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    PHF6 PHD finger protein 6 [ Homo sapiens (human) ]

    Gene ID: 84295, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PHF6provided by HGNC
    Official Full Name
    PHD finger protein 6provided by HGNC
    Primary source
    HGNC:HGNC:18145
    See related
    Ensembl:ENSG00000156531 MIM:300414; AllianceGenome:HGNC:18145
    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
    BFLS; BORJ; CENP-31
    Summary
    This gene is a member of the plant homeodomain (PHD)-like finger (PHF) family. It encodes a protein with two PHD-type zinc finger domains, indicating a potential role in transcriptional regulation, that localizes to the nucleolus. Mutations affecting the coding region of this gene or the splicing of the transcript have been associated with Borjeson-Forssman-Lehmann syndrome (BFLS), a disorder characterized by cognitive disability, epilepsy, hypogonadism, hypometabolism, obesity, swelling of subcutaneous tissue of the face, narrow palpebral fissures, and large ears. Alternate splicing results in multiple transcript variants, encoding different isoforms. [provided by RefSeq, Jun 2010]
    Expression
    Ubiquitous expression in ovary (RPKM 17.4), lymph node (RPKM 13.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHF6 in Genome Data Viewer
    Location:
    Xq26.2
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (134373312..134428790)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (132698463..132753940)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (133507342..133562820)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chrX:133374068-133374687 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:133381318-133381517 Neighboring gene coiled-coil domain containing 160 Neighboring gene NT5DC1 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:133515535-133515735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21008 Neighboring gene origin of replication in promoter/intron 1 of HPRT1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21009 Neighboring gene hypoxanthine phosphoribosyltransferase 1 Neighboring gene ribosomal protein L36a pseudogene 54

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Pathogenesis of Börjeson-Forssman-Lehmann syndrome: Insights from PHF6 function. Jahani-Asl A, et al. Neurobiol Dis, 2016 Dec. PMID 27633282, Free PMC Article
    2. Upregulated Plant Homeodomain Finger Protein 6 Promotes Extracellular Matrix Degradation in Intervertebral Disc Degeneration Based on Microarray Analysis. Rui G, et al. Spine (Phila Pa 1976), 2020 Oct 1. PMID 32453232
    3. Further characterization of Borjeson-Forssman-Lehmann syndrome in females due to de novo variants in PHF6. Gerber CB, et al. Clin Genet, 2022 Sep. PMID 35662002, Free PMC Article
    4. The chromatin-binding protein PHF6 functions as an E3 ubiquitin ligase of H2BK120 via H2BK12Ac recognition for activation of trophectodermal genes. Oh S, et al. Nucleic Acids Res, 2020 Sep 18. PMID 32735658, Free PMC Article
    5. PHF6 Deletions May Cause Borjeson-Forssman-Lehmann Syndrome in Females. Berland S, et al. Mol Syndromol, 2011 Sep. PMID 22190899, Free PMC Article

    See all (157) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression.
      Title: PHF6 cooperates with SWI/SNF complexes to facilitate transcriptional progression.
    2. Investigating the physiological role of S199A and S199D mutants of PHF6 protein in T-cell acute lymphoblastic leukemia.
      Title: Investigating the physiological role of S199A and S199D mutants of PHF6 protein in T-cell acute lymphoblastic leukemia.
    3. Molecular and clinical analyses of PHF6 mutant myeloid neoplasia provide their pathogenesis and therapeutic targeting.
      Title: Molecular and clinical analyses of PHF6 mutant myeloid neoplasia provide their pathogenesis and therapeutic targeting.
    4. PHF6 recruits BPTF to promote HIF-dependent pathway and progression in YAP-high breast cancer.
      Title: PHF6 recruits BPTF to promote HIF-dependent pathway and progression in YAP-high breast cancer.
    5. PHF6 promotes the progression of endometrial carcinoma by increasing cancer cells growth and decreasing T-cell infiltration.
      Title: PHF6 promotes the progression of endometrial carcinoma by increasing cancer cells growth and decreasing T-cell infiltration.
    6. PHF6 mutation is associated with poor outcome in acute myeloid leukaemia.
      Title: PHF6 mutation is associated with poor outcome in acute myeloid leukaemia.
    7. The Role of PHF6 in Hematopoiesis and Hematologic Malignancies.
      Title: The Role of PHF6 in Hematopoiesis and Hematologic Malignancies.
    8. MiR-1306-5p promotes cell proliferation and inhibits cell apoptosis in acute myeloid leukemia by downregulating PHF6 expression.
      Title: MiR-1306-5p promotes cell proliferation and inhibits cell apoptosis in acute myeloid leukemia by downregulating PHF6 expression.
    9. Further characterization of Borjeson-Forssman-Lehmann syndrome in females due to de novo variants in PHF6.
      Title: Further characterization of Borjeson-Forssman-Lehmann syndrome in females due to de novo variants in PHF6.
    10. Functional mapping of PHF6 complexes in chromatin remodeling, replication dynamics, and DNA repair.
      Title: Functional mapping of PHF6 complexes in chromatin remodeling, replication dynamics, and DNA repair.
    Submit: New GeneRIF Correction See all GeneRIFs (55)

