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

Summary

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: mouse all
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Genomic context

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_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
PRDM4 zinc knuckle by NMR spectroscopy.
Title: The PR/SET domain in PRDM4 is preceded by a zinc knuckle.
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 EBI GWAS CatalogPubMed

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

STS-AA005240 (e-PCR)
- UniSTS:33899

WI-18626 (e-PCR)
- UniSTS:67188

STS-T67867 (e-PCR)
- UniSTS:80783

G20329 (e-PCR)
- UniSTS:81063

A005M11 (e-PCR)
- UniSTS:81064

G54223 (e-PCR)
- UniSTS:109490

RH79609 (e-PCR)
- UniSTS:90065

RH103160 (e-PCR)
- UniSTS:97494

RH93454 (e-PCR)
- UniSTS:91879

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	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 cell fate commitment	IBA Inferred from Biological aspect of Ancestor more info
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 transcription by RNA polymerase II	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
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
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)

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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

107732871..107761137 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060936.1 Alternate T2T-CHM13v2.0

Range

107696363..107724788 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q9UFA6, Q9UKN5
XM_054370846.1 → XP_054226821.1 PR domain zinc finger protein 4 isoform X1
XM_054370845.1 → XP_054226820.1 PR domain zinc finger protein 4 isoform X1