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    PRDM6 PR/SET domain 6 [ Homo sapiens (human) ]

    Gene ID: 93166, updated on 8-Dec-2022

    Summary

    Official Symbol
    PRDM6provided by HGNC
    Official Full Name
    PR/SET domain 6provided by HGNC
    Primary source
    HGNC:HGNC:9350
    See related
    Ensembl:ENSG00000061455 MIM:616982; AllianceGenome:HGNC:9350
    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
    PDA3; KMT8C; PRISM
    Summary
    The protein encoded by this gene is a transcriptional repressor and a member of the PRDM family. Family members contain a PR domain and multiple zinc-finger domains. The encoded protein is involved in regulation of vascular smooth muscle cells (VSMC) contractile proteins. Mutations in this gene result in patent ductus arteriosus 3 (PDA3). [provided by RefSeq, Apr 2017]
    Expression
    Broad expression in gall bladder (RPKM 2.3), placenta (RPKM 2.0) and 16 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PRDM6 in Genome Data Viewer
    Location:
    5q23.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    110 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (123089241..123194266)
    110 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (123605724..123710965)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (122424936..122529960)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PPIC antisense RNA 1 Neighboring gene peptidylprolyl isomerase C Neighboring gene RNA, 7SL, cytoplasmic 711, pseudogene Neighboring gene PRDM6 antisense RNA 1 Neighboring gene SUMO1 pseudogene 5 Neighboring gene centrosomal protein 120 Neighboring gene keratin 8 pseudogene 33

    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
    Patent ductus arteriosus 3
    MedGen: C4310753 OMIM: 617039 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2017-12-14)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2017-12-14)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk.
    EBI GWAS Catalog
    Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables histone H4K20 monomethyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in histone methylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of smooth muscle cell differentiation 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 neurogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    putative histone-lysine N-methyltransferase PRDM6
    Names
    PR domain 6
    PR domain containing 6
    PR domain-containing protein 6
    PR-domain zinc finger protein 6
    NP_001129711.1
    XP_011542028.1
    XP_047273834.1

    NCBI Reference Sequences (RefSeq)

    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_053114.1 RefSeqGene

      Range
      5139..110164
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001136239.4NP_001129711.1  putative histone-lysine N-methyltransferase PRDM6

      See identical proteins and their annotated locations for NP_001129711.1

      Status: REVIEWED

      Source sequence(s)
      AC008548, AC106786
      Consensus CDS
      CCDS47259.1
      UniProtKB/Swiss-Prot
      Q9NQW9, Q9NQX0
      Related
      ENSP00000384725.3, ENST00000407847.5
      Conserved Domains (5) summary
      COG5048
      Location:404584
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:503523
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:501523
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:260365
      SET; SET domain
      pfam13465
      Location:544568
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      123089241..123194266
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417878.1XP_047273834.1  putative histone-lysine N-methyltransferase PRDM6 isoform X2

    2. XM_011543726.4XP_011542028.1  putative histone-lysine N-methyltransferase PRDM6 isoform X1

      Conserved Domains (5) summary
      COG5048
      Location:306378
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:303323
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:301323
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:60165
      SET; SET domain
      pfam13465
      Location:344368
      zf-H2C2_2; Zinc-finger double domain

    RNA

    1. XR_001742346.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      123605724..123710965
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)