BRD2

bromodomain containing 2, the group of Bromodomain containing|Bromodomain and extra-terminal domain family

Basic information

Region (hg38): 6:32968594-32981505

Previous symbols: [ "BRD2-IT1" ]

Links

ENSG00000204256 ∙ NCBI:6046 ∙ OMIM:601540 ∙ HGNC:1103 ∙ Uniprot:P25440 ∙ 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 BRD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRD2 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				12	9	21
missense			32	1	5	38
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				6	2	8
non coding					1	1
Total	0	0	32	13	16

Variants in BRD2

This is a list of pathogenic ClinVar variants found in the BRD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-32972917-C-T		not specified	Uncertain significance (Sep 01, 2021)
6-32972923-A-G		not specified	Uncertain significance (Jun 02, 2023)
6-32974446-G-GT		not specified	Benign (-)
6-32974467-C-T		not specified	Uncertain significance (May 12, 2015)
6-32974473-A-C		not specified	Uncertain significance (Aug 03, 2022)
6-32974485-G-C		not specified	Uncertain significance (Jan 04, 2022)
6-32974487-T-C		BRD2-related disorder	Benign (Dec 31, 2019)
6-32974500-G-A			Benign (Dec 31, 2019)
6-32974525-G-A		BRD2-related disorder	Benign (Oct 17, 2019)
6-32974575-T-C		not specified	Uncertain significance (Jan 16, 2024)
6-32974609-C-A			Benign (Dec 31, 2019)
6-32974633-C-T		BRD2-related disorder	Benign (Dec 31, 2019)
6-32974654-A-G			Likely benign (Oct 23, 2018)
6-32974717-C-T		BRD2-related disorder	Likely benign (Jun 22, 2018)
6-32975374-T-C		BRD2-related disorder	Benign (Oct 17, 2019)
6-32975411-A-G		not specified	Uncertain significance (May 14, 2024)
6-32975448-A-G		not specified	Uncertain significance (Jan 23, 2024)
6-32975452-T-C			Benign (Dec 31, 2019)
6-32975509-C-T		BRD2-related disorder	Likely benign (Feb 28, 2019)
6-32976026-C-T		BRD2-related disorder	Likely benign (Mar 08, 2019)
6-32976031-C-G		not specified	Uncertain significance (Apr 22, 2022)
6-32976044-T-C			Uncertain significance (Nov 01, 2023)
6-32976048-C-T			Likely benign (Jun 08, 2018)
6-32976246-C-G		BRD2-related disorder	Benign (Dec 31, 2019)
6-32976251-G-A			Likely benign (May 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRD2	protein_coding	protein_coding	ENST00000395289	13	12846

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000433	125740	0	7	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.593	417	453	0.922	0.0000251	5398
Missense in Polyphen		92	139.23	0.66079		1640
Synonymous	-4.45	236	164	1.44	0.00000836	1682
Loss of Function	5.05	3	35.5	0.0845	0.00000187	459

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000590	0.0000590
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000450	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in spermatogenesis or folliculogenesis (By similarity). Binds hyperacetylated chromatin and plays a role in the regulation of transcription, probably by chromatin remodeling. Regulates transcription of the CCND1 gene. Plays a role in nucleosome assembly. {ECO:0000250, ECO:0000269|PubMed:18406326}.
• Pathway: Chemical Compounds to monitor Proteins;Gene expression (Transcription);RUNX3 regulates p14-ARF;Transcriptional regulation by RUNX3;Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of retinoblastoma protein (Consensus)

Recessive Scores

• pRec: 0.542

Intolerance Scores

• loftool: 0.201
• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.25

Haploinsufficiency Scores

• pHI: 0.412
• hipred: N
• hipred_score: 0.423
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brd2
• Phenotype: craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; vision/eye phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; skeleton phenotype; immune system phenotype; respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype

Zebrafish Information Network

• Gene name: brd2a
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: nucleosome assembly;regulation of transcription by RNA polymerase II;spermatogenesis;viral process
• Cellular component: nucleoplasm;cytoplasm;nuclear speck
• Molecular function: chromatin binding;protein binding;lysine-acetylated histone binding