BRD7
bromodomain containing 7, the group of Bromodomain containing|PBAF complex
Basic information
Region (hg38): 16:50313487-50368988
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (72 variants)
- not_provided (1 variants)
- Granular_cell_cancer (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRD7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013263.5. 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 | 0 | |||||
| missense | 69 | 73 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 69 | 4 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BRD7 | protein_coding | protein_coding | ENST00000394689 | 17 | 55448 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00226 | 125737 | 0 | 7 | 125744 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.489 | 320 | 346 | 0.926 | 0.0000174 | 4340 |
| Missense in Polyphen | 101 | 121.53 | 0.83109 | 1667 | ||
| Synonymous | 0.392 | 118 | 124 | 0.955 | 0.00000682 | 1154 |
| Loss of Function | 4.90 | 4 | 35.5 | 0.113 | 0.00000171 | 468 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000762 | 0.0000544 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.0000181 | 0.0000176 |
| Middle Eastern | 0.0000762 | 0.0000544 |
| South Asian | 0.0000377 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts both as coactivator and as corepressor. May play a role in chromatin remodeling. Activator of the Wnt signaling pathway in a DVL1-dependent manner by negatively regulating the GSK3B phosphotransferase activity. Induces dephosphorylation of GSK3B at 'Tyr-216'. Down-regulates TRIM24-mediated activation of transcriptional activation by AR (By similarity). Transcriptional corepressor that down-regulates the expression of target genes. Binds to target promoters, leading to increased histone H3 acetylation at 'Lys-9' (H3K9ac). Binds to the ESR1 promoter. Recruits BRCA1 and POU2F1 to the ESR1 promoter. Coactivator for TP53-mediated activation of transcription of a set of target genes. Required for TP53-mediated cell-cycle arrest in response to oncogene activation. Promotes acetylation of TP53 at 'Lys-382', and thereby promotes efficient recruitment of TP53 to target promoters. Inhibits cell cycle progression from G1 to S phase. {ECO:0000250, ECO:0000269|PubMed:16265664, ECO:0000269|PubMed:16475162, ECO:0000269|PubMed:20215511, ECO:0000269|PubMed:20228809, ECO:0000269|PubMed:20660729}.;
- Pathway
- Hepatocellular carcinoma - Homo sapiens (human);Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53
(Consensus)
Recessive Scores
- pRec
- 0.180
Intolerance Scores
- loftool
- 0.761
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 74.58
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.674
- ghis
- 0.526
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.640
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Brd7
- Phenotype
- growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); limbs/digits/tail 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;cell cycle;negative regulation of cell population proliferation;Wnt signaling pathway;positive regulation of histone acetylation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;regulation of signal transduction by p53 class mediator;negative regulation of G1/S transition of mitotic cell cycle
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol
- Molecular function
- p53 binding;transcription coactivator activity;transcription corepressor activity;protein binding;transcription factor binding;histone binding;transcription regulatory region DNA binding;lysine-acetylated histone binding