BRPF3

bromodomain and PHD finger containing 3, the group of Bromodomain containing|PHD finger proteins|PWWP domain containing

Basic information

Region (hg38): 6:36196744-36232790

Links

ENSG00000096070 ∙ NCBI:27154 ∙ OMIM:616856 ∙ HGNC:14256 ∙ Uniprot:Q9ULD4 ∙ 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 BRPF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRPF3 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			102	2		104
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	103	2	0

Variants in BRPF3

This is a list of pathogenic ClinVar variants found in the BRPF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-36200339-G-A		not specified	Uncertain significance (Jan 02, 2024)
6-36200348-G-A		not specified	Uncertain significance (Aug 04, 2023)
6-36200381-C-T		not specified	Uncertain significance (Jan 23, 2024)
6-36200437-C-T		not specified	Uncertain significance (Jan 10, 2025)
6-36200456-T-C		not specified	Uncertain significance (Oct 07, 2024)
6-36200474-G-A		not specified	Uncertain significance (Apr 05, 2023)
6-36200616-A-T		not specified	Uncertain significance (May 25, 2022)
6-36200623-G-A		not specified	Uncertain significance (May 16, 2024)
6-36200639-A-G		not specified	Uncertain significance (Jun 19, 2024)
6-36200720-T-G		not specified	Uncertain significance (Jun 17, 2024)
6-36200776-G-A		not specified	Uncertain significance (Dec 03, 2021)
6-36200820-G-A		not specified	Uncertain significance (Oct 17, 2023)
6-36200821-G-A		not specified	Uncertain significance (Feb 06, 2025)
6-36200828-A-G		not specified	Uncertain significance (Nov 07, 2022)
6-36200866-G-C		not specified	Uncertain significance (Oct 20, 2024)
6-36200884-G-A		not specified	Uncertain significance (Jan 20, 2023)
6-36200891-G-A		not specified	Uncertain significance (Sep 29, 2023)
6-36200921-G-A		not specified	Uncertain significance (Jun 03, 2022)
6-36200999-G-A		not specified	Uncertain significance (Jul 12, 2022)
6-36201034-G-A		not specified	Uncertain significance (Dec 07, 2024)
6-36201058-G-A		not specified	Uncertain significance (Feb 28, 2024)
6-36201143-A-G		not specified	Uncertain significance (Jan 17, 2025)
6-36201169-A-G		not specified	Uncertain significance (May 04, 2023)
6-36201277-G-A		not specified	Uncertain significance (Jun 23, 2023)
6-36201427-A-T		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRPF3	protein_coding	protein_coding	ENST00000357641	12	36047

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000187	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.91	516	738	0.699	0.0000467	7867
Missense in Polyphen		177	341.35	0.51853		3559
Synonymous	1.65	254	290	0.877	0.0000164	2446
Loss of Function	5.72	3	43.9	0.0684	0.00000213	545

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000891	0.0000891
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Chromatin modifying enzymes;HATs acetylate histones;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.177
• rvis_EVS: -1.06
• rvis_percentile_EVS: 7.54

Haploinsufficiency Scores

• pHI: 0.235
• hipred: Y
• hipred_score: 0.696
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.975

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Brpf3
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: platelet degranulation;histone H3 acetylation
• Cellular component: extracellular region;cytosol;MOZ/MORF histone acetyltransferase complex
• Molecular function: protein binding;metal ion binding