BRD9

protein-coding

bromodomain containing 9, the group of Bromodomain containing|BAF complex|GBAF complex

Gene summary

Enables histone reader activity. Involved in double-strand break repair via homologous recombination. Located in nucleoplasm. Part of SWI/SNF complex. Is active in site of double-strand break. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_023924.5

Inheritance

—

ClinVar variants

U:100B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr5:850,291-892,801

External References & Databases

Ensembl (ENSG00000028310)

Transcript & Mutation Effects

hg38 • Region Span ~42.5 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 BRD9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 96

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_023924.5. 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			2 clinvar	5 clinvar	1 clinvar	8
missense			91 clinvar	3 clinvar		94
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	100	8	1	109

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 65 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_023924.5	RefSeq	NP_076413.3	16	MANE Select
ENST00000467963.6	Ensembl	ENSP00000419765.1	16	MANE Select
NM_001009877.3	RefSeq	NP_001009877.2	15	Standard
NM_001317951.2	RefSeq	NP_001304880.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

chromatin organization
biological_process

Molecular Function

nucleic acid binding
protein binding
lysine-acetylated histone binding

Cellular Component

SWI/SNF complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000467963
Coding exons: 16
Length: 42534
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125748
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.26	285	352	0.810	0.0000217	3930
Missense (PolyPhen)		70	114.73	0.61014		1362
Synonymous	-0.448	157	150	1.05	0.0000109	1093
Loss of Function	3.57	9	30.1	0.299	0.00000160	380

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in chromatin remodeling and regulation of transcription (PubMed:22464331, PubMed:26365797). Acts as a chromatin reader that recognizes and binds acylated histones: binds histones that are acetylated and/or butyrylated (PubMed:26365797). Component of SWI/SNF chromatin remodeling subcomplex GBAF that carries out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner (PubMed:29374058). {ECO:0000269|PubMed:22464331, ECO:0000269|PubMed:26365797, ECO:0000269|PubMed:29374058}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.329
RVIS EVS: -0.8
RVIS percentile EVS: 12.49

Essentials

Essential (CRISPR): E
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.828

Gene Damage Prediction

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