BRPF1 bromodomain and PHD finger containing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: BRPF1provided by HGNC
Official Full Name: bromodomain and PHD finger containing 1provided by HGNC
Primary source: HGNC:HGNC:14255
See related: Ensembl:ENSG00000156983 MIM:602410; AllianceGenome:HGNC:14255
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: BR140; IDDDFP
Summary: This gene encodes a bromodomain, PHD finger and chromo/Tudor-related Pro-Trp-Trp-Pro (PWWP) domain containing protein. The encoded protein is a component of the MOZ/MORF histone acetyltransferase complexes which function as a transcriptional regulators. This protein binds to the catalytic MYST domains of the MOZ and MORF proteins and may play a role in stimulating acetyltransferase and transcriptional activity of the complex. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression: Ubiquitous expression in testis (RPKM 10.0), bone marrow (RPKM 8.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p25.3

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (9731735..9748015)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (9723693..9739970)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (9773419..9789699)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Broadening the ocular phenotypic spectrum of ultra-rare BRPF1 variants: report of two cases.
Title: Broadening the ocular phenotypic spectrum of ultra-rare BRPF1 variants: report of two cases.
Beyond 'speech delay': Expanding the phenotype of BRPF1-related disorder.
Title: Beyond 'speech delay': Expanding the phenotype of BRPF1-related disorder.
Anemia and thrombocytopenia due to a novel BRPF1 variant in a family from Canakkale with intellectual disability and dysmorphic facies: Case report and review of the literature.
Title: Anemia and thrombocytopenia due to a novel BRPF1 variant in a family from Çanakkale with intellectual disability and dysmorphic facies: Case report and review of the literature.
Pygo2 activates BRPF1 via Pygo2-H3K4me2/3 interaction to maintain malignant progression in colon cancer.
Title: Pygo2 activates BRPF1 via Pygo2-H3K4me2/3 interaction to maintain malignant progression in colon cancer.
Bromodomain-containing protein BRPF1 is a therapeutic target for liver cancer.
Title: Bromodomain-containing protein BRPF1 is a therapeutic target for liver cancer.
Molecular Basis for the PZP Domain of BRPF1 Association with Chromatin.
Title: Molecular Basis for the PZP Domain of BRPF1 Association with Chromatin.
Truncated BRPF1 Cooperates with Smoothened to Promote Adult Shh Medulloblastoma.
Title: Truncated BRPF1 Cooperates with Smoothened to Promote Adult Shh Medulloblastoma.
data indicate that aberrations in the chromatin regulator gene BRPF1 cause histone H3 acetylation deficiency and a previously unrecognized intellectual disability syndrome
Title: Mutations in the Chromatin Regulator Gene BRPF1 Cause Syndromic Intellectual Disability and Deficient Histone Acetylation.
comparison of the clinical symptoms of individuals carrying mutations or small deletions of BRPF1 alone or SETD5 alone with those of individuals with deletions encompassing both BRPF1 and SETD5; leads to conclusion that both genes contribute to the phenotypic severity of 3p25 deletion syndrome but that some specific features, such as ptosis and blepharophimosis, are mostly driven by BRPF1 haploinsufficiency
Title: Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis.
critical insights into the molecular mechanism of ligand binding by the BRPF1 bromodomain
Title: Structural insights into recognition of acetylated histone ligands by the BRPF1 bromodomain.

Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Intellectual developmental disorder with dysmorphic facies and ptosis MedGen: C4310617 OMIM: 617333 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2023-08-23) ClinGen Genome Curation PagePubMed Triplosensitivity No evidence available (Last evaluated 2023-08-23) ClinGen Genome Curation Page

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat upregulates bromodomain and PHD finger-containing protein 1 (BRPF1) in HEK 293T cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-M91585 (e-PCR)
- UniSTS:23603

RH47297 (e-PCR)
- UniSTS:32426

SHGC-76698 (e-PCR)
- UniSTS:36523

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables acetyltransferase activator activity	IDA Inferred from Direct Assay more info	PubMed
contributes_to histone H4K12 acetyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
contributes_to histone H4K5 acetyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
contributes_to histone H4K8 acetyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of developmental process	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of hemopoiesis	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of MOZ/MORF histone acetyltransferase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of MOZ/MORF histone acetyltransferase complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
part_of histone acetyltransferase complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: peregrin

Names: bromodomain-containing protein, 140kD

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_052955.1 RefSeqGene

Range

5007..21287

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001003694.2 → NP_001003694.1 peregrin isoform 1

See identical proteins and their annotated locations for NP_001003694.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AI356310, AK293865, BC053851

Consensus CDS

CCDS33692.1

UniProtKB/TrEMBL

A0A5F9ZH11

Related

ENSP00000373340.2, ENST00000383829.7

Conserved Domains (5) summary

cd05839
Location:1089 → 1204

BR140_related; The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, ...

cd05512
Location:632 → 735

Bromo_brd1_like; Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. ...

COG5141
Location:174 → 657

COG5141; PHD zinc finger-containing protein [General function prediction only]

COG5189
Location:20 → 52

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

cd15701
Location:330 → 450

ePHD_BRPF1; Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins
NM_001319049.2 → NP_001305978.1 peregrin isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site and lacks an exon compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AC022382, AK293865, BC068262

Consensus CDS

CCDS82729.1

UniProtKB/TrEMBL

A0A5F9ZH11

Related

ENSP00000402485.2, ENST00000433861.6

Conserved Domains (5) summary

cd05839
Location:988 → 1103

BR140_related; The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, ...

cd05512
Location:632 → 729

Bromo_brd1_like; Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. ...

