Alternative titles; symbols
HGNC Approved Gene Symbol: CHD8
Cytogenetic location: 14q11.2 Genomic coordinates (GRCh38) : 14:21,385,199-21,456,123 (from NCBI)
Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
---|---|---|---|---|
14q11.2 | Intellectual developmental disorder with autism and macrocephaly | 615032 | Autosomal dominant | 3 |
CHD8 is an ATP-dependent chromatin-remodeling factor that regulates transcription of beta-catenin (CTNNB1; 116806) target genes (Thompson et al., 2008).
By sequencing clones from a size-fractionated fetal brain cDNA library, Nagase et al. (2000) cloned CHD8, which they designated KIAA1564. The deduced protein contains 1,417 amino acids. RT-PCR ELISA detected moderate expression in all adult and fetal tissues and specific brain regions examined.
Sakamoto et al. (2000) cloned rat Chd8, which they called Duplin. The deduced 749-amino acid protein was expressed mainly in the nuclear fraction of transfected COS cells.
Ishihara et al. (2006) cloned mouse Chd8. The deduced 2,582-amino acid protein has 2 chromodomains, followed by a central helicase/ATPase domain and 2 C-terminal BRK domains. Northern blot analysis detected ubiquitous Chd8 expression in mouse tissues, with highest levels in heart and testis. Western blot analysis of HeLa cells detected endogenous CHD8 at an apparent molecular mass of 240 kD.
Nishiyama et al. (2004) determined that the mouse Chd8 gene contains 9 exons and spans about 13 kb.
By transient transfection assays in HEK293 cells, Kunkel et al. (2020) showed that human CHD8 was transcribed from 2 far upstream promoters. RNA polymerase II (see 180660) occupancy levels on each of the promoters were similar in HEK293 cells. RACE analysis showed that both promoters drove CHD8 transcription from a dispersed set of transcriptional start sites.
Gross (2021) mapped the CHD8 gene to chromosome 14q11.2 based on an alignment of the CHD8 sequence (GenBank AB046784) with the genomic sequence (GRCh38).
Nishiyama et al. (2004) mapped the mouse Duplin gene to chromosome 14.
Sakamoto et al. (2000) found that rat Duplin bound directly to the armadillo repeats of beta-catenin (see CTNNB1; 116806) in the nuclei of mammalian cells, thereby inhibiting binding of TCF4 (TCF7L2; 602228) to beta-catenin and beta-catenin-dependent activation of TCF4. Expression of Duplin in Xenopus embryos inhibited axis formation and beta catenin-dependent axis duplication, and it countered the ability of beta-catenin to rescue ventralizing phenotypes induced by ultraviolet irradiation. Sakamoto et al. (2000) concluded that Duplin is a nuclear protein that negatively regulates Wnt (see 164820) signaling by binding beta-catenin.
By yeast 2-hybrid analysis of a mouse brain cDNA library, followed by studies in COS cells, Kobayashi et al. (2002) found that importin-alpha (see KPNA2; 600685) bound a cluster of basic amino acids in rat Duplin. Interaction with importin-alpha caused Duplin to translocate to the nucleus, and nuclear localization of Duplin was essential for inhibition of Wnt-dependent activation of TCF4 in mammalian cells and ventralization in Xenopus embryos. Additional experiments in Xenopus embryos showed that Duplin also inhibited the Wnt signaling pathway downstream of beta-catenin target genes.
Using yeast 2-hybrid analysis and pull-down assays, Ishihara et al. (2006) found that the C-terminal region of mouse Chd8 interacted with the zinc finger domain of Ctcf (604167). Chromatin immunoprecipitation analysis of a human hepatoma cell line revealed that CHD8 was present at CTCF target sites, such as the differentially methylated region of H19 (103280), the locus control region of beta-globin (141900), and the promoter regions of the BRCA1 (113705) and MYC (190080) genes. Immunoprecipitation analysis demonstrated an endogenous complex of CHD8 and CTCF in HeLa cells. Knockdown of CHD8 in HeLa cells by RNA interference abolished the CTCF-dependent insulator activity of the H19 differentially methylated region, leading to reactivation of imprinted IGF2 (147470) from the maternal chromosome. Lack of CHD8 affected CpG methylation and histone acetylation around the CTCF-binding sites, which are adjacent to heterochromatin, of the BRCA1 and MYC genes. Ishihara et al. (2006) concluded that CTCF-CHD8 has a role in insulation and epigenetic regulation at active insulator sites.
Using purified recombinant human protein, Thompson et al. (2008) showed that CHD8 was a remodeling enzyme capable of altering nucleosomal structure in an ATP-dependent manner. Purification of CHD8 from HeLa cells revealed that CHD8 was part of a 900-kD complex that also included WDR5 (609012), which interacted directly with CHD8 in the complex. CHD8 interacted directly with beta-catenin and bound to the proximal promoter regions of beta-catenin target genes to regulate beta-catenin-mediated transcription.
