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    DPF3 double PHD fingers 3 [ Homo sapiens (human) ]

    Gene ID: 8110, updated on 28-Oct-2024

    Summary

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    Official Symbol
    DPF3provided by HGNC
    Official Full Name
    double PHD fingers 3provided by HGNC
    Primary source
    HGNC:HGNC:17427
    See related
    Ensembl:ENSG00000205683 MIM:601672; AllianceGenome:HGNC:17427
    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
    CERD4; BAF45C; SMARCG3
    Summary
    This gene encodes a member of the D4 protein family. The encoded protein is a transcription regulator that binds acetylated histones and is a component of the BAF chromatin remodeling complex. Alternate splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
    Expression
    Biased expression in ovary (RPKM 2.9), heart (RPKM 2.2) and 11 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DPF3 in Genome Data Viewer
    Location:
    14q24.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (72609034..72894101, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (66814656..67099787, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (73075742..73360809, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene regulator of G protein signaling 6 Neighboring gene uncharacterized LOC105370559 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:72917516-72918293 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:72923240-72923442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:72981479-72981979 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8686 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:73011529-73012307 Neighboring gene microRNA 7843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73066667-73067182 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:73085384-73086583 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:73087954-73088634 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:73109733-73110932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73118269-73119105 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73146128-73146975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73174572-73175072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:73208790-73209747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73257468-73257968 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:73276522-73277721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73318647-73319224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8689 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:73331388-73331571 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73342399-73343100 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr14:73343101-73343801 Neighboring gene MPRA-validated peak2194 silencer Neighboring gene Sharpr-MPRA regulatory region 237 Neighboring gene uncharacterized LOC107984711 Neighboring gene uncharacterized LOC124903429

    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. Non-canonical role for the BAF complex subunit DPF3 in mitosis and ciliogenesis. Verrillo G, et al. J Cell Sci, 2024 May 1. PMID 38661008, Free PMC Article
    2. Genetic polymorphisms in DPF3 associated with risk of breast cancer and lymph node metastases. Hoyal CR, et al. J Carcinog, 2005 Aug 19. PMID 16109180, Free PMC Article
    3. Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Zeng L, et al. Nature, 2010 Jul 8. PMID 20613843, Free PMC Article
    4. DPF3 polymorphisms increased the risk of pulmonary tuberculosis in the Northwest Chinese Han population. Liu C, et al. Gene, 2024 Nov 15. PMID 38795855
    5. The renal cancer risk allele at 14q24.2 activates a novel hypoxia-inducible transcription factor-binding enhancer of DPF3 expression. Protze J, et al. J Biol Chem, 2022 Mar. PMID 35148991, Free PMC Article

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DPF3 polymorphisms increased the risk of pulmonary tuberculosis in the Northwest Chinese Han population.
      Title: DPF3 polymorphisms increased the risk of pulmonary tuberculosis in the Northwest Chinese Han population.
    2. Non-canonical role for the BAF complex subunit DPF3 in mitosis and ciliogenesis.
      Title: Non-canonical role for the BAF complex subunit DPF3 in mitosis and ciliogenesis.
    3. The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-beta signaling.
      Title: The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling.
    4. The renal cancer risk allele at 14q24.2 activates a novel hypoxia-inducible transcription factor-binding enhancer of DPF3 expression.
      Title: The renal cancer risk allele at 14q24.2 activates a novel hypoxia-inducible transcription factor-binding enhancer of DPF3 expression.
    5. Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locus.
      Title: Altered regulation of DPF3, a member of the SWI/SNF complexes, underlies the 14q24 renal cancer susceptibility locus.
    6. downregulation of DPF3 plays an indispensable function in the progression of breast cancer
      Title: Downregulation of DPF3 promotes the proliferation and motility of breast cancer cells through activating JAK2/STAT3 signaling.
    7. DPF3 single nucleotide polymorphisms were significantly correlated with male infertility in a Japanese population.
      Title: Association of TUSC1 and DPF3 gene polymorphisms with male infertility.
    8. SLC1A1 and DPF3 were strongly associated with idiopathic male infertility and were significantly correlated with semen quality alterations
      Title: Strong association of SLC1A1 and DPF3 gene variants with idiopathic male infertility in Han Chinese.
    9. the high resolution crystal structure of the tandem PHD fingers of DPF3b in complex with an H3K14ac peptide.
      Title: Crystal structure of DPF3b in complex with an acetylated histone peptide.
    10. Activation of DPF3a upon hypertrophic stimuli in cardiac hypertrophy switches cardiac fetal gene expression from being silenced by HEY to being activated by BRG1.
      Title: Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    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)

