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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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See PRDM8 in Genome Data Viewer
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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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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