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

Gene ID: 93166, updated on 17-Jun-2019

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
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

Genomic context

See PRDM6 in Genome Data Viewer
Location:
5q23.2
Exon count:
11
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (123089148..123194266)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (122424841..122529960)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene sorting nexin 24 Neighboring gene uncharacterized LOC107986447 Neighboring gene peptidylprolyl isomerase C Neighboring gene uncharacterized LOC105379152 Neighboring gene RNA, 7SL, cytoplasmic 711, pseudogene 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

NHGRI GWAS Catalog

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

Pathways from BioSystems

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 transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone-lysine N-methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
histone lysine methylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of smooth muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neurogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
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

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_053114.1 RefSeqGene

    Range
    5001..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
    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 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    123089148..123194266
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543726.3XP_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_948304.1 RNA Sequence

  2. XR_001742346.1 RNA Sequence

  3. XR_948305.1 RNA Sequence

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