PHF1 PHD finger protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PHF1provided by HGNC
Official Full Name: PHD finger protein 1provided by HGNC
Primary source: HGNC:HGNC:8919
See related: Ensembl:ENSG00000112511 MIM:602881; AllianceGenome:HGNC:8919
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: PCL1; PHF2; hPHF1; MTF2L2; TDRD19C
Summary: This gene encodes a Polycomb group protein. The protein is a component of a histone H3 lysine-27 (H3K27)-specific methyltransferase complex, and functions in transcriptional repression of homeotic genes. The protein is also recruited to double-strand breaks, and reduced protein levels results in X-ray sensitivity and increased homologous recombination. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
Expression: Ubiquitous expression in ovary (RPKM 47.5), testis (RPKM 44.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.32

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (33410412..33416439)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (33231158..33237801)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (33378791..33384216)

Chromosome 6 - NC_000006.12 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 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?

When molecular outsmarts morphology: Malignant ossifying fibromyxoid tumors masquerading as osteosarcomas, including a novel CREBZF::PHF1 fusion.
Title: When molecular outsmarts morphology: Malignant ossifying fibromyxoid tumors masquerading as osteosarcomas, including a novel CREBZF::PHF1 fusion.
A PHF1-TFE3 fusion atypical ossifying fibromyxoid tumor with prominent collagenous rosettes: Case report with a brief review.
Title: A PHF1-TFE3 fusion atypical ossifying fibromyxoid tumor with prominent collagenous rosettes: Case report with a brief review.
Primary malignant ossifying fibromyxoid tumour of the bone. A clinicopathologic and molecular report of two cases.
Title: Primary malignant ossifying fibromyxoid tumour of the bone. A clinicopathologic and molecular report of two cases.
PHF1 fusions cause distinct gene expression and chromatin accessibility profiles in ossifying fibromyxoid tumors and mesenchymal cells.
Title: PHF1 fusions cause distinct gene expression and chromatin accessibility profiles in ossifying fibromyxoid tumors and mesenchymal cells.
A novel MBTD1-PHF1 gene fusion in endometrial stromal sarcoma: A case report and literature review.
Title: A novel MBTD1-PHF1 gene fusion in endometrial stromal sarcoma: A case report and literature review.
PHF1 promotes cell proliferation, invasion, and tumorigenesis in vivo and in vitro and its expression is markedly upregulated in a variety of human cancers
Title: PHD finger protein 1 (PHF1) is a novel reader for histone H4R3 symmetric dimethylation and coordinates with PRMT5-WDR77/CRL4B complex to promote tumorigenesis.
the increase of DNA accessibility within the H3K36me3-containing nucleosome, instigated by the Tudor domain of PHF1 binding to H3K36me3, is dramatically enhanced by the PHF1 N-terminal domain.
Title: PHF1 Tudor and N-terminal domains synergistically target partially unwrapped nucleosomes to increase DNA accessibility.
ZC3H7B-BCOR and MEAF6-PHF1 fusions occurred predominantly in S100 protein-negative and malignant ossifying fibromyxoid tumors.
Title: Novel ZC3H7B-BCOR, MEAF6-PHF1, and EPC1-PHF1 fusions in ossifying fibromyxoid tumors--molecular characterization shows genetic overlap with endometrial stromal sarcoma.
the F61L/S86F mutant of MTF2 Tudor-PHD1 was able to bind to H3K36me3 as strong as the PHF1 Tudor bound to this PTM . We concluded that the hydrophobic patch plays an essential role in binding of these Tudors to methylated chromatin
Title: An aromatic cage is required but not sufficient for binding of Tudor domains of the Polycomblike protein family to H3K36me3.
PCL1 binds to and stabilizes p53 to induce cellular quiescence
Title: A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence.

Submit: New GeneRIF Correction See all GeneRIFs (27)

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

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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Replication interactions

Interaction	Pubs
Knockdown of PHD finger protein 1 (PHF1) by siRNA has both activating and inhibiting activities on HIV-1 replication in HeLa P4/R5 cells, suggesting a regulatory role in HIV replication	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_5865-5866:996691399:1 (e-PCR)
- UniSTS:269593

PHF1 (e-PCR)
- UniSTS:505635

STS-Z40841 (e-PCR)
- UniSTS:65333

STS-D14678 (e-PCR)
- UniSTS:32835

RH1523 (e-PCR)
- UniSTS:31404

D6S1834 (e-PCR)
- UniSTS:20155

RH15807 (e-PCR)
- UniSTS:18644

G44723 (e-PCR)
- UniSTS:95198

STS-Z41506 (e-PCR)
- UniSTS:29179

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone methyltransferase binding	IPI Inferred from Physical Interaction more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA repair-dependent chromatin remodeling	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of gene expression, epigenetic	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of ESC/E(Z) complex	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in site of double-strand break	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: PHD finger protein 1

Names: hPCl1; polycomb-like 1; polycomb-like protein 1; testicular tissue protein Li 140; tudor domain containing 19C

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.

mRNA and Protein(s)

NM_002636.5 → NP_002627.2 PHD finger protein 1 isoform a

Status: REVIEWED

Description

Transcript Variant: This variant (1), uses an alternate splice site and lacks an alternate exon in the 3' coding region resulting in a frameshift, compared to variant 2. The resulting isoform (a) has a shorter and distinct C-terminus, compared to isoform b.

Source sequence(s)

AL662799

Consensus CDS

CCDS4778.1

UniProtKB/TrEMBL

A0A140VJR4, A0A1U9X8A3

Related

ENSP00000363636.3, ENST00000374512.7

Conserved Domains (3) summary

cd15500
Location:89 → 139

PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)

cd15582
Location:188 → 239

PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)

pfam18104
Location:34 → 69

Tudor_2; Jumonji domain-containing protein 2A Tudor domain
NM_024165.3 → NP_077084.2 PHD finger protein 1 isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2), also called variant PHF2, represents the longest transcript and encodes the longer isoform (b).

Source sequence(s)

AL662799

Consensus CDS

CCDS4777.1

UniProtKB/Swiss-Prot

B1AZX2, B1AZX3, O43189, O60929, Q5SU07, Q5SU08, Q96KM7

Related

ENSP00000363640.3, ENST00000374516.8

Conserved Domains (4) summary

cd15500
Location:89 → 139

PHD1_PHF1; PHD finger 1 found in PHD finger protein1 (PHF1)

cd15582
Location:188 → 239

PHD2_PHF1; PHD finger 2 found in PHD finger protein1 (PHF1)

pfam14061
Location:539 → 565

Mtf2_C; Polycomb-like MTF2 factor 2

pfam18104
Location:34 → 69

Tudor_2; Jumonji domain-containing protein 2A Tudor domain

RNA

NR_027692.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site, compared to variant 2. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL662799