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PRDM4 PR/SET domain 4 [ Homo sapiens (human) ]

Gene ID: 11108, updated on 14-Nov-2024

Summary

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Official Symbol
PRDM4provided by HGNC
Official Full Name
PR/SET domain 4provided by HGNC
Primary source
HGNC:HGNC:9348
See related
Ensembl:ENSG00000110851 MIM:605780; AllianceGenome:HGNC:9348
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
PFM1
Summary
The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell differentiation and tumorigenesis. An elevated expression level of this gene has been observed in PC12 cells treated with nerve growth factor, beta polypeptide (NGF). This gene is located in a chromosomal region that is thought to contain tumor suppressor genes. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in kidney (RPKM 10.4), esophagus (RPKM 8.7) and 25 other tissues See more
Orthologs
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Genomic context

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See PRDM4 in Genome Data Viewer
Location:
12q23.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (107732871..107761137, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (107696363..107724788, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (108126648..108154914, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene PWP1 homolog, endonuclein Neighboring gene uncharacterized LOC124903010 Neighboring gene ribosomal protein L17 pseudogene 38 Neighboring gene PRDM4 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4823 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6956 Neighboring gene achaete-scute family bHLH transcription factor 4 Neighboring gene uncharacterized LOC105369963

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. The PR/SET domain in PRDM4 is preceded by a zinc knuckle. Briknarová K, et al. Proteins, 2011 Jul. PMID 21604305
  2. PFM1 (PRDM4), a new member of the PR-domain family, maps to a tumor suppressor locus on human chromosome 12q23-q24.1. Yang XH, et al. Genomics, 1999 Nov 1. PMID 10552934
  3. PRDM4 mediates YAP-induced cell invasion by activating leukocyte-specific integrin β2 expression. Liu H, et al. EMBO Rep, 2018 Jun. PMID 29669796, Free PMC Article
  4. Identification of Prdm genes in human corneal endothelium. Rolev K, et al. Exp Eye Res, 2017 Jun. PMID 28228349, Free PMC Article
  5. Control of the cell cycle by neurotrophins: lessons from the p75 neurotrophin receptor. López-Sánchez N, et al. Histol Histopathol, 2002 Oct. PMID 12371150

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. results demonstrate that YAP promotes cell invasion by inducing leukocyte-specific integrin expression, and identify PRDM4 as a novel transcription factor for YAP targets.
    Title: PRDM4 mediates YAP-induced cell invasion by activating leukocyte-specific integrin β2 expression.
  2. Both Prdm 4 and Prdm 5 are expressed in human corneal endothelium, primary hCECs and in HCECs-12 cells, characterised by expression of the Na(+)/K(+)-ATPase.
    Title: Identification of Prdm genes in human corneal endothelium.
  3. PRDM4 zinc knuckle by NMR spectroscopy.
    Title: The PR/SET domain in PRDM4 is preceded by a zinc knuckle.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

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
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
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)

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

  • MGC45046

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISS
Inferred from Sequence or Structural Similarity
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone methyltransferase binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of histone methyltransferase complex NAS
Non-traceable Author Statement
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
PR domain zinc finger protein 4
Names
PR domain 4
PR domain containing 4
PR domain-containing protein 4
PR-domain zinc-finger protein PFM1

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_012406.4 → NP_036538.3  PR domain zinc finger protein 4

    See identical proteins and their annotated locations for NP_036538.3

    Status: REVIEWED

    Source sequence(s)
    AK056378, AL133083, BU502236
    Consensus CDS
    CCDS9115.1
    UniProtKB/Swiss-Prot
    Q9UFA6, Q9UKN5
    UniProtKB/TrEMBL
    B3KPI0
    Related
    ENSP00000228437.5, ENST00000228437.10
    Conserved Domains (4) summary
    sd00017
    Location:620 → 640
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:618 → 640
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:632 → 657
    zf-H2C2_2; Zinc-finger double domain
    cl02566
    Location:426 → 533
    SET; SET domain

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    107732871..107761137 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005268593.2 → XP_005268650.1  PR domain zinc finger protein 4 isoform X1

    See identical proteins and their annotated locations for XP_005268650.1

    UniProtKB/TrEMBL
    B3KPI0
    Conserved Domains (4) summary
    sd00017
    Location:627 → 647
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:625 → 647
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:639 → 664
    zf-H2C2_2; Zinc-finger double domain
    cl02566
    Location:433 → 540
    SET; SET domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    107696363..107724788 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370847.1 → XP_054226822.1  PR domain zinc finger protein 4 isoform X2

    UniProtKB/Swiss-Prot
    Q9UFA6, Q9UKN5

  2. XM_054370846.1 → XP_054226821.1  PR domain zinc finger protein 4 isoform X1

  3. XM_054370845.1 → XP_054226820.1  PR domain zinc finger protein 4 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UKN5.3 GenPept UniProtKB/Swiss-Prot:Q9UKN5

Gene LinkOut

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

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