CHD9

protein-coding

chromodomain helicase DNA binding protein 9

Gene summary

Predicted to enable ATP binding activity; ATP hydrolysis activity; and DNA binding activity. Predicted to be involved in DNA-templated transcription. Predicted to act upstream of or within chromatin organization. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001308319.2

Inheritance

—

ClinVar variants

U:359B:11

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr16:53,054,991-53,329,150

External References & Databases

Ensembl (ENSG00000177200)

Transcript & Mutation Effects

hg38 • Region Span ~274.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CHD9 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 329

not providedTotal: 16

Neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001308319.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	5 clinvar		10
missense			340 clinvar	5 clinvar	1 clinvar	346
nonsense			4 clinvar			4
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	359	10	1	370

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 69 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001308319.2	RefSeq	NP_001295248.1	38	MANE Select
ENST00000447540.6	Ensembl	ENSP00000396345.2	38	MANE Select
NM_001352127.3	RefSeq	NP_001339056.1	38	Standard
NM_001352156.3	RefSeq	NP_001339085.1	38	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
Metabolism of lipids
Metabolism

Biological Process

chromatin organization
regulation of lipid metabolic process

Molecular Function

DNA binding
helicase activity
ATP binding

Cellular Component

nucleoplasm
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000566029
Coding exons: 38
Length: 274118
Individuals with no LoFs: 124630
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 124653
p: 0.0000923

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.77	1050	1.45e+3	0.722	0.0000742	18846
Missense (PolyPhen)		318	556.05	0.57189		7315
Synonymous	0.353	488	498	0.980	0.0000251	5455
Loss of Function	9.62	15	136	0.110	0.00000769	1710

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00015	0.00014	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. Proposed to be a ATP-dependent chromatin remodeling protein. Has DNA-dependent ATPase activity and binds to A/T-rich DNA. Associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis (By similarity). {ECO:0000250, ECO:0000269|PubMed:16095617, ECO:0000269|PubMed:16554032}.;

Recessive Scores

pRec: 0.149

Intolerance Scores

LoFtool: 0.0877
RVIS EVS: -2.18
RVIS percentile EVS: 1.4

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.510

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium