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

Gene ID: 8110, updated on 14-Nov-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
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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)

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 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
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
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

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