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    PHF10 PHD finger protein 10 [ Homo sapiens (human) ]

    Gene ID: 55274, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PHF10provided by HGNC
    Official Full Name
    PHD finger protein 10provided by HGNC
    Primary source
    HGNC:HGNC:18250
    See related
    Ensembl:ENSG00000130024 MIM:613069; AllianceGenome:HGNC:18250
    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
    BAF45A; XAP135; SMARCG4
    Summary
    This gene contains a predicted ORF that encodes a protein with two zinc finger domains. The function of the encoded protein is not known. Sequence analysis suggests that multiple alternatively spliced transcript variants are derived from this gene but the full-length nature of only two of them is known. These two splice variants encode different isoforms. A pseudogene for this gene is located on Xq28. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in adrenal (RPKM 31.1), ovary (RPKM 25.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PHF10 in Genome Data Viewer
    Location:
    6q27
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (169703902..169724500, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (171057816..171078422, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (170103998..170124596, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169829202-169829769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169849141-169850015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169850016-169850889 Neighboring gene WD repeat domain 27 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169952752-169953720 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:169956378-169956538 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:169964074-169964574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17796 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:170017112-170017650 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:170019030-170019674 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:170019675-170020319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170024255-170024754 Neighboring gene uncharacterized LOC124901471 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170040667-170041282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170047131-170048124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25463 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:170056229-170057024 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:170057025-170057820 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170061015-170061514 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:170062913-170064112 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:170067058-170067246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170067590-170068090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170068091-170068591 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170092723-170093223 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17797 Neighboring gene chromosome 6 open reading frame 120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17798 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:170124719-170125261 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17799 Neighboring gene MPRA-validated peak6328 silencer Neighboring gene dynein light chain Tctex-type 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170171824-170172324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:170172325-170172825 Neighboring gene ER membrane associated RNA degradation Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:170183046-170183546 Neighboring gene long intergenic non-protein coding RNA 242 Neighboring gene long intergenic non-protein coding RNA 574

    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. PHF10 is required for cell proliferation in normal and SV40-immortalized human fibroblast cells. Banga SS, et al. Cytogenet Genome Res, 2009. PMID 20068294, Free PMC Article
    2. The sequential phosphorylation of PHF10 subunit of the PBAF chromatin-remodeling complex determines different properties of the PHF10 isoforms. Sheynov AA, et al. Biol Open, 2020 Jan 15. PMID 31911482, Free PMC Article
    3. Mammalian cells contain two functionally distinct PBAF complexes incorporating different isoforms of PHF10 signature subunit. Brechalov AV, et al. Cell Cycle, 2014. PMID 24763304, Free PMC Article
    4. Stability of the PHF10 subunit of PBAF signature module is regulated by phosphorylation: role of β-TrCP. Tatarskiy VV, et al. Sci Rep, 2017 Jul 17. PMID 28717195, Free PMC Article
    5. [PHF10 isoforms are phosphorylated in the PBAF mammalian chromatin remodeling complex]. Brechalov AV, et al. Mol Biol (Mosk), 2016 Mar-Apr. PMID 27239853