Using a yeast 2-hybrid library screen, Batsukh et al. (2010) identified CHD8 as an interacting partner of CHD7 (608892), mutations in which cause the autosomal dominant malformation syndrome CHARGE (214800). In a direct yeast 2-hybrid system, the CHD7-CHD8 interaction was disrupted by CHD7 missense mutations found in CHARGE patients, including gly2108 to arg (608892.0011), whereas in coimmunoprecipitation studies disruption of the CHD7-CHD8 interaction by the mutations could not be observed. The authors hypothesized that CHD7 and CHD8 proteins interact directly and indirectly via additional linker proteins. Disruption of the direct CHD7-CHD8 interaction may change the conformation of a putative large CHD7-CHD8 complex and could be a disease mechanism in CHARGE syndrome.
Using RNA-sequencing and chromatin immunoprecipitation-sequencing analyses in CHD8-knockdown human neural progenitor cells (NPCs), Sugathan et al. (2014) found that CHD8 regulated many functionally distinct genes associated with autism spectrum disorder (ASD; 209850) and neurodevelopmental pathways. CHD8 also appeared to play a role in cancer formation through regulation of a distinct set of genes.
O'Roak et al. (2012) performed whole-exome sequencing for parent-child trios from the Simons Simplex collection of autism spectrum disorder patients, including 189 new trios and 20 that were previously reported (O'Roak et al., 2011). Some of the patients had significantly impaired intellectual development In addition, O'Roak et al. (2012) sequenced the exomes of 50 unaffected sibs corresponding to 31 of the new and 19 of the previously reported trios, for a total of 677 individual exomes from 209 families. In proband exomes, O'Roak et al. (2012) reported 2 de novo disruptive mutations in CHD8, which they described as a nonsense mutation and a frameshift indel, in patients with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032).
In a study of exonic de novo mutations in autism spectrum disorders, Neale et al. (2012) stated that they had identified 3 loss-of-function mutations in the CHD8 gene among 935 cases and no mutations in CHD8 among 870 controls.
Among 2,446 probands from the Simons Simplex Collection including patients with impaired intellectual development, O'Roak et al. (2012) identified 9 de novo mutations in the CHD8 gene, including 3 frameshift (e.g., 610528.0002), 4 nonsense (e.g., 610528.0001), an in-frame deletion (610528.0009), and a splice site mutation (610528.0003) in 9 children (2 females and 7 males).
In a 17-year-old boy with IDDAM, Merner et al. (2016) identified a de novo heterozygous 1-bp duplication in the CHD8 gene (610528.0010).
In 10 newly identified, unrelated patients with IDDAM, Douzgou et al. (2019) identified 10 different heterozygous mutations in the CHD8 gene, including 2 splicing, 6 nonsense, and 2 frameshift. Eight of the mutations were confirmed to be de novo; in the other 2 cases, parental inheritance was unknown. None of the mutations were present in the gnomAD database. Functional studies were not performed.
In 27 patients with IDDAM, 10 of whom had previously been reported, Ostrowski et al. (2019) identified heterozygous mutations in the CHD8 gene, including 2 missense and 24 null mutations. The null mutations were distributed throughout the gene. One mutation (R564X) was identified in 2 unrelated patients. Twenty-four mutations were determined to be de novo and 3 were maternally inherited. One of these mothers had mild intellectual disability. In this patient cohort, there was a male to female ratio of 21:6. Ostrowski et al. (2019) suggested that females might present with a milder, subclinical phenotype due to gender-specific effects on transcriptional regulation.
An et al. (2020) screened a cohort of 96 patients with autism spectrum disorder by next-generation sequencing of a gene panel including the CHD8 gene. Three patients were identified with de novo heterozygous mutations in CHD8 (R1188X, 610528.0011; c.4818-1G-A, 610528.0013; Y1168N, 610528.0014). An et al. (2020) identified an additional patient with autism spectrum disorder and a de novo heterozygous mutation (E689X; 610528.0012) in the CHD8 gene by trio whole-exome sequencing. Functional studies were not performed.
Associations Pending Confirmation
Lee et al. (2020) reported 14-year-old female monozygotic twins with a congenital myasthenic syndrome (see, e.g., 601462) with a de novo c.1732C-T transition (NM_001170629) in the CHD8 gene, resulting in an R578C substitution at a highly conserved residue in the glutamine-rich domain. The mutation was identified by whole-exome sequencing and confirmed by Sanger sequencing. The mutation was predicted to affect protein folding and interactions with CHD8 binding partners. The sibs' clinical features included myasthenia, muscle weakness, ptosis, macrocephaly, and overgrowth. They were assessed as having average school performance with slightly below average long-term retrieval and fluid reasoning skills.
