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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
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Genomic context

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See PRDM6 in Genome Data Viewer
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
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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

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