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

Gene ID: 56978, updated on 1-Jun-2020

Summary

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
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

Genomic context

See PRDM8 in Genome Data Viewer
Location:
4q21.21
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (80183418..80204329)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (81105033..81125483)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene CRISPRi-validated cis-regulatory element chr4.2006 Neighboring gene uncharacterized LOC105377303 Neighboring gene ribosomal protein SA pseudogene 39 Neighboring gene fibroblast growth factor 5 Neighboring gene mitochondrial ribosomal protein S25 pseudogene 1 Neighboring gene cilia and flagella associated protein 299

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

Associated conditions

Description Tests
Epilepsy, progressive myoclonic, 10
MedGen: C4225258 OMIM: 616640 GeneReviews: Not available
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NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
methylation IEA
Inferred from Electronic Annotation
more info
 
oligodendrocyte development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    5001..24060
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001099403.2NP_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
    Q9NQV8
    UniProtKB/TrEMBL
    A0A024RDC4, Q05CA1
    Related
    ENSP00000406998.2, ENST00000415738.3
    Conserved Domains (3) summary
    sd00017
    Location:627647
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:667688
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:29131
    SET; SET domain
  2. NM_020226.3NP_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
    Q9NQV8
    UniProtKB/TrEMBL
    A0A024RDC4, Q05CA1
    Related
    ENSP00000339764.4, ENST00000339711.8
    Conserved Domains (3) summary
    sd00017
    Location:627647
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:667688
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:29131
    SET; SET domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    80183418..80204329
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532135.2XP_011530437.1  PR domain zinc finger protein 8 isoform X3

    Conserved Domains (3) summary
    sd00017
    Location:861881
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:901922
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:262364
    SET; SET domain
  2. XM_011532133.2XP_011530435.1  PR domain zinc finger protein 8 isoform X2

    Conserved Domains (3) summary
    sd00017
    Location:908928
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:948969
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:309411
    SET; SET domain
  3. XM_005263144.2XP_005263201.1  PR domain zinc finger protein 8 isoform X7

    See identical proteins and their annotated locations for XP_005263201.1

    Conserved Domains (3) summary
    sd00017
    Location:628648
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:668689
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:29131
    SET; SET domain
  4. XM_005263145.2XP_005263202.1  PR domain zinc finger protein 8 isoform X7

    See identical proteins and their annotated locations for XP_005263202.1

    Conserved Domains (3) summary
    sd00017
    Location:628648
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:668689
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:29131
    SET; SET domain
  5. XM_011532141.3XP_011530443.1  PR domain zinc finger protein 8 isoform X6

    Conserved Domains (3) summary
    sd00017
    Location:766786
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:806827
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:167269
    SET; SET domain
  6. XM_011532140.2XP_011530442.1  PR domain zinc finger protein 8 isoform X5

    See identical proteins and their annotated locations for XP_011530442.1

    Conserved Domains (3) summary
    sd00017
    Location:812832
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:852873
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:213315
    SET; SET domain
  7. XM_005263146.4XP_005263203.1  PR domain zinc finger protein 8 isoform X8

    See identical proteins and their annotated locations for XP_005263203.1

    UniProtKB/Swiss-Prot
    Q9NQV8
    UniProtKB/TrEMBL
    A0A024RDC4
    Related
    ENSP00000423985.1, ENST00000504452.5
    Conserved Domains (3) summary
    sd00017
    Location:627647
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:667688
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:29131
    SET; SET domain
  8. XM_017008469.1XP_016863958.1  PR domain zinc finger protein 8 isoform X4

  9. XM_017008470.1XP_016863959.1  PR domain zinc finger protein 8 isoform X5

    Conserved Domains (3) summary
    sd00017
    Location:812832
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:852873
    zf-C2H2; Zinc finger, C2H2 type
    pfam00856
    Location:213315
    SET; SET domain
  10. XM_017008468.1XP_016863957.1  PR domain zinc finger protein 8 isoform X1

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