though only the results at P8 were statistically significant.
 Monitoring ultrasonic vocalizations
 P4, P6, P8, P10
 Size/growth1
 Decreased
Description: Vcp mutant mice fed 19% protein chow exhibited decreased body weight at 18 months compared to wildtype controls.
 Body weight measurement
 18 months
Size/growth1
 No change
 Body weight measurement
 12 months
Size/growth1
 No change
 Body weight measurement
 12 weeks
Size/growth1
 No change
 Body weight measurement
 9 weeks
Skeletal development1
 No change
 Skeletal X-rays
 24 weeks
Anxiety1
 No change
 Open field test
 8 weeks
Anxiety1
 No change
 Elevated plus maze test
 8 weeks
Anxiety1
 No change
 Light-dark exploration test
 8 weeks
Spatial working memory1
 No change
 Y-maze test
 8 weeks
General locomotor activity1
 No change
 Open field test
 8 weeks
Grip strength1
 No change
 Grip strength test
 12 months
Grip strength1
 No change
 Grip strength test
 12 weeks
Grip strength1
 No change
 Grip strength test
 9 weeks
Motor coordination and balance1
 No change
 Accelerating rotarod test
 10-12 weeks
Rearing behavior1
 No change
 Open field test
 8 weeks
Brain morphology1
 No change
 General observations
 24 months
Self grooming1
 No change
 Open field test
 8 weeks
Social memory1
 No change
 Three-chamber social approach test
 9-10 weeks
 Not Reported:

 

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