    See all (83) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Neuronal and Muscle Differentiation of Mammalian Cells Is Accompanied by a Change in PHF10 Isoform Expression.
      Title: Neuronal and Muscle Differentiation of Mammalian Cells Is Accompanied by a Change in PHF10 Isoform Expression.
    2. ZC3H13-mediated N6-methyladenosine modification of PHF10 is impaired by fisetin which inhibits the DNA damage response in pancreatic cancer.
      Title: ZC3H13-mediated N6-methyladenosine modification of PHF10 is impaired by fisetin which inhibits the DNA damage response in pancreatic cancer.
    3. PHF10 subunit of PBAF complex mediates transcriptional activation by MYC.
      Title: PHF10 subunit of PBAF complex mediates transcriptional activation by MYC.
    4. The sequential phosphorylation of PHF10 subunit of the PBAF chromatin-remodeling complex determines different properties of the PHF10 isoforms.
      Title: The sequential phosphorylation of PHF10 subunit of the PBAF chromatin-remodeling complex determines different properties of the PHF10 isoforms.
    5. PHF10 expression in cells of different lines is activated by the c-MYC oncogene. Since PHF10 stimulates cell proliferation, its c-MYC-dependent activation in cancer cells should lead to an increase in their proliferation rate.
      Title: Oncogene c-MYC Controls the Expression of PHF10 Subunit of PBAF Chromatin Remodeling Complex in SW620 Cell Line.
    6. Data show that PHF10 subunit of the PBAF signature module is the most unstable PBAF subunit, and demonstrate an important role of beta-TrCP ubiquitin ligase in regulation of PHF10 level and PBAF in general. Also, PHF10 isoforms contained two non-canonical beta-TrCP degrons and are degraded by beta-TrCP in a phospho-dependent manner.
      Title: Stability of the PHF10 subunit of PBAF signature module is regulated by phosphorylation: role of β-TrCP.
    7. We studied the expression of S100A4 and the total PHF10 protein in some human cancer cell lines. We have found that, in the cell lines studied, the PHF10 expression is correlated with the S100A4 expression.
      Title: The level of the Phf10 protein, a PBAF chromatin-remodeling complex subunit, correlates with the Mts1/S100A4 expression in human cancer cell lines.
    8. Phosphorylation of PHF10 isoforms occurs while they are incorporated as a subunit of the PBAF complex, and therefore phosphorylation of PHF10 isoforms may play an essential role in regulation of PBAF complex's function and mechanism of action.
      Title: [PHF10 isoforms are phosphorylated in the PBAF mammalian chromatin remodeling complex].
    9. The study demonstrates the existence of functionally different PBAF complexes in mammalian cell. It also provides an insight into the molecular structure and role of human PHF10/BAF45a and characterizes it as an essential PBAF subunit.
      Title: Mammalian cells contain two functionally distinct PBAF complexes incorporating different isoforms of PHF10 signature subunit.
    10. PHF10 repressed caspase-3 expression and impaired the programmed cell death pathway in human gastric cancer at the transcriptional level.
      Title: A novel plant homeodomain finger 10-mediated antiapoptotic mechanism involving repression of caspase-3 in gastric cancer cells.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis of six type 1 diabetes cohorts identifies multiple associated loci.
    EBI GWAS Catalog
    Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10975, MGC111009

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone acetyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of T cell differentiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of cell differentiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of double-strand break repair NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of myoblast differentiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of stem cell population maintenance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of G0 to G1 transition NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of G1/S transition of mitotic cell cycle NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of mitotic metaphase/anaphase transition NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of nucleotide-excision repair 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
    		  
    involved_in regulation of transcription by RNA polymerase II NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of RSC-type complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of SWI/SNF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in kinetochore NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of npBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of npBAF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nuclear matrix NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    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 10
    Names
    BRG1-associated factor 45a
    BRG1-associated factor, 45-KD, A
    PHD zinc finger protein XAP135

    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.

    mRNA and Protein(s)

    1. NM_018288.4 → NP_060758.2  PHD finger protein 10 isoform a

      See identical proteins and their annotated locations for NP_060758.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform.
      Source sequence(s)
      AL513547, BC110323, DB460742
      Consensus CDS
      CCDS5308.2
      UniProtKB/Swiss-Prot
      Q2YDA3, Q53HG8, Q8WUB8, Q9BXD2, Q9NV26
      UniProtKB/TrEMBL
      S5FMB0
      Related
      ENSP00000341805.4, ENST00000339209.9
      Conserved Domains (3) summary
      cd15528
      Location:379 → 433
      PHD1_PHF10; PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins
      cd15529
      Location:435 → 478
      PHD2_PHF10; PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins
      cd21085
      Location:73 → 161
      WH_NTD_PHF10; N-terminal winged helix DNA-binding domain found in PHD finger protein 10 (PHF10) and similar proteins

    2. NM_133325.3 → NP_579866.2  PHD finger protein 10 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction which results in 6 fewer nt when compared to variant 1. It encodes an isoform (b) that lacks 2 internal amino acids compared to isoform a.
      Source sequence(s)
      AL513547
      Consensus CDS
      CCDS5309.2
      UniProtKB/TrEMBL
      S5FMB0
      Related
      ENSP00000355743.4, ENST00000366780.8
      Conserved Domains (2) summary
      cd15528
      Location:377 → 431
      PHD1_PHF10; PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins
      cd15529
      Location:433 → 476
      PHD2_PHF10; PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      169703902..169724500 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      171057816..171078422 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355780.1 → XP_054211755.1  PHD finger protein 10 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WUB8.3 GenPept UniProtKB/Swiss-Prot:Q8WUB8

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools