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    PRDM8 PR/SET domain 8 [ Homo sapiens (human) ]

    Gene ID: 56978, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PRDM8provided by HGNC
    Official Full Name
    PR/SET domain 8provided by HGNC
    Primary source
    HGNC:HGNC:13993
    See related
    Ensembl:ENSG00000152784 MIM:616639; AllianceGenome:HGNC:13993
    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
    PFM5; EPM10; KMT8D
    Summary
    This gene encodes a protein that belongs to a conserved family of histone methyltransferases that predominantly act as negative regulators of transcription. The encoded protein contains an N-terminal Su(var)3-9, Enhancer-of-zeste, and Trithorax (SET) domain and a double zinc-finger domain. Knockout of this gene in mouse results in mistargeting by neurons of the dorsal telencephalon, abnormal itch-like behavior, and impaired differentiation of rod bipolar cells. In humans, the protein has been shown to interact with the phosphatase laforin and the ubiquitin ligase malin, which regulate glycogen construction in the cytoplasm. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
    Expression
    Broad expression in prostate (RPKM 8.4), brain (RPKM 5.3) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    4q21.21
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (80185270..80204329)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (83515641..83534739)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (81106424..81125483)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900724 Neighboring gene CRISPRi-validated cis-regulatory element chr4.2002 Neighboring gene CRISPRi-validated cis-regulatory element chr4.2004 Neighboring gene ribosomal protein SA pseudogene 39 Neighboring gene CRISPRi-validated cis-regulatory element chr4.2006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15518 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15519 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15520 Neighboring gene Sharpr-MPRA regulatory region 11700 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:81111011-81111527 Neighboring gene PRDM8 antisense RNA 1 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:81111528-81112043 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:81117267-81117884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:81117885-81118500 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:81121978-81123177 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15521 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15522 Neighboring gene uncharacterized LOC124900725 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:81184495-81184996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:81187513-81188044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:81189787-81190357 Neighboring gene fibroblast growth factor 5

    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. PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation. Cypris O, et al. Clin Epigenetics, 2020 Aug 20. PMID 32819411, Free PMC Article
    2. PRDM8 internal promoter hyperhydroxymethylation correlates with increased expression of the corresponding transcript in Down syndrome. Lu Z, et al. Mol Med Rep, 2016 Aug. PMID 27278638
    3. DNA methylation in PRDM8 is indicative for dyskeratosis congenita. Weidner CI, et al. Oncotarget, 2016 Mar 8. PMID 26909595, Free PMC Article
    4. Transcription factor PRDM8 is required for rod bipolar and type 2 OFF-cone bipolar cell survival and amacrine subtype identity. Jung CC, et al. Proc Natl Acad Sci U S A, 2015 Jun 9. PMID 26023183, Free PMC Article
    5. PRDM8 exhibits antitumor activities toward hepatocellular carcinoma by targeting NAP1L1. Chen Z, et al. Hepatology, 2018 Sep. PMID 29572888

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation.
      Title: PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation.
    2. Through regulating NAP1L1, PRDM8 inhibits PI3K/AKT/mTOR signaling in hepatocellular carcinoma.
      Title: PRDM8 exhibits antitumor activities toward hepatocellular carcinoma by targeting NAP1L1.
    3. Aberrant hypermethylation is particularly observed in PRDM8 and this may support identification and classification of bone marrow failure syndromes
      Title: DNA methylation in PRDM8 is indicative for dyskeratosis congenita.
    4. alteration of hydroxymethylation and methylation of PRDM8 correlates with changes in its expression in the peripheral blood of children with DS. Given the proposed function of PRDM8 in cognitive disability in DS
      Title: PRDM8 internal promoter hyperhydroxymethylation correlates with increased expression of the corresponding transcript in Down syndrome.
    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

    Associated conditions

    Description Tests
    Early-onset Lafora body disease
    MedGen: C4225258 OMIM: 616640 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Gene-age interactions in blood pressure regulation: a large-scale investigation with the CHARGE, Global BPgen, and ICBP Consortia.
    EBI GWAS Catalog
    Genome-wide association study identifies eight loci associated with blood pressure.
    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)

    Genotypes

    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9 methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription corepressor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in corpus callosum morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in corticospinal tract morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in oligodendrocyte development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear body 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 

    General protein information

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    Preferred Names
    PR domain zinc finger protein 8
    Names
    PR domain 8
    PR-domain containing protein 8

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_046725.1 RefSeqGene

      Range
      17234..24060
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001099403.2 → NP_001092873.1  PR domain zinc finger protein 8

      See identical proteins and their annotated locations for NP_001092873.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AI077328, BC027929, BC058908, BC071584, BP219935
      Consensus CDS
      CCDS43243.1
      UniProtKB/Swiss-Prot
      A8K7X2, Q6IQ36, Q9NQV8
      Related
      ENSP00000406998.2, ENST00000415738.3
      Conserved Domains (3) summary
      sd00017
      Location:627 → 647
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:667 → 688
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:29 → 131
      SET; SET domain

    2. NM_020226.4 → NP_064611.3  PR domain zinc finger protein 8

      See identical proteins and their annotated locations for NP_064611.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AF275815, AI077328, BC027929, BC058908, BC071584
      Consensus CDS
      CCDS43243.1
      UniProtKB/Swiss-Prot
      A8K7X2, Q6IQ36, Q9NQV8
      Related
      ENSP00000339764.4, ENST00000339711.8
      Conserved Domains (3) summary
      sd00017
      Location:627 → 647
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:667 → 688
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:29 → 131
      SET; SET domain

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      80185270..80204329
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      83515641..83534739
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQV8.3 GenPept UniProtKB/Swiss-Prot:Q9NQV8

    Gene LinkOut

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

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