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

Gene ID: 5252, updated on 6-Jul-2026
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; 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
all
Try the new Gene page
Try the new Transcripts and proteins table
See PHF1 in Genome Data Viewer
Location:
6p21.32
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (33410412..33416439)
RS_2025_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_000006.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L35a pseudogene 4 Neighboring gene kinesin family member C1 Neighboring gene ribosomal protein L12 pseudogene 1 Neighboring gene synaptic Ras GTPase activating protein 1 Neighboring gene cutA divalent cation tolerance homolog Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:33393157-33393699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:33396849-33397470 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:33405630-33405807 Neighboring gene SYNGAP1 antisense RNA 1 Neighboring gene microRNA 5004

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. PHF1 Tudor and N-terminal domains synergistically target partially unwrapped nucleosomes to increase DNA accessibility. Gibson MD, et al. Nucleic Acids Res, 2017 Apr 20. PMID 28082396, Free PMC Article
  2. A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence. Brien GL, et al. Genes Dev, 2015 Nov 1. PMID 26494712, Free PMC Article
  3. Recurrent rearrangement of the PHF1 gene in ossifying fibromyxoid tumors. Gebre-Medhin S, et al. Am J Pathol, 2012 Sep. PMID 22796436
  4. Endometrial stromal sarcomas with sex cord differentiation are associated with PHF1 rearrangement. D'Angelo E, et al. Am J Surg Pathol, 2013 Apr. PMID 23211293
  5. PHF1 fusions cause distinct gene expression and chromatin accessibility profiles in ossifying fibromyxoid tumors and mesenchymal cells. Hofvander J, et al. Mod Pathol, 2020 Jul. PMID 31932680

See all (66) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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)

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

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

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

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 H3K36me3 reader activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables histone H3K36me3 reader activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K4me3 reader activity IDA
Inferred from Direct Assay
more info
 PubMed 
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 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 heterochromatin formation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of gene expression, epigenetic IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of transcription by RNA polymerase II NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of ESC/E(Z) complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of ESC/E(Z) complex IEA
Inferred from Electronic Annotation
more info
  
part_of ESC/E(Z) complex NAS
Non-traceable Author Statement
more info
 PubMed 
colocalizes_with centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in centrosome IEA
Inferred from Electronic Annotation
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 nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
located_in site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 
Preferred Names
PHD finger protein 1
Names
polycomb-like 1
polycomb-like protein 1
testicular tissue protein Li 140
tudor domain containing 19C

NEW Try the new Transcript table

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)

  1. 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
    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

  2. NM_024165.3 → NP_077084.2  PHD finger protein 1 isoform b

    Status: REVIEWED

    Source sequence(s)
    AL662799
    Consensus CDS
    CCDS4777.1
    UniProtKB/Swiss-Prot
    B1AZX2, B1AZX3, O43189, O60929, Q5SU07, Q5SU08, Q96KM7
    UniProtKB/TrEMBL
    A0ACI8R9E3
    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

  1. 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
    Related
    ENST00000941047.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    33410412..33416439
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047418879.1 → XP_047274835.1  PHD finger protein 1 isoform X6

    UniProtKB/Swiss-Prot
    B1AZX2, B1AZX3, O43189, O60929, Q5SU07, Q5SU08, Q96KM7
    UniProtKB/TrEMBL
    A0ACI8R9E3
    Related
    ENSP00000529059.1, ENST00000859000.1

  2. XM_011514665.2 → XP_011512967.2  PHD finger protein 1 isoform X4

  3. XM_011514666.2 → XP_011512968.2  PHD finger protein 1 isoform X5

  4. XM_011514662.2 → XP_011512964.2  PHD finger protein 1 isoform X1

    UniProtKB/TrEMBL
    A0ACI8R9E3

  5. XM_011514663.2 → XP_011512965.2  PHD finger protein 1 isoform X2

    UniProtKB/TrEMBL
    A0ACI8R9E3

  6. XM_011514669.2 → XP_011512971.2  PHD finger protein 1 isoform X7

    UniProtKB/TrEMBL
    A0A140VJR4

  7. XM_011514664.2 → XP_011512966.2  PHD finger protein 1 isoform X3

    UniProtKB/TrEMBL
    A0ACI8U6L2
    Related
    ENSP00000529068.1, ENST00000859009.1

  8. XM_011514670.3 → XP_011512972.2  PHD finger protein 1 isoform X8

    UniProtKB/TrEMBL
    E9PQT8

  9. XM_047418881.1 → XP_047274837.1  PHD finger protein 1 isoform X9

RNA

  1. XR_007059274.1 RNA Sequence

  2. XR_926250.2 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    4858494..4865164
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331354.1 → XP_054187329.1  PHD finger protein 1 isoform X6

