BRD3

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

Basic information

Region (hg38): 9:134030305-134068535

Links

ENSG00000169925 ∙ NCBI:8019 ∙ OMIM:601541 ∙ HGNC:1104 ∙ Uniprot:Q15059 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BRD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRD3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			40	4		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	40	4	2

Variants in BRD3

This is a list of pathogenic ClinVar variants found in the BRD3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-134034697-G-GT			Benign (Sep 11, 2018)
9-134036143-A-C		not specified	Uncertain significance (Dec 18, 2023)
9-134036148-C-T		not specified	Uncertain significance (Sep 11, 2024)
9-134036203-C-T		not specified	Uncertain significance (Apr 08, 2023)
9-134036286-T-C		not specified	Uncertain significance (Aug 17, 2022)
9-134040044-T-C		not specified	Likely benign (Dec 21, 2022)
9-134040118-T-G		not specified	Uncertain significance (Apr 07, 2022)
9-134040119-T-C		not specified	Uncertain significance (Apr 07, 2022)
9-134040250-T-C		not specified	Uncertain significance (May 07, 2024)
9-134041858-C-T		not specified	Likely benign (Sep 26, 2024)
9-134041878-G-A		not specified	Uncertain significance (Dec 28, 2022)
9-134041881-G-A		not specified	Uncertain significance (Dec 10, 2024)
9-134041897-C-G		not specified	Uncertain significance (Jun 10, 2024)
9-134041899-G-A		not specified	Uncertain significance (Jan 19, 2025)
9-134041903-C-A		not specified	Uncertain significance (Jun 16, 2023)
9-134041935-C-T		not specified	Uncertain significance (May 08, 2023)
9-134041957-G-A			Likely benign (Feb 01, 2024)
9-134045303-C-T		not specified	Uncertain significance (Jun 26, 2024)
9-134045359-C-T		Premature ovarian failure	Uncertain significance (Mar 02, 2020)
9-134048121-C-T		not specified	Uncertain significance (Jun 24, 2022)
9-134048249-T-C		not specified	Uncertain significance (Feb 13, 2024)
9-134048265-C-T		not specified	Uncertain significance (May 11, 2022)
9-134048266-G-A			Benign (Sep 11, 2018)
9-134048313-T-C		not specified	Uncertain significance (Jul 21, 2021)
9-134048349-T-G		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRD3	protein_coding	protein_coding	ENST00000303407	11	38231

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.975	0.0253	125707	0	10	125717	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.64	302	461	0.655	0.0000301	4718
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.000118	0.0000924
European (Non-Finnish)	0.0000362	0.0000352
Middle Eastern	0.000110	0.000109
South Asian	0.0000658	0.0000653
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Chemical Compounds to monitor Proteins (Consensus)

Recessive Scores

• pRec: 0.181

Intolerance Scores

• loftool: 0.226
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.78

Haploinsufficiency Scores

• pHI: 0.481
• hipred: Y
• hipred_score: 0.728
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.792

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brd3

Zebrafish Information Network

• Gene name: brd3a
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: chromatin organization;regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: chromatin binding;protein binding;lysine-acetylated histone binding