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
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (83 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 14 | 20 | ||||
| missense | 83 | 88 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 83 | 15 | 10 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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