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PRDM2 PR/SET domain 2 [ Homo sapiens (human) ]

Gene ID: 7799, updated on 3-Jun-2018
Official Symbol
PRDM2provided by HGNC
Official Full Name
PR/SET domain 2provided by HGNC
Primary source
HGNC:HGNC:9347
See related
Ensembl:ENSG00000116731 MIM:601196; Vega:OTTHUMG00000007917
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
RIZ; KMT8; RIZ1; RIZ2; KMT8A; MTB-ZF; HUMHOXY1
Summary
This tumor suppressor gene is a member of a nuclear histone/protein methyltransferase superfamily. It encodes a zinc finger protein that can bind to retinoblastoma protein, estrogen receptor, and the TPA-responsive element (MTE) of the heme-oxygenase-1 gene. Although the functions of this protein have not been fully characterized, it may (1) play a role in transcriptional regulation during neuronal differentiation and pathogenesis of retinoblastoma, (2) act as a transcriptional activator of the heme-oxygenase-1 gene, and (3) be a specific effector of estrogen action. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 10.7), ovary (RPKM 8.6) and 25 other tissues See more
Orthologs
mouse all
See PRDM2 in Genome Data Viewer
Location:
1p36.21
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (13698874..13825079)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (14026714..14151574)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378612 Neighboring gene uncharacterized LOC105376756 Neighboring gene kazrin, periplakin interacting protein Neighboring gene RNA, U6 small nuclear 1265, pseudogene Neighboring gene uncharacterized LOC107985467

Go to nucleotide: Graphics FASTA GenBank

  • Project title: 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 Jun 15 11:32:44 2016

Related articles in PubMed

  1. RIZ1 and histone methylation status in pituitary adenomas. Xue Y, et al. Tumour Biol, 2017 Jul. PMID 28718376
  2. A deletion polymorphism in the RIZ gene is associated with increased progression of imatinib treated chronic myeloid leukemia patients. Mir R, et al. Leuk Lymphoma, 2017 Jul. PMID 27830966
  3. Methylation Status of the RIZ1 Gene Promoter in Human Glioma Tissues and Cell Lines. Zhang C, et al. Cell Mol Neurobiol, 2017 Aug. PMID 27757741
  4. RIZ1: a potential tumor suppressor in glioma. Zhang C, et al. BMC Cancer, 2015 Dec 21. PMID 26690953, Free PMC Article
  5. Aberrant Methylation of the 1p36 Tumor Suppressor Gene RIZ1 in Renal Cell Carcinoma. Ge P, et al. Asian Pac J Cancer Prev, 2015. PMID 25987089