    UniProtKB/TrEMBL
    A0ACI8R9E3

  2. XM_054331356.1 → XP_054187331.1  PHD finger protein 1 isoform X11

    UniProtKB/TrEMBL
    A0ACI8R9E3

  3. XM_054331362.1 → XP_054187337.1  PHD finger protein 1 isoform X13

  4. XM_054331358.1 → XP_054187333.1  PHD finger protein 1 isoform X12

    UniProtKB/TrEMBL
    A0ACI8U6L2

  5. XM_054331353.1 → XP_054187328.1  PHD finger protein 1 isoform X5

  6. XM_054331360.1 → XP_054187335.1  PHD finger protein 1 isoform X8

    UniProtKB/TrEMBL
    B4DI51

  7. XM_054331352.1 → XP_054187327.1  PHD finger protein 1 isoform X4

  8. XM_054331351.1 → XP_054187326.1  PHD finger protein 1 isoform X10

    UniProtKB/TrEMBL
    A0ACI8U6L2

  9. XM_054331348.1 → XP_054187323.1  PHD finger protein 1 isoform X1

    UniProtKB/TrEMBL
    A0ACI8R9E3

  10. XM_054331349.1 → XP_054187324.1  PHD finger protein 1 isoform X2

    UniProtKB/TrEMBL
    A0ACI8R9E3

  11. XM_054331359.1 → XP_054187334.1  PHD finger protein 1 isoform X7

    UniProtKB/TrEMBL
    A0A140VJR4

  12. XM_054331350.1 → XP_054187325.1  PHD finger protein 1 isoform X3

    UniProtKB/TrEMBL
    A0ACI8U6L2

  13. XM_054331361.1 → XP_054187336.1  PHD finger protein 1 isoform X13

  14. XM_054331355.1 → XP_054187330.1  PHD finger protein 1 isoform X11

    UniProtKB/TrEMBL
    A0ACI8R9E3

  15. XM_054331357.1 → XP_054187332.1  PHD finger protein 1 isoform X12

    UniProtKB/TrEMBL
    A0ACI8U6L2

  16. XM_054331364.1 → XP_054187339.1  PHD finger protein 1 isoform X9

  17. XM_054331363.1 → XP_054187338.1  PHD finger protein 1 isoform X14

RNA

  1. XR_008485716.1 RNA Sequence

  2. XR_008485717.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    33231158..33237801
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355619.1 → XP_054211594.1  PHD finger protein 1 isoform X6

    UniProtKB/Swiss-Prot
    B1AZX2, B1AZX3, O43189, O60929, Q5SU07, Q5SU08, Q96KM7
    UniProtKB/TrEMBL
    A0ACI8R9E3

  2. XM_054355621.1 → XP_054211596.1  PHD finger protein 1 isoform X16

    UniProtKB/TrEMBL
    A0ACI8Q7C3, A0ACI8R9E3

  3. XM_054355627.1 → XP_054211602.1  PHD finger protein 1 isoform X18

  4. XM_054355623.1 → XP_054211598.1  PHD finger protein 1 isoform X17

    UniProtKB/TrEMBL
    A0ACI8PFY4, A0ACI8U6L2

  5. XM_054355618.1 → XP_054211593.1  PHD finger protein 1 isoform X5

  6. XM_054355625.1 → XP_054211600.1  PHD finger protein 1 isoform X8

    UniProtKB/TrEMBL
    E9PQT8

  7. XM_054355617.1 → XP_054211592.1  PHD finger protein 1 isoform X4

  8. XM_054355616.1 → XP_054211591.1  PHD finger protein 1 isoform X15

    UniProtKB/TrEMBL
    A0ACI8U6L2

  9. XM_054355613.1 → XP_054211588.1  PHD finger protein 1 isoform X1

    UniProtKB/TrEMBL
    A0ACI8R9E3

  10. XM_054355614.1 → XP_054211589.1  PHD finger protein 1 isoform X2

    UniProtKB/TrEMBL
    A0ACI8R9E3

  11. XM_054355624.1 → XP_054211599.1  PHD finger protein 1 isoform X7

    UniProtKB/TrEMBL
    A0A140VJR4

  12. XM_054355615.1 → XP_054211590.1  PHD finger protein 1 isoform X3

    UniProtKB/TrEMBL
    A0ACI8U6L2

  13. XM_054355626.1 → XP_054211601.1  PHD finger protein 1 isoform X18

  14. XM_054355620.1 → XP_054211595.1  PHD finger protein 1 isoform X16

    UniProtKB/TrEMBL
    A0ACI8Q7C3, A0ACI8R9E3

  15. XM_054355622.1 → XP_054211597.1  PHD finger protein 1 isoform X17

    UniProtKB/TrEMBL
    A0ACI8PFY4, A0ACI8U6L2

  16. XM_054355629.1 → XP_054211604.1  PHD finger protein 1 isoform X9

  17. XM_054355628.1 → XP_054211603.1  PHD finger protein 1 isoform X19

RNA

  1. XR_008487345.1 RNA Sequence

  2. XR_008487346.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43189.3 GenPept UniProtKB/Swiss-Prot:O43189

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