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.

not_specified (142 variants)
not_provided (3 variants)
Autism (1 variants)
Colitis (1 variants)
Cranial_asymmetry (1 variants)
Delayed_speech_and_language_development (1 variants)

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. These statistics are base on transcript: NM_000015695.3. 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			143 clinvar	2 clinvar		145
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	144	2	0

Loading clinvar variants...

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