See all (79) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  1. Promoter hypermethylation may play an important role in the epigenetic silencing of RIZ1 expression in human glioma tissues and glioblastoma cell lines.
    Title: Methylation Status of the RIZ1 Gene Promoter in Human Glioma Tissues and Cell Lines.
  2. the Pro704 p-/- allele of RIZ is significantly more common in CML patients with Loss of hematological response than good responders (p = .001). We showed that LOH p-/- homozygosity of RIZ1 was common event in BC than proline p+/+ homozygosity and proline p+/+ homozygosity more common feature in CP phase CML.
    Title: A deletion polymorphism in the RIZ gene is associated with increased progression of imatinib treated chronic myeloid leukemia patients.
  3. Promoter region methylation of RIZ1 may play an important role in the epigenetic silencing of RIZ1 expression in pituitary adenomas, which may translate into important diagnostic and therapeutic applications
    Title: RIZ1 and histone methylation status in pituitary adenomas.
  4. RIZ1 expression is negatively correlated with glioma differentiation and can serve as a predictor of glioma prognosis and thus could be a potential therapeutic target for patients with gliomas.
    Title: RIZ1: a potential tumor suppressor in glioma.
  5. Loss of RIZ1 expression due to methylation is associated with Renal Cell Carcinoma.
    Title: Aberrant Methylation of the 1p36 Tumor Suppressor Gene RIZ1 in Renal Cell Carcinoma.
  6. PRDM2 downregulation may play a role in dopamine-agonist resistance and tumor recurrence in prolactinomas.
    Title: Lower PRDM2 expression is associated with dopamine-agonist resistance and tumor recurrence in prolactinomas.
  7. Results suggest that high expression of SMYD3 is related to the occurrence of esophageal squamous cell carcinoma. Also, its suppression promoted the expression of RIZ1 suggesting a signal transduction pathway between SMYD3 and RIZ1.
    Title: Effect of the downregulation of SMYD3 expression by RNAi on RIZ1 expression and proliferation of esophageal squamous cell carcinoma.
  8. PRDM2, PRDM5, PRDM16 promoters are methylated and their expression is suppressed in lung cancer cells.
    Title: Methylation of PRDM2, PRDM5 and PRDM16 genes in lung cancer cells.
  9. The development and progression of esophageal squamous cell carcinoma are related to the inactivation of RIZ1.
    Title: Alteration in gene expression profile and oncogenicity of esophageal squamous cell carcinoma by RIZ1 upregulation.
  10. RIZ1 expression is significantly downregulated as the formation of meningiomas progressed, and suggest that RIZ1 may represent a promising candidate tumor suppressor gene that contributes to malignant meningiomas.
    Title: Retinoblastoma protein-interacting zinc-finger gene 1 (RIZ1) dysregulation in human malignant meningiomas.
Submit: New GeneRIF Correction See all GeneRIFs (48)

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Replication interactions

Interaction Pubs
Knockdown of PR domain containing 2, with ZNF domain (PRDM2) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
 PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
RNA polymerase II transcription factor activity, sequence-specific DNA binding ISA
Inferred from Sequence Alignment
more info
  
RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM
Inferred from Sequence Model
more info
 PubMed 
RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS
Non-traceable Author Statement
more info
 PubMed 
chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
histone-lysine N-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
zinc ion binding NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
determination of adult lifespan IEA
Inferred from Electronic Annotation
more info
  
histone lysine methylation IEA
Inferred from Electronic Annotation
more info
  
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
 PubMed 
transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
  
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
Preferred Names
PR domain zinc finger protein 2
Names
GATA-3 binding protein G3B
MTE-binding protein
PR domain 2
PR domain containing 2, with ZNF domain
PR domain-containing protein 2
lysine N-methyltransferase 8
retinoblastoma protein-binding zinc finger protein
retinoblastoma protein-interacting zinc finger protein
zinc finger protein RIZ
zinc-finger DNA-binding protein
NP_001007258.1
NP_001129082.1
NP_036363.2
NP_056950.2
XP_016857744.1
XP_016857745.1
XP_016857746.1
XP_016857748.1
XP_016857749.1
XP_016857750.1
XP_016857751.1
XP_016857752.1
XP_016857753.1

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_001007257.2 → NP_001007258.1  PR domain zinc finger protein 2 isoform c

    See identical proteins and their annotated locations for NP_001007258.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) is shorter at the 5' end and differs in the 3' UTR and coding region compared to variant 1. Expression of this transcript is under the control of an internal promoter in the gene (PMID: 9006946), which is why it is shorter at the 5' end than variant 1. The resulting isoform (c, also called RIZ2) is shorter at the N-terminus and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AI651991, BC014468, BC032768, D45132, U17838
    Consensus CDS
    CCDS30603.1
    UniProtKB/Swiss-Prot
    Q13029
    Related
    ENSP00000411103.1, OTTHUMP00000009686, ENST00000413440.5, OTTHUMT00000021940
    Conserved Domains (2) summary
    sd00017
    Location:935 → 955
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:159 → 181
    zf-C2H2; Zinc finger, C2H2 type

  2. NM_001135610.1 → NP_001129082.1  PR domain zinc finger protein 2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an alternate 5' UTR and lacks two internal coding exons compared to variant 1. The resulting isoform (d) is much shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AK307377, AL031277, BC014468, BU621515
    Consensus CDS
    CCDS44061.1
    UniProtKB/Swiss-Prot
    Q13029
    Related
    ENSP00000365216.5, OTTHUMP00000009685, ENST00000376048.9, OTTHUMT00000021939
    Conserved Domains (1) summary
    smart00317
    Location:28 → 147
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

