BRD1

bromodomain containing 1, the group of Bromodomain containing|PHD finger proteins|PWWP domain containing

Basic information

Region (hg38): 22:49773278-49827873

Links

ENSG00000100425 ∙ NCBI:23774 ∙ OMIM:604589 ∙ HGNC:1102 ∙ Uniprot:O95696 ∙ 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 BRD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRD1 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				14	6	20
missense			61	6	5	72
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	61	20	11

Variants in BRD1

This is a list of pathogenic ClinVar variants found in the BRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-49774254-G-A			Likely benign (May 21, 2018)
22-49774268-C-T		not specified	Uncertain significance (Aug 02, 2021)
22-49774275-G-A			Likely benign (Dec 27, 2017)
22-49774298-G-A		not specified	Uncertain significance (Dec 28, 2022)
22-49774367-T-C		not specified	Uncertain significance (May 27, 2022)
22-49775658-C-G		not specified	Uncertain significance (Feb 14, 2025)
22-49775663-A-G		not specified	Uncertain significance (Feb 27, 2023)
22-49775668-C-T			Likely benign (Feb 01, 2023)
22-49775674-G-T		not specified	Uncertain significance (Dec 28, 2024)
22-49775698-G-C			Benign (May 30, 2018)
22-49775700-C-T		not specified	Uncertain significance (Feb 25, 2025)
22-49775724-G-A		not specified	Uncertain significance (Jun 22, 2023)
22-49776066-G-C		not specified	Uncertain significance (Jan 22, 2025)
22-49776122-G-A			Benign (Jan 04, 2019)
22-49776148-T-C		not specified	Uncertain significance (Dec 15, 2023)
22-49776153-C-G		not specified	Uncertain significance (Oct 20, 2023)
22-49776154-C-T		not specified	Uncertain significance (Jan 23, 2025)
22-49776163-C-T			Likely benign (Sep 20, 2018)
22-49777040-C-T		not specified	Uncertain significance (Jul 07, 2022)
22-49777081-G-A		not specified	Uncertain significance (May 30, 2024)
22-49777093-C-G		not specified	Uncertain significance (Nov 14, 2023)
22-49777094-T-C		not specified	Uncertain significance (Feb 27, 2025)
22-49777095-G-A			Benign (Jan 04, 2019)
22-49777096-C-T		not specified	Uncertain significance (Aug 23, 2021)
22-49777115-G-A		not specified	Uncertain significance (Jan 19, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRD1	protein_coding	protein_coding	ENST00000216267	12	54230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000513	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.76	501	708	0.708	0.0000506	6920
Missense in Polyphen		126	293.14	0.42983		2871
Synonymous	-2.34	369	316	1.17	0.0000256	2115
Loss of Function	5.64	6	48.3	0.124	0.00000291	495

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.0000545	0.0000544
South Asian	0.000163	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the MOZ/MORF complex which has a histone H3 acetyltransferase activity. {ECO:0000269|PubMed:16387653, ECO:0000269|PubMed:21880731}.
• Pathway: Pathways Affected in Adenoid Cystic Carcinoma;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.350
• rvis_EVS: -1.72
• rvis_percentile_EVS: 2.49

Haploinsufficiency Scores

• pHI: 0.569
• hipred: Y
• hipred_score: 0.649
• ghis: 0.571

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.796

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brd1
• Phenotype: cellular phenotype; hematopoietic system 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); 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); vision/eye 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); liver/biliary system phenotype; embryo phenotype

Gene ontology

• Biological process: response to immobilization stress;histone H3 acetylation;response to electrical stimulus
• Cellular component: nucleus;nuclear speck;dendrite;perikaryon;MOZ/MORF histone acetyltransferase complex
• Molecular function: histone binding;metal ion binding