    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

    • FLJ14079

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in chromatin remodeling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in muscle organ development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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 NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of SWI/SNF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of brahma complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in chromatin NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of nBAF complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    part_of nBAF complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    zinc finger protein DPF3
    Names
    BRG1-associated factor 45C
    D4, zinc and double PHD fingers, family 3
    zinc finger protein cer-d4

    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_001280542.3 → NP_001267471.1  zinc finger protein DPF3 isoform 2

      See identical proteins and their annotated locations for NP_001267471.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' CDS and the 3' UTR compared to variant 1. The encoded isoform (2, also known as DPF3b) has a distinct C-terminus and is longer than isoform 1.
      Source sequence(s)
      AC004828, AC006360, AC007160, AL392024
      Consensus CDS
      CCDS61497.1
      UniProtKB/Swiss-Prot
      A8MSI3, B7Z276, F5H575, Q32UJ0, Q6P9E6, Q6ZT41, Q92784, Q9H7Y5
      Related
      ENSP00000450518.1, ENST00000556509.6
      Conserved Domains (4) summary
      COG5189
      Location:195 → 222
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      cd15530
      Location:318 → 363
      PHD2_d4; PHD finger 2 found in d4 gene family proteins
      cd15692
      Location:261 → 317
      PHD1_DPF3; PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3)
      pfam14051
      Location:13 → 79
      Requiem_N; N-terminal domain of DPF2/REQ

    2. NM_001280543.2 → NP_001267472.1  zinc finger protein DPF3 isoform 3

      See identical proteins and their annotated locations for NP_001267472.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is longer than isoform 1.
      Source sequence(s)
      AC004828, AK123045, AK126074, AK294425, BC026305, DB172058
      Consensus CDS
      CCDS61495.1
      UniProtKB/Swiss-Prot
      Q92784
      Related
      ENSP00000481992.1, ENST00000614862.5
      Conserved Domains (2) summary
      pfam14051
      Location:23 → 94
      Requiem_N; N-terminal domain of DPF2/REQ
      cl22851
      Location:271 → 302
      PHD_SF; PHD finger superfamily

    3. NM_001280544.2 → NP_001267473.1  zinc finger protein DPF3 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) has a distinct N-terminus and is longer than isoform 1.
      Source sequence(s)
      AC004828, AC007160, AK124946, AK126933, BC026305
      Consensus CDS
      CCDS61496.1
      UniProtKB/TrEMBL
      F8W7T1
      Related
      ENSP00000381791.3, ENST00000366353.8
      Conserved Domains (2) summary
      pfam14051
      Location:68 → 139
      Requiem_N; N-terminal domain of DPF2/REQ
      cl22851
      Location:316 → 347
      PHD_SF; PHD finger superfamily

    4. NM_012074.5 → NP_036206.3  zinc finger protein DPF3 isoform 1

      See identical proteins and their annotated locations for NP_036206.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the shortest isoform (1, also known as DPF3a).
      Source sequence(s)
      AC004828, AK126933, BC026305, BC060801
      Consensus CDS
      CCDS45133.1
      UniProtKB/Swiss-Prot
      Q92784
      Related
      ENSP00000370614.4, ENST00000381216.8
      Conserved Domains (3) summary
      COG5189
      Location:195 → 222
      SFP1; Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
      pfam14051
      Location:13 → 79
      Requiem_N; N-terminal domain of DPF2/REQ
      cl22851
      Location:261 → 292
      PHD_SF; PHD finger superfamily

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      72609034..72894101 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      66814656..67099787 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q92784.3 GenPept UniProtKB/Swiss-Prot:Q92784

    Gene LinkOut

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

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