BRD7

bromodomain containing 7, the group of Bromodomain containing|PBAF complex

Basic information

Region (hg38): 16:50313487-50368988

Links

ENSG00000166164 ∙ NCBI:29117 ∙ OMIM:618489 ∙ HGNC:14310 ∙ Uniprot:Q9NPI1 ∙ 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 BRD7 gene.

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.

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						0
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in BRD7

This is a list of pathogenic ClinVar variants found in the BRD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-50314005-C-T			Likely benign (Aug 01, 2022)
16-50314038-C-T			Benign (Dec 31, 2019)
16-50315365-G-A		not specified	Uncertain significance (Mar 25, 2022)
16-50315415-T-C			Benign (Jul 23, 2018)
16-50315428-G-A		not specified	Uncertain significance (Nov 20, 2023)
16-50315495-G-C		not specified	Uncertain significance (Jul 20, 2021)
16-50319953-G-A		Granular cell cancer	Likely pathogenic (Jul 16, 2015)
16-50319995-G-C		not specified	Uncertain significance (Sep 06, 2022)
16-50320016-T-C		not specified	Uncertain significance (Apr 19, 2024)
16-50320025-G-C		not specified	Uncertain significance (Mar 25, 2024)
16-50320256-A-T		not specified	Uncertain significance (Apr 25, 2023)
16-50320274-C-T		not specified	Uncertain significance (Jun 13, 2024)
16-50320329-C-T		not specified	Uncertain significance (May 20, 2024)
16-50320716-G-A		not specified	Uncertain significance (Jul 19, 2023)
16-50320747-A-C		not specified	Uncertain significance (Sep 12, 2023)
16-50320765-C-T		not specified	Likely benign (Oct 26, 2021)
16-50321998-G-T		not specified	Uncertain significance (Jun 10, 2024)
16-50322005-G-C		not specified	Uncertain significance (Oct 13, 2023)
16-50323615-T-A		not specified	Uncertain significance (Apr 07, 2022)
16-50323645-C-G		not specified	Uncertain significance (Nov 22, 2022)
16-50325833-A-T		not specified	Uncertain significance (May 25, 2022)
16-50326293-C-T		not specified	Uncertain significance (Jan 03, 2024)
16-50326377-G-A		not specified	Uncertain significance (Dec 20, 2023)
16-50333602-T-C		not specified	Uncertain significance (Jun 28, 2022)
16-50334771-C-A		not specified	Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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