Nishiyama et al. (2004) found that development of Duplin -/- mouse embryos was arrested at gastrulation, with the embryos manifesting massive apoptosis. In contrast, Duplin +/- mice appeared normal and were fertile. Expression of beta-catenin target genes was not increased in Duplin -/- embryos, suggesting that the lack of Duplin did not result in constitutive activation of Wnt signaling during embryogenesis.
Sugathan et al. (2014) found that knockdown of chd8 expression in zebrafish resulted in macrocephaly, likely caused by disturbed neuronal proliferation at early developmental stages.
Katayama et al. (2016) demonstrated that mice heterozygous for Chd8 mutations manifest ASD-like behavioral characteristics including increased anxiety, repetitive behavior, and altered social behavior. CHD8 haploinsufficiency did not result in prominent changes in the expression of a few specific genes but instead gave rise to small but global changes in gene expression in the mouse brain, reminiscent of those in the brains of patients with ASD. Gene set enrichment analysis revealed that neurodevelopment was delayed in the mutant mouse embryos. Furthermore, reduced expression of CHD8 was associated with abnormal activation of RE-1 silencing transcription factor (REST; 600571), which suppresses the transcription of many neuronal genes. REST activation was also observed in the brains of humans with ASD, and CHD8 was found to interact physically with REST in the mouse brain. Katayama et al. (2016) concluded that their results were consistent with the notion that CHD8 haploinsufficiency is a highly penetrant risk factor for ASD, with disease pathogenesis probably resulting from a delay in neurodevelopment.
Kawamura et al. (2021) found that mice with Chd8 deletion in brain were born approximately at the expected mendelian ratio, but that they subsequently showed growth retardation and cerebellar hypoplasia, and most died before 3 weeks of age. Analysis of mice with cerebellar granule neuron progenitor (GNP)-specific deletion of Chd8 showed that cerebellar hypoplasia resulted from a GNP-autonomous defect induced by Chd8 loss. Chd8 regulated proliferation and differentiation of GNPs, and cerebellar hypoplasia associated with Chd8 ablation resulted from attenuated proliferation and premature differentiation of Chd8-deficient GNPs. Chd8 was also required for pre- and postsynaptic integrity of CGNs, as electrophysiologic analysis revealed reduction in both pre- and postsynaptic function in mice with GNP-specific deletion of Chd8. Behavioral tests showed that GNP-specific Chd8-deficient mice manifested a motor behavioral defect, but not ASD-related behaviors. Chd8 was essential for activation of neuronal gene expression during GNP differentiation, and Chd8 deficiency attenuated proliferative capacity of progenitor cells by inhibiting expression of cell-cycle regulators at the transcriptional level. By conferring an accessible chromatin landscape and transactivating genes, CHD8 promoted GNP differentiation and contributed to GNP development.
In a 55-month-old non-Hispanic white male with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), O'Roak et al. (2012) identified a de novo heterozygous nonsense mutation in the CHD8 gene, a ser-to-ter substitution at codon 62 (S62X). The boy had a low verbal IQ of 75, nonverbal IQ of 78, and below average adaptive score of 80. His head circumference was 53 cm (z score = 1.0).
In a 67-month-old non-Hispanic white male with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), O'Roak et al. (2012) detected a heterozygous de novo 1-basepair insertion in the CHD8 gene that resulted in premature termination of the protein (tyr747 to ter; Y747X). The proband was nonverbal with extremely low verbal IQ of 25, nonverbal IQ of 38, and adaptive score of 57. His head circumference was 55 cm (z score = 2.0). He was diagnosed with cerebral palsy and was excessively clumsy and uncoordinated at 18 months. MRI/CT at 18 months was normal; EEG was normal at 24 months. The proband had a healthy 4-year-old sister.
In a 96-month-old non-Hispanic white female with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), O'Roak et al. (2012) detected a de novo heterozygous splice site mutation (3519-2A-G) in the helicase superfamily C-terminal (HELC) domain of the CHD8 gene. She had a verbal IQ of 47 and a nonverbal IQ of 41, with clinical range deficits in social responsiveness and adaptive skills. She had experienced a delay in phrased speech. Her head circumference was 55.2 (z score = 2.3). She had a history of antiepileptic and antibiotic medication use, but not of seizures. MRI and EEG at age 5 were normal. A 6-year-old sister was healthy with normal head circumference.
In an 8-year-old non-Hispanic white male with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), O'Roak et al. (2012) detected a heterozygous de novo nonsense mutation in the CHD8 gene, gln1238 to ter (Q1238X). In addition to the CHD8 mutation, the patient also carried a CUBN (602997) de novo nonsense mutation and 2 inherited copy number variations. The patient had an extremely low verbal IQ of 20, nonverbal IQ of 34, and low adaptive score of 59. He had macrocephaly (z score = 2.62) and normal BMI.
