BRPF3

protein-coding

bromodomain and PHD finger containing 3, the group of Bromodomain containing|PHD finger proteins|PWWP domain containing

Gene summary

Contributes to histone acetyltransferase activity. Involved in positive regulation of DNA replication. Located in nucleus. Part of MOZ/MORF histone acetyltransferase complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015695.3

Inheritance

—

ClinVar variants

U:169B:2

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr6:36,196,744-36,232,790

External References & Databases

Ensembl (ENSG00000096070)

Transcript & Mutation Effects

hg38 • Region Span ~36.0 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 BRPF3 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 159

not providedTotal: 4

AutismTotal: 1

ColitisTotal: 1

Cranial asymmetryTotal: 1

Delayed speech and language developmentTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015695.3. 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			1 clinvar			1
missense			163 clinvar	2 clinvar		165
nonsense			1 clinvar			1
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	169	2	0	171

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015695.3	RefSeq	NP_056510.2	12	MANE Select
ENST00000357641.10	Ensembl	ENSP00000350267.6	12	MANE Select
ENST00000339717.11	Ensembl	ENSP00000345419.7	10	Standard
ENST00000339717.12	Ensembl	ENSP00000345419.7	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in leukocytes - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase
Gene expression (Transcription)

Biological Process

platelet degranulation
histone H3 acetylation

Molecular Function

protein binding
metal ion binding

Cellular Component

extracellular region
cytosol
MOZ/MORF histone acetyltransferase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357641
Coding exons: 12
Length: 36047
Individuals with no LoFs: 125742
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125748
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.91	516	738	0.699	0.0000467	7867
Missense (PolyPhen)		177	341.35	0.51853		3559
Synonymous	1.65	254	290	0.877	0.0000164	2446
Loss of Function	5.72	3	43.9	0.0684	0.00000213	545

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000089	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. {ECO:0000269|PubMed:16387653}.;

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.177
RVIS EVS: -1.06
RVIS percentile EVS: 7.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.975

Gene Damage Prediction

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