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

Gene ID: 55274, updated on 2-Nov-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
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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)

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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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