In a 63-month-old non-Hispanic white male with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), O'Roak et al. (2012) detected a heterozygous de novo substitution at codon 1337 of the CHD8 gene (arg1337 to ter, R1337X). The patient was 1 of 4 children born to the same parents and the third of 6 pregnancies (the mother's first and fourth pregnancies resulted in miscarriage within 13 weeks). Verbal IQ was low (79), nonverbal IQ average (92), and adaptive score low (58). His head circumference was 55.4 cm (z score = 2.5).
In a 12-year-old non-Hispanic white male with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), O'Roak et al. (2012) identified a de novo heterozygous frameshift mutation in the CHD8 gene (Glu2103ArgfsTer3). The patient had a verbal IQ of 60, nonverbal IQ of 67, and adaptive score of 73. He was diagnosed as excessively clumsy and uncoordinated at age 3. The patient showed clinical range deficits in social responsiveness and elevation in anxious/depressed mood, and had a mixed expressive-receptive language disorder and pragmatic language disorder. He had chronic diarrhea from age 5 to 8 years. He had an abnormal EEG and seizures at age 12 years concurrent with a head injury. His head circumference was 58 cm (z score = 2.7).
In a 55-month-old non-Hispanic white female with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), O'Roak et al. (2012) identified a heterozygous de novo frameshift mutation in the CHD8 gene, a 2-basepair deletion resulting in premature termination of the protein (Leu2120ProfsTer13). The patient also carried a de novo nonsense mutations in the ETFB gene (130410) and the IQGAP2 gene (605401). She had normative range verbal IQ of 90 and nonverbal IQ of 93, but low adaptive behavioral skills score of 59. She had a large head (z score = 2.40).
In a 16-year-old non-Hispanic white male with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), O'Roak et al. (2012) identified a heterozygous de novo 1-basepair insertion of a T nucleotide in the CHD8 gene, resulting in frameshift and premature termination of the protein (Asn2371LysfsTer2). The patient had an extremely low verbal IQ of 6, nonverbal IQ of 19, and adaptive score of 39. His head circumference was 60.8 cm (z score = 3.0). Loss of language skills during early development and attention problems were reported.
In a 13-year-old non-Hispanic white male with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), O'Roak et al. (2012) identified a heterozygous de novo in-frame deletion of 3 nucleotides in the CHD8 gene resulting in deletion of histidine-2498 (His2498del). The patient had a verbal IQ of 84, nonverbal IQ of 98, and very low adaptive score of 66. His head circumference was 57 cm (z score = 1.6).
In a 17-year-old boy with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), Merner et al. (2016) identified a heterozygous 1-bp duplication (c.6276dupA, NM_020920.3) in the CHD8 gene, predicted to result in a frameshift and premature termination (Asn2092LysfsTer2). The mutation, which was identified by sequencing of the CHD8 gene, occurred de novo. The mutation was not present in the dbSNP and ExAC databases. CHD8 mRNA and protein expression was reduced in patient lymphoblastoid cell lines compared to controls.
In a 16-year-old boy with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), An et al. (2020) identified a de novo heterozygous c.3562C-T transition (c.3562C-T, NM_001170629.1) in exon 17 of the CHD8 gene, resulting in an arg1188-to-ter (R1188X) substitution. The mutation, which was found by next-generation sequencing of a panel of genes and confirmed by Sanger sequencing, was not identified in either parent. Functional studies were not performed.
In a 6-year-old boy with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), An et al. (2020) identified a de novo heterozygous c.2065C-A transversion (c.2065C-A, NM_001170629.1) in exon 8 of the CHD8 gene, resulting in a glu689-to-ter (E689X) substitution. The mutation, which was identified by trio whole-exome sequencing and confirmed by Sanger sequencing, was not identified in the parents. Functional studies were not performed.
In an 11-year-old boy with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), An et al. (2020) identified a de novo heterozygous c.4818-1G-A transition (c.4818-1G-A, NM_0011700629.1) in intron 24 the CHD8 gene, predicted to result in a splicing abnormality and skipping of exon 25. The mutation, which was found by next-generation sequencing of a panel of genes and confirmed by Sanger sequencing, was not identified in either parent. Functional studies were not performed.
In a 12-year-old boy with intellectual developmental disorder with autism and macrocephaly (IDDAM; 615032), An et al. (2020) identified a de novo heterozygous c.3502T-A transversion (c.3502T-A, NM_001170629.1) in exon 16 of the CHD8 gene, resulting in a tyr1168-to-asn (Y1168N) substitution. The mutation, which was identified by next-generation sequencing of a panel of genes and confirmed by Sanger sequencing, was not identified in either parent. Functional studies were not performed.
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