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Relevance to Autism

Karimi et al., 2025 performed DNA methylation analysis studies on a cohort of individuals with Sifrim-Hitz-Weiss syndrome and found a recognizable episignature in individuals with pathogenic CHD4 missense variants within the ATP helicase domain; conversely, individuals with truncating CHD4 variants exhibited a different episignature and phenotype with a higher rate of autism spectrum disorder (6/7 individuals with truncating variants vs. 1/20 with missense variants). De novo and inherited loss-of-function variants and damaging de novo missense variants in CHD4 have also been reported in ASD probands from the Simons Simplex Collection, the SPARK cohort, the Autism Sequencing Consortium, the Autism Simplex Collection, and the iHART cohort (Iossifov et al., 2014; Stessman et al., 2017; Ruzzo et al., 2019; Zhou et al., 2022; Fu et al., 2022). Larrigan et al., 2023 demonstrated that telecephalon-specific conditional knockout of Chd4 in mice resulted in increased repetitive behaviors, a phenotype that was more apparent in female animals.

Molecular Function

The product of this gene belongs to the SNF2/RAD54 helicase family. It represents the main component of the nucleosome remodeling and deacetylase complex and plays an important role in epigenetic transcriptional repression. Heterozygous mutations in the CHD4 gene are responsible for Sifrim-Hitz-Weiss syndrome (OMIM 617159), an autosomal dominant intellectual developmental disorder with variable congenital defects affecting other systems, including cardiac, skeletal, and urogenital.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Discovery of a DNA methylation profile in individuals with Sifrim-Hitz-Weiss syndrome
Sifrim-Hitz-Weiss syndrome, DD, ID
ASD, ADHD, epilepsy/seizures
Support
Integrating de novo and inherited variants in 42
ASD
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD
Support
Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.
ASD
Support
Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases.
ASD
DD, ID
Support
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Support
Divergent phenotypes in constitutive versus conditional mutant mouse models of Sifrim-Hitz-Weiss syndrome
Sifrim-Hitz-Weiss syndrome
Support
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1487R001 
 missense_variant 
 c.2975G>A 
 p.Arg992Gln 
 De novo 
  
  
 GEN1487R002 
 missense_variant 
 c.3280G>A 
 p.Glu1094Lys 
 De novo 
  
  
 GEN1487R003 
 missense_variant 
 c.3326T>C 
 p.Ile1109Thr 
 De novo 
  
  
 GEN1487R004 
 missense_variant 
 c.3338A>T 
 p.Asn1113Ile 
 Unknown 
  
  
 GEN1487R005 
 missense_variant 
 c.3380G>A 
 p.Arg1127Gln 
 De novo 
  
  
 GEN1487R006 
 missense_variant 
 c.3401A>G 
 p.Asn1134Ser 
 Unknown 
  
  
 GEN1487R007 
 missense_variant 
 c.2860A>G 
 p.Met954Val 
 De novo 
  
  
 GEN1487R008 
 missense_variant 
 c.2903C>T 
 p.Ser968Phe 
 Familial 
 Paternal 
  
 GEN1487R009 
 missense_variant 
 c.3653T>C 
 p.Ile1218Thr 
 De novo 
  
  
 GEN1487R010 
 missense_variant 
 c.3739A>G 
 p.Ile1247Val 
 De novo 
  
  
 GEN1487R011 
 missense_variant 
 c.1342C>T 
 p.His448Tyr 
 De novo 
  
  
 GEN1487R012 
 missense_variant 
 c.3938A>G 
 p.Tyr1313Cys 
 Unknown 
  
  
 GEN1487R013 
 missense_variant 
 c.4217G>A 
 p.Arg1406His 
 Unknown 
  
  
 GEN1487R014 
 missense_variant 
 c.4989G>C 
 p.Lys1663Asn 
 Familial 
 Maternal 
  
 GEN1487R015 
 missense_variant 
 c.5624T>C 
 p.Ile1875Thr 
 Familial 
 Paternal 
  
 GEN1487R016 
 stop_gained 
 c.214A>T 
 p.Lys72Ter 
 Unknown 
  
  
 GEN1487R017 
 stop_gained 
 c.895G>T 
 p.Gly299Ter 
 Familial 
 Maternal 
  
 GEN1487R018 
 frameshift_variant 
 c.1442del 
 p.Pro481GlnfsTer18 
 Familial 
 Paternal 
  
 GEN1487R019 
 stop_gained 
 c.1876C>T 
 p.Arg626Ter 
 Familial 
 Maternal 
  
 GEN1487R020 
 frameshift_variant 
 c.3234dup 
 p.Leu1079AlafsTer11 
 Unknown 
  
  
 GEN1487R021a 
 missense_variant 
 c.1486C>G 
 p.Pro496Ala 
 Familial 
 Paternal 
  
 GEN1487R021b 
 missense_variant 
 c.3862C>T 
 p.Arg1288Trp 
 Familial 
 Maternal 
  
 GEN1487R022 
 stop_gained 
 c.1671G>A 
 p.Trp557Ter 
 De novo 
  
  
 GEN1487R023 
 stop_gained 
 c.1714C>T 
 p.Arg572Ter 
 Familial 
 Maternal 
 Multiplex 
 GEN1487R024 
 missense_variant 
 c.2861T>C 
 p.Met954Thr 
 De novo 
  
  
 GEN1487R025 
 missense_variant 
 c.2975G>A 
 p.Arg992Gln 
 De novo 
  
  
 GEN1487R026 
 missense_variant 
 c.2986G>A 
 p.Ala996Thr 
 Familial 
 Maternal 
  
 GEN1487R027 
 missense_variant 
 c.3203G>A 
 p.Arg1068His 
 De novo 
  
  
 GEN1487R028 
 missense_variant 
 c.3203G>A 
 p.Arg1068His 
 De novo 
  
  
 GEN1487R029 
 missense_variant 
 c.3280G>A 
 p.Glu1094Lys 
 De novo 
  
  
 GEN1487R030 
 missense_variant 
 c.3283C>T 
 p.Arg1095Cys 
 De novo 
  
  
 GEN1487R031 
 missense_variant 
 c.3403C>G 
 p.Leu1135Val 
 De novo 
  
  
 GEN1487R032 
 missense_variant 
 c.3518G>A 
 p.Arg1173Gln 
 Familial 
 Paternal 
  
 GEN1487R033 
 missense_variant 
 c.2612T>C 
 p.Ile871Thr 
 De novo 
  
 Simplex 
 GEN1487R034 
 synonymous_variant 
 c.5172G>A 
 p.Lys1724= 
 De novo 
  
 Simplex 
 GEN1487R035 
 stop_gained 
 c.5179G>T 
 p.Glu1727Ter 
 De novo 
  
 Simplex 
 GEN1487R036 
 splice_site_variant 
 C>T 
 p.? 
 Familial 
 Paternal 
 Simplex 
 GEN1487R037 
 missense_variant 
 c.284G>A 
 p.Arg95His 
 Unknown 
  
  
 GEN1487R038 
 missense_variant 
 c.1810C>T 
 p.Arg604Cys 
 Unknown 
  
  
 GEN1487R039 
 stop_gained 
 c.131C>G 
 p.Ser44Ter 
 Familial 
 Maternal 
 Multiplex 
 GEN1487R040 
 splice_region_variant 
 c.100+4A>G 
 p.? 
 De novo 
  
 Simplex 
 GEN1487R041 
 missense_variant 
 c.3748G>A 
 p.Asp1250Asn 
 De novo 
  
 Simplex 
 GEN1487R042 
 synonymous_variant 
 c.4821C>G 
 p.Val1607= 
 De novo 
  
 Simplex 
 GEN1487R043 
 missense_variant 
 c.2642A>G 
 p.Asn881Ser 
 De novo 
  
  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
12
Deletion-Duplication
 27
 
12
Duplication
 5
 
12
Deletion
 1
 
12
Duplication
 2
 
12
Duplication
 1
 
12
Duplication
 4
 
12
Duplication
 1
 

No Animal Model Data Available

 

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