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

    Gene ID: 7799, updated on 3-Apr-2024

    Summary

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    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; AllianceGenome:HGNC:9347
    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
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    Genomic context

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    Location:
    1p36.21
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (13700188..13825079)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (13142270..13267189)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (14026683..14151574)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376756 Neighboring gene small Cajal body-specific RNA 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 288 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 217 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 219 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:14075835-14076053 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 220 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:14107388-14107556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:14119276-14119776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:14128246-14129019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:14130567-14131339 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:14129793-14130566 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 222 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:14170707-14171281 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_267 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:14273321-14273553 Neighboring gene kazrin, periplakin interacting protein Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_268 Neighboring gene MPRA-validated peak76 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:14462209-14462755 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:14462756-14463301 Neighboring gene RNA, U6 small nuclear 1265, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:14493737-14494238 Neighboring gene uncharacterized LOC107985467

    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
    • 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 absence of PRDM2 involved the tumorigenesis of somatotroph adenomas through regulating c-Myc. Wei D, et al. Gene, 2020 May 5. PMID 32044406
    2. RIZ1 and histone methylation status in pituitary adenomas. Xue Y, et al. Tumour Biol, 2017 Jul. PMID 28718376
    3. 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
    4. 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
    5. RIZ1: a potential tumor suppressor in glioma. Zhang C, et al. BMC Cancer, 2015 Dec 21. PMID 26690953, Free PMC Article

    See all (91) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RIZ2 at the crossroad of the EGF/EGFR signaling in colorectal cancer.
      Title: RIZ2 at the crossroad of the EGF/EGFR signaling in colorectal cancer.
    2. Exploring the putative role of PRDM1 and PRDM2 transcripts as mediators of T lymphocyte activation.
      Title: Exploring the putative role of PRDM1 and PRDM2 transcripts as mediators of T lymphocyte activation.
    3. PRDM2 negatively regulated the expression of c-Myc in somatotroph adenomas, and testified the synergism between PRDM2 gene therapy and c-Myc inhibitor in vitro experiment
      Title: The absence of PRDM2 involved the tumorigenesis of somatotroph adenomas through regulating c-Myc.
    4. The authors have found that overexpression of RIZ1 in HEK293 cells reduced the expression of Akt3 protein.
      Title: Repression of Akt3 gene transcription by the tumor suppressor RIZ1.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (52)

    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

    HIV-1 interactions

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    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables histone H3K9 trimethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in determination of adult lifespan IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    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_001380915.1
    NP_001380916.1
    NP_001380917.1
    NP_036363.2
    NP_056950.2
    XP_016857749.1
    XP_016857750.1
    XP_047285950.1
    XP_047285951.1
    XP_047285952.1
    XP_047285953.1
    XP_047285954.1
    XP_054194628.1
    XP_054194629.1
    XP_054194630.1
    XP_054194631.1
    XP_054194632.1
    XP_054194633.1
    XP_054194634.1

    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_001007257.3 → 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, AL031277, BC014468, BC032768, D45132, U17838
      Consensus CDS
      CCDS30603.1
      UniProtKB/TrEMBL
      Q59H82
      Related
      ENSP00000411103.1, ENST00000413440.5
      Conserved Domains (3) summary
      sd00017
      Location:935 → 955
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:161 → 181
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:159 → 181
      zf-C2H2; Zinc finger, C2H2 type

    2. NM_001135610.2 → 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, AL359771, BC014468, BU621515
      Consensus CDS
      CCDS44061.1
      UniProtKB/Swiss-Prot
      Q13029
      Related
      ENSP00000365216.5, ENST00000376048.9
      Conserved Domains (1) summary
      smart00317
      Location:28 → 147
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

    3. NM_001393986.1 → NP_001380915.1  PR domain zinc finger protein 2 isoform a

      Status: REVIEWED

      Source sequence(s)
      AL031277, AL359771, AL583942
      Consensus CDS
      CCDS150.1
      UniProtKB/Swiss-Prot
      B1AJZ4, B5MC68, Q13029, Q13149, Q14550, Q5THJ1, Q5VUL9
      UniProtKB/TrEMBL
      Q59H82
      Related
      ENSP00000312352.6, ENST00000311066.10
      Conserved Domains (5) summary
      sd00017
      Location:1136 → 1156
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:362 → 382
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd19188
      Location:23 → 145
      PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
      pfam00096
      Location:360 → 382
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:483 → 506
      zf-C2H2_4; C2H2-type zinc finger

