BRD3

protein-coding

bromodomain containing 3, the group of Bromodomain and extra-terminal domain family|Bromodomain containing

Gene summary

This gene was identified based on its homology to the gene encoding the RING3 protein, a serine/threonine kinase. The gene localizes to 9q34, a region which contains several major histocompatibility complex (MHC) genes. The function of the encoded protein is not known. [provided by RefSeq, Jul 2008]

MANE transcript

NM_007371.4

Inheritance

—

ClinVar variants

U:78B:8

Top phenotype

Premature ovarian failure

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr9:134,030,305-134,068,535

External References & Databases

Ensembl (ENSG00000169925)

Transcript & Mutation Effects

hg38 • Region Span ~38.2 kb

Loading mutation effect viewer...

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 BRD3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 7

Premature ovarian failureTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007371.4. 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			4 clinvar		2 clinvar	6
missense			68 clinvar	6 clinvar		74
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	78	6	2	86

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007371.4	RefSeq	NP_031397.1	11	MANE Select
ENST00000303407.12	Ensembl	ENSP00000305918.6	11	MANE Select
ENST00000371834.6	Ensembl	ENSP00000360900.2	9	Standard
ENST00000371834.7	Ensembl	ENSP00000360900.2	9	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
brd3a	Danio rerio	Structure: thrombocyte Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

brd3a

Danio rerio

Structure: thrombocyte

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Chemical Compounds to monitor Proteins

Biological Process

chromatin organization
regulation of transcription by RNA polymerase II

Molecular Function

chromatin binding
protein binding
lysine-acetylated histone binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000303407
Coding exons: 11
Length: 38231
Individuals with no LoFs: 125707
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125717
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.64	302	461	0.655	0.0000301	4718
Missense (PolyPhen)		89	191.45	0.46487		2009
Synonymous	-1.16	227	206	1.10	0.0000161	1417
Loss of Function	4.30	4	28.9	0.138	0.00000132	381

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00012	0.000092	rare
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Chromatin reader that recognizes and binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling and interaction with transcription factors (PubMed:18406326, PubMed:27105114). Regulates transcription by promoting the binding of the transcription factor GATA1 to its targets (By similarity). {ECO:0000250|UniProtKB:Q8K2F0, ECO:0000269|PubMed:18406326, ECO:0000269|PubMed:27105114}.;
Disease: DISEASE: Note=A chromosomal aberration involving BRD3 is found in a rare, aggressive, and lethal carcinoma arising in midline organs of young people. Translocation t(15;9)(q14;q34) with NUT which produces a BRD3-NUT fusion protein. {ECO:0000269|PubMed:17934517}.;

Recessive Scores

pRec: 0.181

Intolerance Scores

LoFtool: 0.226
RVIS EVS: -0.71
RVIS percentile EVS: 14.78

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.792

Gene Damage Prediction

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