COG5141
Location:174 → 657

COG5141; PHD zinc finger-containing protein [General function prediction only]

COG5189
Location:20 → 52

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

cd15701
Location:330 → 450

ePHD_BRPF1; Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins
NM_001319050.2 → NP_001305979.1 peregrin isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses two alternate splice sites compared to variant 1. The encoded isoform (4) is shorter than isoform 1.

Source sequence(s)

AC022382, AL713696, BC068262

Consensus CDS

CCDS82730.1

UniProtKB/TrEMBL

A0A5F9ZH11

Related

ENSP00000508256.1, ENST00000684333.1

Conserved Domains (5) summary

cd05839
Location:1082 → 1197

BR140_related; The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, ...

cd05512
Location:632 → 729

Bromo_brd1_like; Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. ...

COG5141
Location:174 → 657

COG5141; PHD zinc finger-containing protein [General function prediction only]

COG5189
Location:20 → 52

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

cd15701
Location:330 → 450

ePHD_BRPF1; Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins
NM_001410704.1 → NP_001397633.1 peregrin isoform 5

Status: REVIEWED

Source sequence(s)

AC022382

Consensus CDS

CCDS93197.1

UniProtKB/TrEMBL

A0A5F9ZH11, A0A8C8KWW5

Related

ENSP00000398863.2, ENST00000424362.7
NM_004634.3 → NP_004625.2 peregrin isoform 2

See identical proteins and their annotated locations for NP_004625.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame segment in the coding region, as compared to variant 1. The encoded isoform 2 is thus shorter than isoform 1.

Source sequence(s)

AC022382, AI356310, BC036374, BC053851

Consensus CDS

CCDS2575.1

UniProtKB/Swiss-Prot

B4DEZ6, P55201, Q7Z6E0, Q8TCM6, Q9UHI0

UniProtKB/TrEMBL

A0A5F9ZH11

Related

ENSP00000507469.1, ENST00000683743.1

Conserved Domains (5) summary

cd05839
Location:1083 → 1198

BR140_related; The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, ...

cd05512
Location:632 → 729

Bromo_brd1_like; Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. ...

COG5141
Location:174 → 657

COG5141; PHD zinc finger-containing protein [General function prediction only]

COG5189
Location:20 → 52

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

cd15701
Location:330 → 450

ePHD_BRPF1; Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins

RNA

NR_160918.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC022382

Related

ENST00000673551.2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

9731735..9748015

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047448878.1 → XP_047304834.1 peregrin isoform X5

UniProtKB/TrEMBL

A0A5F9ZH11
XM_047448879.1 → XP_047304835.1 peregrin isoform X6

UniProtKB/TrEMBL

A0A5F9ZH11, A0A804HL48

Related

ENSP00000508198.1, ENST00000682980.1
XM_011534101.2 → XP_011532403.1 peregrin isoform X1

See identical proteins and their annotated locations for XP_011532403.1

UniProtKB/TrEMBL

A0A5F9ZH11, A0A804HI52

Related

ENSP00000506903.1, ENST00000683639.1

Conserved Domains (5) summary

cd05839
Location:1117 → 1232

BR140_related; The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, ...

cd05512
Location:632 → 729

Bromo_brd1_like; Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. ...

COG5141
Location:174 → 657

COG5141; PHD zinc finger-containing protein [General function prediction only]

COG5189
Location:20 → 52

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

cd15701
Location:330 → 450

ePHD_BRPF1; Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins
XM_005265449.2 → XP_005265506.1 peregrin isoform X2

See identical proteins and their annotated locations for XP_005265506.1

UniProtKB/TrEMBL

A0A5F9ZH11, A0A804HKY8

Related

ENSP00000508123.1, ENST00000682208.1

Conserved Domains (5) summary

cd05839
Location:1116 → 1231

BR140_related; The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, ...

cd05512
Location:632 → 729

Bromo_brd1_like; Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. ...

COG5141
Location:174 → 657

COG5141; PHD zinc finger-containing protein [General function prediction only]

COG5189
Location:20 → 52

SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]

cd15701
Location:330 → 450

ePHD_BRPF1; Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins
XM_047448881.1 → XP_047304837.1 peregrin isoform X7

UniProtKB/TrEMBL

A0A5F9ZH11, A0A804HIN1

Related

ENSP00000507148.1, ENST00000684206.1
XM_047448875.1 → XP_047304831.1 peregrin isoform X1

UniProtKB/TrEMBL

A0A5F9ZH11, A0A804HI52
XM_047448877.1 → XP_047304833.1 peregrin isoform X4

UniProtKB/TrEMBL

A0A5F9ZH11

Related

ENSP00000410210.2, ENST00000457855.2
XM_047448876.1 → XP_047304832.1 peregrin isoform X3

UniProtKB/TrEMBL

A0A5F9ZH11

Related

ENSP00000506921.1, ENST00000684199.1
XM_047448882.1 → XP_047304838.1 peregrin isoform X7

UniProtKB/TrEMBL

A0A5F9ZH11, A0A804HIN1