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    PRDM16 PR/SET domain 16 [ Homo sapiens (human) ]

    Gene ID: 63976, updated on 8-Jul-2021

    Summary

    Official Symbol
    PRDM16provided by HGNC
    Official Full Name
    PR/SET domain 16provided by HGNC
    Primary source
    HGNC:HGNC:14000
    See related
    Ensembl:ENSG00000142611 MIM:605557
    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
    MEL1; KMT8F; LVNC8; PFM13; CMD1LL
    Summary
    The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). This gene is located near the 1p36.3 breakpoint and has been shown to be specifically expressed in the t(1:3)(p36,q21)-positive MDS/AML. The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal PR domain. The translocation results in the overexpression of a truncated version of this protein that lacks the PR domain, which may play an important role in the pathogenesis of MDS and AML. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in stomach (RPKM 3.4), thyroid (RPKM 3.1) and 17 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See PRDM16 in Genome Data Viewer
    Location:
    1p36.32
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (3069203..3438621)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (2985767..3355185)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene opioid growth factor receptor pseudogene Neighboring gene actin related protein T2 Neighboring gene PRDM16 divergent transcript Neighboring gene uncharacterized LOC105378606 Neighboring gene microRNA 4251 Neighboring gene uncharacterized LOC107984909 Neighboring gene uncharacterized LOC105378605 Neighboring gene Sharpr-MPRA regulatory region 1148 Neighboring gene VISTA enhancer hs705 Neighboring gene Sharpr-MPRA regulatory region 1987 Neighboring gene uncharacterized LOC105378604 Neighboring gene Sharpr-MPRA regulatory region 11957 Neighboring gene VISTA enhancer hs1912 Neighboring gene Rho guanine nucleotide exchange factor 16 Neighboring gene MEGF6 intron CAGE-defined mid-level expression enhancer Neighboring gene multiple EGF like domains 6

    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 Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Genome-wide association of lipid-lowering response to statins in combined study populations.
    GeneReviews: Not available
    Genome-wide association study reveals three susceptibility loci for common migraine in the general population.
    GeneReviews: Not available
    Genome-wide meta-analysis identifies new susceptibility loci for migraine.
    GeneReviews: Not available
    Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
    GeneReviews: Not available
    Integrated Genome-wide Association, Coexpression Network, and Expression Single Nucleotide Polymorphism Analysis Identifies Novel Pathway in Allergic Rhinitis.
    GeneReviews: Not available
    Left ventricular noncompaction 8
    MedGen: C3809288 OMIM: 615373 GeneReviews: Not available
    Compare labs

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA1675, MGC166915

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in brown fat cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in heterochromatin organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in histone H3-K9 methylation 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 negative regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transcription, DNA-templated ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT involved_in negative regulation of transforming growth factor beta receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of transforming growth factor beta receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription, DNA-templated ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cellular respiration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in aggresome IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of transcription repressor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    histone-lysine N-methyltransferase PRDM16
    Names
    MDS1/EVI1-like gene 1
    PR domain 16
    PR domain containing 16
    PR domain zinc finger protein 16
    transcription factor MEL1
    NP_071397.3
    NP_955533.2

    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_029576.2 RefSeqGene

      Range
      5026..374444
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_022114.4NP_071397.3  histone-lysine N-methyltransferase PRDM16 isoform 1

      See identical proteins and their annotated locations for NP_071397.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL354743, BC161614, BX092842
      Consensus CDS
      CCDS41236.2
      UniProtKB/Swiss-Prot
      Q9HAZ2
      Related
      ENSP00000270722.5, ENST00000270722.10
      Conserved Domains (6) summary
      smart00317
      Location:84209
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      COG5048
      Location:9311083
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:953973
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:951973
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:965989
      zf-H2C2_2; Zinc-finger double domain
      pfam15909
      Location:369450
      zf-C2H2_8; C2H2-type zinc ribbon
    2. NM_199454.3NP_955533.2  histone-lysine N-methyltransferase PRDM16 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AB078876, AI623202, AL354743, BX092842
      Consensus CDS
      CCDS44048.2
      UniProtKB/Swiss-Prot
      Q9HAZ2
      Related
      ENSP00000367643.2, ENST00000378391.6
      Conserved Domains (6) summary
      smart00317
      Location:84209
      SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
      COG5048
      Location:9311083
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:953973
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:951973
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:965989
      zf-H2C2_2; Zinc-finger double domain
      pfam15909
      Location:369450
      zf-C2H2_8; C2H2-type zinc ribbon

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      3069203..3438621
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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