BRD9

bromodomain containing 9, the group of Bromodomain containing|BAF complex|GBAF complex

Basic information

Region (hg38): 5:850290-892801

Links

ENSG00000028310 ∙ NCBI:65980 ∙ OMIM:618465 ∙ HGNC:25818 ∙ Uniprot:Q9H8M2 ∙ 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 BRD9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRD9 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				1	1	2
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding					3	3
Total	0	0	23	2	4

Variants in BRD9

This is a list of pathogenic ClinVar variants found in the BRD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-850383-C-G		not specified	Uncertain significance (Dec 20, 2021)
5-850385-T-C		not specified	Uncertain significance (Jan 26, 2022)
5-850389-C-T		not specified	Uncertain significance (Dec 13, 2023)
5-850399-C-G		not specified	Uncertain significance (Mar 17, 2023)
5-850411-C-T			Likely benign (Nov 01, 2023)
5-850416-A-G		not specified	Likely benign (Jun 16, 2024)
5-850430-C-T		not specified	Uncertain significance (Apr 24, 2024)
5-850485-A-C		not specified	Uncertain significance (Sep 22, 2022)
5-850490-A-T		not specified	Uncertain significance (Jan 16, 2024)
5-850524-G-A		not specified	Uncertain significance (Apr 25, 2022)
5-850526-G-A		not specified	Uncertain significance (Feb 15, 2023)
5-850529-G-A		not specified	Uncertain significance (Dec 15, 2022)
5-850547-T-C		not specified	Uncertain significance (Jun 06, 2023)
5-850562-T-G		not specified	Uncertain significance (Oct 18, 2021)
5-850572-C-A			Benign (Apr 19, 2018)
5-850587-C-T		not specified	Likely benign (Jul 14, 2021)
5-864514-T-C		not specified	Uncertain significance (Jun 18, 2021)
5-864521-C-T		not specified	Uncertain significance (Nov 07, 2022)
5-864557-G-A		not specified	Uncertain significance (Jun 16, 2024)
5-865443-T-G		not specified	Uncertain significance (Aug 02, 2022)
5-865483-C-A		not specified	Uncertain significance (Feb 23, 2023)
5-865512-T-C		not specified	Uncertain significance (May 09, 2024)
5-865539-T-G		not specified	Uncertain significance (May 14, 2024)
5-865587-T-C			Benign (Dec 18, 2017)
5-870496-T-G		not specified	Uncertain significance (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRD9	protein_coding	protein_coding	ENST00000467963	16	42534

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0154	0.985	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	285	352	0.810	0.0000217	3930
Missense in Polyphen		70	114.73	0.61014		1362
Synonymous	-0.448	157	150	1.05	0.0000109	1093
Loss of Function	3.57	9	30.1	0.299	0.00000160	380

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.000164	0.000163
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in chromatin remodeling and regulation of transcription (PubMed:22464331, PubMed:26365797). Acts as a chromatin reader that recognizes and binds acylated histones: binds histones that are acetylated and/or butyrylated (PubMed:26365797). Component of SWI/SNF chromatin remodeling subcomplex GBAF that carries out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner (PubMed:29374058). {ECO:0000269|PubMed:22464331, ECO:0000269|PubMed:26365797, ECO:0000269|PubMed:29374058}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.329
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.49

Haploinsufficiency Scores

• pHI: 0.123
• hipred: Y
• hipred_score: 0.605
• ghis: 0.584

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.828

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brd9

Gene ontology

• Biological process: chromatin organization;biological_process
• Cellular component: SWI/SNF complex
• Molecular function: nucleic acid binding;protein binding;lysine-acetylated histone binding