    4. NM_001393987.1 → NP_001380916.1  PR domain zinc finger protein 2 isoform e

      Status: REVIEWED

      Source sequence(s)
      AL031277
      UniProtKB/TrEMBL
      Q59H82
      Conserved Domains (4) summary
      sd00017
      Location:935 → 955
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:161 → 181
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:159 → 181
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:282 → 305
      zf-C2H2_4; C2H2-type zinc finger

    5. NM_001393988.1 → NP_001380917.1  PR domain zinc finger protein 2 isoform c

      Status: REVIEWED

      Source sequence(s)
      AL031277
      Consensus CDS
      CCDS30603.1
      UniProtKB/TrEMBL
      Q59H82
      Related
      ENSP00000341621.4, ENST00000343137.8
      Conserved Domains (3) summary
      sd00017
      Location:935 → 955
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:161 → 181
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:159 → 181
      zf-C2H2; Zinc finger, C2H2 type

    6. NM_012231.5 → NP_036363.2  PR domain zinc finger protein 2 isoform a

      See identical proteins and their annotated locations for NP_036363.2

      Status: REVIEWED

      Source sequence(s)
      AL031277, AL359771, AL583942
      Consensus CDS
      CCDS150.1
      UniProtKB/Swiss-Prot
      B1AJZ4, B5MC68, Q13029, Q13149, Q14550, Q5THJ1, Q5VUL9
      UniProtKB/TrEMBL
      Q59H82
      Related
      ENSP00000235372.6, ENST00000235372.11
      Conserved Domains (5) summary
      sd00017
      Location:1136 → 1156
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:362 → 382
      ZF_C2H2; C2H2 Zn finger [structural motif]
      cd19188
      Location:23 → 145
      PR-SET_PRDM2; PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins
      pfam00096
      Location:360 → 382
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:483 → 506
      zf-C2H2_4; C2H2-type zinc finger

    7. NM_015866.6 → NP_056950.2  PR domain zinc finger protein 2 isoform b

      See identical proteins and their annotated locations for NP_056950.2

      Status: REVIEWED

      Source sequence(s)
      AL031277, AL359771, AL583942
      UniProtKB/TrEMBL
      Q59H82
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      13700188..13825079
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047429994.1 → XP_047285950.1  PR domain zinc finger protein 2 isoform X1

    2. XM_047429995.1 → XP_047285951.1  PR domain zinc finger protein 2 isoform X2

    3. XM_047429996.1 → XP_047285952.1  PR domain zinc finger protein 2 isoform X3

    4. XM_047429998.1 → XP_047285954.1  PR domain zinc finger protein 2 isoform X5

    5. XM_047429997.1 → XP_047285953.1  PR domain zinc finger protein 2 isoform X4

    6. XM_017002261.3 → XP_016857750.1  PR domain zinc finger protein 2 isoform X4

      UniProtKB/TrEMBL
      Q59H82
      Conserved Domains (4) summary
      sd00017
      Location:935 → 955
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:161 → 181
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:159 → 181
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:282 → 305
      zf-C2H2_4; C2H2-type zinc finger

    7. XM_017002260.3 → XP_016857749.1  PR domain zinc finger protein 2 isoform X4

      UniProtKB/TrEMBL
      Q59H82
      Conserved Domains (4) summary
      sd00017
      Location:935 → 955
      ZF_C2H2; C2H2 Zn finger [structural motif]
      sd00019
      Location:161 → 181
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:159 → 181
      zf-C2H2; Zinc finger, C2H2 type
      pfam13894
      Location:282 → 305
      zf-C2H2_4; C2H2-type zinc finger

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      13142270..13267189
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338653.1 → XP_054194628.1  PR domain zinc finger protein 2 isoform X1

    2. XM_054338654.1 → XP_054194629.1  PR domain zinc finger protein 2 isoform X2

    3. XM_054338655.1 → XP_054194630.1  PR domain zinc finger protein 2 isoform X3

    4. XM_054338659.1 → XP_054194634.1  PR domain zinc finger protein 2 isoform X5

    5. XM_054338656.1 → XP_054194631.1  PR domain zinc finger protein 2 isoform X4

    6. XM_054338658.1 → XP_054194633.1  PR domain zinc finger protein 2 isoform X4

    7. XM_054338657.1 → XP_054194632.1  PR domain zinc finger protein 2 isoform X4

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

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