CHD2

Chr 15AD

chromodomain helicase DNA binding protein 2

Also known as: DEE94, EEOC

NCBI Gene: 1106ENSG00000173575UniProt: O14647OMIM: 602119

The CHD family of proteins is characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. CHD genes alter gene expression possibly by modification of chromatin structure thus altering access of the transcriptional apparatus to its chromosomal DNA template. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Developmental and epileptic encephalopathy 94MIM #615369
AD

Clinical highlights

Gene-disease validity (ClinGen)
complex neurodevelopmental disorder · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
48
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.07
LOEUF· LoF intol.
LOF
Mechanism· G2P
📖
GeneReview available — CHD2
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?
0.07LOEUF
pLI 1.000
Z-score 9.50
OE 0.03 (0.01–0.07)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
5.21Z-score
OE missense 0.53 (0.49–0.57)
523 obs / 982.0 exp
Constrained

Extremely missense-constrained (top ~0.01%)

Observed / Expected Ratios?
LoF OE?0.03 (0.01–0.07)
0≤0.351.4
Missense OE?0.53 (0.49–0.57)
0≤0.61.4
Synonymous OE?0.95
0≤1.21.6
LoF obs/exp: 3 / 111.0Missense obs/exp: 523 / 982.0Syn Z: 0.71

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

CHD2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients