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

Gene ID: 63976, updated on 13-Mar-2020

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

Genomic context

See PRDM16 in Genome Data Viewer
Location:
1p36.32
Exon count:
17
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (3069203..3438621)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (2985565..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 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
Left ventricular noncompaction 8
MedGen: C3809288 OMIM: 615373 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association of lipid-lowering response to statins in combined study populations.
NHGRI GWA Catalog
Genome-wide association study reveals three susceptibility loci for common migraine in the general population.
NHGRI GWA Catalog
Genome-wide meta-analysis identifies new susceptibility loci for migraine.
NHGRI GWA Catalog
Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
NHGRI GWA Catalog
Integrated Genome-wide Association, Coexpression Network, and Expression Single Nucleotide Polymorphism Analysis Identifies Novel Pathway in Allergic Rhinitis.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1675, MGC166915

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SMAD binding IEA
Inferred from Electronic Annotation
more info
 
activating transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
histone methyltransferase activity (H3-K9 specific) ISS
Inferred from Sequence or Structural Similarity
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription coactivator activity ISS
Inferred from Sequence or Structural Similarity
more info
 
transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
brown fat cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
heterochromatin organization ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K9 methylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
NOT negative regulation of transforming growth factor beta receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transforming growth factor beta receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
neurogenesis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of brown fat cell differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cellular respiration ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
roof of mouth development IEA
Inferred from Electronic Annotation
more info
 
somatic stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
tongue development IEA
Inferred from Electronic Annotation
more info
 
white fat cell differentiation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
aggresome IDA
Inferred from Direct Assay
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcriptional 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)

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.

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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