• 3
    Haplo
    Score
  • 0
    Triplo
    Score

Gene Facts External Data Attribution

HGNC Symbol
CHD2 (HGNC:1917) HGNC Entrez Ensembl OMIM UCSC Uniprot GeneReviews LOVD LSDB ClinVar
HGNC Name
chromodomain helicase DNA binding protein 2
Gene type
protein-coding gene
Locus type
gene with protein product
Previous symbols
No previous names found
Alias symbols
FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200
%HI
20.62(Read more about the DECIPHER Haploinsufficiency Index)
pLI
1(Read more about gnomAD pLI score)
LOEUF
0.07(Read more about gnomAD LOEUF score)
Cytoband
15q26.1
Genomic Coordinates
GRCh37/hg19: chr15:93443554-93571226 NCBI Ensembl UCSC
GRCh38/hg38: chr15:92900324-93027996 NCBI Ensembl UCSC
MANE Select Transcript
NM_001271.4 ENST00000394196.9 (Read more about MANE Select)
Function
DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. Involved in myogenesis via interaction with MYOD1: binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression (By similarity). {ECO:0000250}. (Source: Uniprot)

Dosage Sensitivity Summary (Gene)

Dosage ID:
ISCA-29570
Curation Status:
Complete
Issue Type:
Dosage Curation - Gene
Haploinsufficiency:
Sufficient Evidence for Haploinsufficiency (3)
Triplosensitivity:
No Evidence for Triplosensitivity (0)
Last Evaluated:
10/23/2019

Haploinsufficiency (HI) Score Details

HI Score:
3
HI Evidence Strength:
Sufficient Evidence for Haploinsufficiency (Disclaimer)
HI Disease:
  • developmental and epileptic encephalopathy 94 Monarch
HI Evidence:
  • PUBMED: 23708187
    Carvill et al. 2013: Describes six de novo mutations in CHD2, including one nonsense and 3 frameshift mutations, found in unrelated individuals with various epilepsy phenotypes and intellectual disability, ranging from moderate to severe. Two individuals were also described as having autism spectrum disorders (one with a frameshift mutation, one with a missense). The authors concluded that there was no apparent genotype-phenotype correlations between type of mutation, seizure type, or level of neurocognitive impairment.
  • PUBMED: 23020937
    Rauch et al. 2012: Describes a single, de novo, heterozygous frameshift mutation found in a German female with intellectual disability and absence seizures. The authors did not see any additional loss of function variants in CHD2 in "roughly 1600 control exomes, [in] a post-hoc test in the 6500 exomes from the Exome Variant Server (version 0.0.14), [or] in 179 low coverage genomes of the 1000 Genomes project."
  • PUBMED: 24207121
    Suls et al. (2013) identified three de novo heterozygous variants in CHD2. 1) c.4971G-A (p.W1657X) variant in CHD2 was found in a patient with childhood-onset epileptic encephalopathy (EEOC; 615369). The variant was found by WES and confirmed by Sanger sequencing. The variant was not present in general population databases. The patient had normal development until the onset of febrile seizures at age 2 years. She had mild to moderate intellectual disability at age 24 years. 2) c.1810-2A-C variant in CHD2 was found in a patient with childhood-onset epileptic encephalopathy (EEOC; 615369). Studies of patient cells showed that the mutant transcript was not subject to nonsense-mediated mRNA decay, but resulted in complex alternative splicing events. The patient showed normal development until the onset of febrile seizures at age 14 months. At age 6 years, he had mild to moderate intellectual disability, dysarthria, and ataxia. 3) c.1396C-T, p. R466X variant in CHD2 was found in a patient with childhood-onset epileptic encephalopathy (EEOC; 615369) by sequencing the CHD2 gene in a cohort of 150 patients with epileptic encephalopathy. The patient had slightly delayed psychomotor development before the onset of febrile seizures at age 3.5 years. He later developed multiple seizure types and had mild intellectual disability, autism spectrum disorder, attention deficit-hyperactivity disorder, and mild ataxia. Brain MRI showed atrophic changes.
HI Evidence Comments:
PubMed: 29740950 Petersen et al. (2018) identified a heterozygous variant c.628G-T, p. E210X in CHD2 in a 5 yro proband with childhood-onset epileptic encephalopathy (EEOC; 615369) and her mildly affected mother. The daughter had global developmental delay, first noted at age 12 months, and onset of medically refractory generalized epilepsy at age 13 months. Her mother had generalized tonic-clonic epilepsy with seizure onset at age 5 years, which was well-controlled with medications, and completed high school in mainstream classes without difficulty. PMID:22178256: Capelli et al. (2012) describe a patient with DD, epilepsy, autistic behavior, and dysmorphic facial features with a de novo 511 kb deletion involving only 2 genes (CHD2 and RGMA). This patient data has been submitted to DECIPHER (249888). Of note, Carvill et al. (mentioned in PMID1 above) also mention a previously unreported individual (in Supplementary Figure 3) with photosensitive generalized early-onset epilepsy and ID and a deletion involving only CHD2 and an uncharacterized non-coding RNA (LOC100507217).

Triplosensitivity (TS) Score Details

TS Score:
0
TS Evidence Strength:
No Evidence for Triplosensitivity (Disclaimer)
TS Evidence Comments:
ISCA Database: nssv580871: de novo duplication involving only this gene (hg18: chr15:91245028-91356680) in a patient with multiple congenital anomalies. The laboratory classified this imbalance as uncertain. Further studies of this case would be needed to determine whether an additional copy of the protein is present or whether the duplication disrupts this gene.

Genomic View

Select assembly: (NC_000015.9) (NC_000015.10)