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

    Gene ID: 93166, updated on 7-Apr-2024

    Summary

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    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
    mouse all
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    Genomic context

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    Location:
    5q23.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (123089241..123194266)
    RS_2023_10 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 ATAC-STARR-seq lymphoblastoid silent region 16272 Neighboring gene PPIC antisense RNA 1 Neighboring gene peptidylprolyl isomerase C Neighboring gene RNA, 7SL, cytoplasmic 711, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:122423586-122424130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:122424131-122424675 Neighboring gene PRDM6 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr5:122486848-122487353 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:122493602-122493821 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:122498660-122499160 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:122551508-122552100 Neighboring gene SUMO1 pseudogene 5 Neighboring gene centrosomal protein 120 Neighboring gene keratin 8 pseudogene 33

    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. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. Li N, et al. Am J Hum Genet, 2016 Oct 6. PMID 27716515, Free PMC Article
    2. Genetic architecture of human thinness compared to severe obesity. Riveros-McKay F, et al. PLoS Genet, 2019 Jan. PMID 30677029, Free PMC Article
    3. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus. Li N, et al. Am J Hum Genet, 2016 Jun 2. PMID 27181681, Free PMC Article
    4. PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells. Davis CA, et al. Mol Cell Biol, 2006 Apr. PMID 16537907, Free PMC Article
    5. Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians. Hong KW, et al. Hum Mol Genet, 2014 Dec 15. PMID 25035420

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Patent ductus arteriosus and coarctation of the aorta in association with PRDM6 variants.
      Title: Patent ductus arteriosus and coarctation of the aorta in association with PRDM6 variants.
    2. we detected a novel obesity and BMI-associated locus at PKHD1 and novel variants driving associations at previously established signals (e.g. rs205262 at the SNRPC/C6orf106 locus and rs112446794 at the PRDM6-CEP120 locus).
      Title: Genetic architecture of human thinness compared to severe obesity.
    3. Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus.
      Title: Mutations in the Histone Modifier PRDM6 Are Associated with Isolated Nonsyndromic Patent Ductus Arteriosus.
    4. Three novel loci were identified in East Asians with cardiac arrhythmias: rs2483280 (PRDM16 locus) and rs335206 (PRDM6 locus) were associated with QRS duration; and rs17026156 (SLC8A1 locus) correlated with PR interval.
      Title: Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
    5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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
    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

    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 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 remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in 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
    		  
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    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
    XP_054209774.1
    XP_054209775.1

    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.

    Genomic

    1. NG_053114.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001136239.4 → NP_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
      B5MCJ4, Q9NQW9, Q9NQX0
      Related
      ENSP00000384725.3, ENST00000407847.5
      Conserved Domains (5) summary
      COG5048
      Location:404 → 584
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:503 → 523
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:501 → 523
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:260 → 365
      SET; SET domain
      pfam13465
      Location:544 → 568
      zf-H2C2_2; Zinc-finger double 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_000005.10 Reference GRCh38.p14 Primary Assembly

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

    mRNA and Protein(s)

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

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

      Conserved Domains (5) summary
      COG5048
      Location:306 → 378
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:303 → 323
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:301 → 323
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:60 → 165
      SET; SET domain
      pfam13465
      Location:344 → 368
      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)

    mRNA and Protein(s)

    1. XM_054353800.1 → XP_054209775.1  putative histone-lysine N-methyltransferase PRDM6 isoform X2

    2. XM_054353799.1 → XP_054209774.1  putative histone-lysine N-methyltransferase PRDM6 isoform X1

    RNA

    1. XR_008487198.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQX0.2 GenPept UniProtKB/Swiss-Prot:Q9NQX0

    Gene LinkOut

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

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