BRPF1

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

Basic information

Region (hg38): 3:9731729-9748019

Links

ENSG00000156983

∙ NCBI:7862 ∙ OMIM:602410 ∙ HGNC:14255 ∙ Uniprot:P55201 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

intellectual developmental disorder with dysmorphic facies and ptosis (Strong), mode of inheritance: AD
intellectual developmental disorder with dysmorphic facies and ptosis (Strong), mode of inheritance: AD
intellectual developmental disorder with dysmorphic facies and ptosis (Strong), mode of inheritance: AD
intellectual developmental disorder with dysmorphic facies and ptosis (Definitive), mode of inheritance: AD
intellectual developmental disorder with dysmorphic facies and ptosis (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual disability disorder with dysmorphic facies and ptosis (IDDDFP)	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	27939639; 27939640

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BRPF1 gene.

not_provided (219 variants)
Inborn_genetic_diseases (131 variants)
Intellectual_developmental_disorder_with_dysmorphic_facies_and_ptosis (99 variants)
BRPF1-related_disorder (34 variants)
not_specified (11 variants)
Intellectual_disability (7 variants)
Neurodevelopmental_disorder (3 variants)
See_cases (3 variants)
Global_developmental_delay (1 variants)
Neurodevelopmental_delay (1 variants)
Neurofibromatosis,_type_1 (1 variants)
Sudden_unexplained_death_in_childhood (1 variants)
Developmental_disorder (1 variants)
Autistic_behavior (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BRPF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001003694.2. 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				40 clinvar	8 clinvar	48
missense	6 clinvar	9 clinvar	253 clinvar	40 clinvar	1 clinvar	309
nonsense	23 clinvar	4 clinvar	2 clinvar			29
start loss	1	1				2
frameshift	36 clinvar	15 clinvar	2 clinvar			53
splice donor/acceptor (+/-2bp)	1 clinvar	4 clinvar	1 clinvar			6
Total	67	33	258	80	9

Highest pathogenic variant AF is 0.0000109745

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BRPF1	protein_coding	protein_coding	ENST00000383829	13	16290

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000459	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.83	464	761	0.609	0.0000498	8011
Missense in Polyphen		170	383.36	0.44344		4004
Synonymous	-0.714	307	291	1.05	0.0000177	2387
Loss of Function	6.17	4	52.1	0.0768	0.00000289	589

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000530	0.0000527
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 (PubMed:16387653, PubMed:27939640). Preferentially mediates histone H3-K23 acetylation (PubMed:27939640). Positively regulates the transcription of RUNX1 and RUNX2 (PubMed:18794358). {ECO:0000269|PubMed:16387653, ECO:0000269|PubMed:18794358, ECO:0000269|PubMed:27939640}.;
Disease: DISEASE: Intellectual developmental disorder with dysmorphic facies and ptosis (IDDDFP) [MIM:617333]: An autosomal dominant neurodevelopmental disorder characterized by delayed psychomotor development, intellectual disability, delayed language, and facial dysmorphisms, most notably ptosis. Additional features may include poor growth, hypotonia, and seizures. {ECO:0000269|PubMed:27939639, ECO:0000269|PubMed:27939640}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: 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: 0.123

Intolerance Scores

loftool: 0.252
rvis_EVS: -2.26
rvis_percentile_EVS: 1.27

Haploinsufficiency Scores

pHI: 0.622
hipred: Y
hipred_score: 0.765
ghis: 0.630

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.837

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Brpf1
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); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; 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); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;

Zebrafish Information Network

Gene name: brpf1
Affected structure: hypobranchial 2 cartilage
Phenotype tag: abnormal
Phenotype quality: aplastic

Gene ontology

Biological process: histone H3 acetylation;histone H3-K23 acetylation;positive regulation of transcription, DNA-templated;regulation of signal transduction by p53 class mediator
Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;MOZ/MORF histone acetyltransferase complex
Molecular function: DNA binding;protein binding;histone acetyltransferase activity (H3-K23 specific);metal ion binding