  3. NM_012231.4 → NP_036363.2  PR domain zinc finger protein 2 isoform a

    See identical proteins and their annotated locations for NP_036363.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a, also called RIZ1).
    Source sequence(s)
    AK311678, AL031277, AL359771, BC014468, BU621515, D45132, U17838
    Consensus CDS
    CCDS150.1
    UniProtKB/Swiss-Prot
    Q13029
    Related
    ENSP00000235372.6, OTTHUMP00000009642, ENST00000235372.11, OTTHUMT00000021792
    Conserved Domains (3) summary
    smart00317
    Location:28 → 147
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    sd00017
    Location:1136 → 1156
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:360 → 382
    zf-C2H2; Zinc finger, C2H2 type

  4. NM_015866.4 → NP_056950.2  PR domain zinc finger protein 2 isoform b

    See identical proteins and their annotated locations for NP_056950.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding region compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AI651991, AL359771, BC014468, BC032768, D45132, U17838
    Consensus CDS
    CCDS151.1
    UniProtKB/Swiss-Prot
    Q13029
    Related
    ENSP00000312352.5, ENST00000311066.9
    Conserved Domains (4) summary
    smart00317
    Location:28 → 147
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    sd00017
    Location:1136 → 1156
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:362 → 382
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:360 → 382
    zf-C2H2; Zinc finger, C2H2 type

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    13698874..13825079
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002264.2 → XP_016857753.1  PR domain zinc finger protein 2 isoform X5

  2. XM_017002256.1 → XP_016857745.1  PR domain zinc finger protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q13029
    Conserved Domains (3) summary
    smart00317
    Location:28 → 147
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    sd00017
    Location:1136 → 1156
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:360 → 382
    zf-C2H2; Zinc finger, C2H2 type

  3. XM_017002255.1 → XP_016857744.1  PR domain zinc finger protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q13029
    Conserved Domains (3) summary
    smart00317
    Location:28 → 147
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    sd00017
    Location:1136 → 1156
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:360 → 382
    zf-C2H2; Zinc finger, C2H2 type

  4. XM_017002257.1 → XP_016857746.1  PR domain zinc finger protein 2 isoform X2

    UniProtKB/Swiss-Prot
    Q13029
    Conserved Domains (4) summary
    smart00317
    Location:28 → 147
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    sd00017
    Location:1136 → 1156
    ZF_C2H2; C2H2 Zn finger [structural motif]
    sd00019
    Location:362 → 382
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:360 → 382
    zf-C2H2; Zinc finger, C2H2 type

  5. XM_017002259.2 → XP_016857748.1  PR domain zinc finger protein 2 isoform X3

    UniProtKB/Swiss-Prot
    Q13029

  6. XM_017002262.1 → XP_016857751.1  PR domain zinc finger protein 2 isoform X4

    UniProtKB/Swiss-Prot
    Q13029
    Related
    ENSP00000341621.4, OTTHUMP00000009687, ENST00000343137.8, OTTHUMT00000021941
    Conserved Domains (2) summary
    sd00017
    Location:935 → 955
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:159 → 181
    zf-C2H2; Zinc finger, C2H2 type

  7. XM_017002261.2 → XP_016857750.1  PR domain zinc finger protein 2 isoform X3

    UniProtKB/Swiss-Prot
    Q13029

  8. XM_017002263.2 → XP_016857752.1  PR domain zinc finger protein 2 isoform X3

    UniProtKB/Swiss-Prot
    Q13029

  9. XM_017002260.2 → XP_016857749.1  PR domain zinc finger protein 2 isoform X3

    UniProtKB/Swiss-Prot
    Q13029

RNA

  1. XR_002957562.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13029.3 GenPept UniProtKB/Swiss-Prot:Q13029

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