    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
    Borjeson-Forssman-Lehmann syndrome
    MedGen: C0265339 OMIM: 301900 GeneReviews: Not available
    		Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-02-24)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2021-02-24)

    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)

    Genotypes

    Pathways from PubChem

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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

    Homology

    Clone Names

    • MGC14797

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables histone deacetylase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone deacetylase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoprotein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ribonucleoprotein complex binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables scaffold protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tubulin binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in blastocyst hatching IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in kinetochore IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    PHD finger protein 6
    Names
    PHD-like zinc finger protein
    centromere protein 31

    NCBI Reference Sequences (RefSeq)

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    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.

    Genomic

    1. NG_008886.1 RefSeqGene

      Range
      5001..60481
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_629

    mRNA and Protein(s)

    1. NM_001015877.2 → NP_001015877.1  PHD finger protein 6 isoform 1

      See identical proteins and their annotated locations for NP_001015877.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also called the "PHF6a" variant) represents the shortest transcript and encodes the shortest isoform (1).
      Source sequence(s)
      AB058726, AW297001, AY157622, BG122271, CF242973
      Consensus CDS
      CCDS14639.1
      UniProtKB/Swiss-Prot
      A8K230, B4E0G4, D3DTG3, E9PC97, Q5JRC7, Q5JRC8, Q8IWS0, Q96JK3, Q9BRU0
      UniProtKB/TrEMBL
      Q5JRC6
      Related
      ENSP00000359839.4, ENST00000370803.8
      Conserved Domains (2) summary
      cd15710
      Location:17 → 131
      ePHD1_PHF6; Extended PHD finger 1 found in PHD finger protein 6 (PHF6)
      cd15711
      Location:212 → 329
      ePHD2_PHF6; Extended PHD finger 2 found in PHD finger protein 6 (PHF6)

    2. NM_032335.3 → NP_115711.2  PHD finger protein 6 isoform 2

      See identical proteins and their annotated locations for NP_115711.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate termination site, resulting in a distinct C-terminus (isoform 2).
      Source sequence(s)
      AK290095, BC005994, DR000282
      Consensus CDS
      CCDS14640.1
      UniProtKB/TrEMBL
      Q5JRC6
      Related
      ENSP00000359836.4, ENST00000370800.4
      Conserved Domains (2) summary
      cd15710
      Location:17 → 131
      ePHD1_PHF6; Extended PHD finger 1 found in PHD finger protein 6 (PHF6)
      cl22851
      Location:213 → 283
      PHD_SF; PHD finger superfamily

    3. NM_032458.3 → NP_115834.1  PHD finger protein 6 isoform 1

      See identical proteins and their annotated locations for NP_115834.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also called the 'PHF6b' variant) differs in the 3' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AB058726, AW297001, AY157622, BG122271
      Consensus CDS
      CCDS14639.1
      UniProtKB/Swiss-Prot
      A8K230, B4E0G4, D3DTG3, E9PC97, Q5JRC7, Q5JRC8, Q8IWS0, Q96JK3, Q9BRU0
      UniProtKB/TrEMBL
      Q5JRC6
      Related
      ENSP00000329097.3, ENST00000332070.7
      Conserved Domains (2) summary
      cd15710
      Location:17 → 131
      ePHD1_PHF6; Extended PHD finger 1 found in PHD finger protein 6 (PHF6)
      cd15711
      Location:212 → 329
      ePHD2_PHF6; Extended PHD finger 2 found in PHD finger protein 6 (PHF6)

    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

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      134373312..134428790
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      132698463..132753940
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IWS0.1 GenPept UniProtKB/Swiss-Prot:Q8IWS0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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