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.

• not_specified (95 variants)
• not_provided (30 variants)
• BRD2-related_disorder (12 variants)

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. These statistics are base on transcript: NM_000005104.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			6	14	6	26
missense			109	1	4	114
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	117	15	10

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
		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

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

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