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

Gene ID: 63976, updated on 21-Mar-2023

Summary

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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; AllianceGenome:HGNC:14000
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
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Genomic context

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See PRDM16 in Genome Data Viewer
Location:
1p36.32
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3069203..3438621)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (2571244..2943423)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (2985767..3355185)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene translation initiation factor IF-2 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 collagen alpha-5(IV) chain-like Neighboring gene VISTA enhancer hs705 Neighboring gene Sharpr-MPRA regulatory region 1987 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3229262-3230461 Neighboring gene uncharacterized LOC105378604 Neighboring gene VISTA enhancer hs1912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3272921-3273812 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

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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. Novel association of SNP rs2297828 in PRDM16 gene with predisposition to type 2 diabetes. Zhang H, et al. Gene, 2023 Jan 15. PMID 36174906
  2. Prognostic impact of PRDM16 expression in acute myeloid leukemia with normal cytogenetics. Xiang X, et al. Hematology, 2022 Dec. PMID 35473465
  3. The relationship between PRDM16 promoter methylation in abdominal subcutaneous and omental adipose tissue and obesity. Liu L, et al. Clin Nutr, 2021 Apr. PMID 33127174
  4. High PRDM16 expression predicts poor outcomes in adult acute myeloid leukemia patients with intermediate cytogenetic risk: a comprehensive cohort study from a single Chinese center. Dao FT, et al. Leuk Lymphoma, 2021 Jan. PMID 32902355
  5. Cardiomyopathy due to PRDM16 mutation: First description of a fetal presentation, with possible modifier genes. Delplancq G, et al. Am J Med Genet C Semin Med Genet, 2020 Mar. PMID 31965688

See all (93) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. miR-1275 Inhibits Human Omental Adipose-Derived Stem Cells Differentiation Toward the Beige Phenotype via PRDM16.
    Title: miR-1275 Inhibits Human Omental Adipose-Derived Stem Cells Differentiation Toward the Beige Phenotype via PRDM16.
  2. Novel association of SNP rs2297828 in PRDM16 gene with predisposition to type 2 diabetes.
    Title: Novel association of SNP rs2297828 in PRDM16 gene with predisposition to type 2 diabetes.
  3. Prognostic impact of PRDM16 expression in acute myeloid leukemia with normal cytogenetics.
    Title: Prognostic impact of PRDM16 expression in acute myeloid leukemia with normal cytogenetics.
  4. Deciphering the Role of the rs2651899, rs10166942, and rs11172113 Polymorphisms in Migraine: A Meta-Analysis.
    Title: Deciphering the Role of the rs2651899, rs10166942, and rs11172113 Polymorphisms in Migraine: A Meta-Analysis.
  5. Genomic alterations and evolution of cell clusters in metastatic invasive micropapillary carcinoma of the breast.
    Title: Genomic alterations and evolution of cell clusters in metastatic invasive micropapillary carcinoma of the breast.
  6. Adipose tissue expression of UCP1 and PRDM16 genes and their association with postprandial triglyceride metabolism and glucose intolerance.
    Title: Adipose tissue expression of UCP1 and PRDM16 genes and their association with postprandial triglyceride metabolism and glucose intolerance.
  7. Prdm16 Deficiency Leads to Age-Dependent Cardiac Hypertrophy, Adverse Remodeling, Mitochondrial Dysfunction, and Heart Failure.
    Title: Prdm16 Deficiency Leads to Age-Dependent Cardiac Hypertrophy, Adverse Remodeling, Mitochondrial Dysfunction, and Heart Failure.
  8. The relationship between PRDM16 promoter methylation in abdominal subcutaneous and omental adipose tissue and obesity.
    Title: The relationship between PRDM16 promoter methylation in abdominal subcutaneous and omental adipose tissue and obesity.
  9. High PRDM16 expression predicts poor outcomes in adult acute myeloid leukemia patients with intermediate cytogenetic risk: a comprehensive cohort study from a single Chinese center.
    Title: High PRDM16 expression predicts poor outcomes in adult acute myeloid leukemia patients with intermediate cytogenetic risk: a comprehensive cohort study from a single Chinese center.
  10. Association of rs2651899 Polymorphism in the Positive Regulatory Domain 16 and Common Migraine Subtypes: A Meta-Analysis.
    Title: Association of rs2651899 Polymorphism in the Positive Regulatory Domain 16 and Common Migraine Subtypes: A Meta-Analysis.
Submit: New GeneRIF Correction See all GeneRIFs (61)

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
Left ventricular noncompaction 8
MedGen: C3809288 OMIM: 615373 GeneReviews: Not available
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EBI GWAS Catalog

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1675, MGC166915

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables histone H3K9 methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables histone H3K9 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables histone H3K9me2 methyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription cis-regulatory region binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription coactivator activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables transcription coregulator activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
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 modification IEA
Inferred from Electronic Annotation
more info
  
involved_in methylation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
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 DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription ISS
Inferred from Sequence or Structural Similarity
more info
  
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 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

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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_022114.4 → NP_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
    Q9C0I8, Q9HAZ2
    Related
    ENSP00000270722.5, ENST00000270722.10
    Conserved Domains (6) summary
    smart00317
    Location:84 → 209
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:931 → 1083
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:953 → 973
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:951 → 973
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:965 → 989
    zf-H2C2_2; Zinc-finger double domain
    pfam15909
    Location:369 → 450
    zf-C2H2_8; C2H2-type zinc ribbon

  2. NM_199454.3 → NP_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:84 → 209
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    COG5048
    Location:931 → 1083
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:953 → 973
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:951 → 973
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:965 → 989
    zf-H2C2_2; Zinc-finger double domain
    pfam15909
    Location:369 → 450
    zf-C2H2_8; C2H2-type zinc ribbon

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    2571244..2943423
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HAZ2.3 GenPept UniProtKB/Swiss-Prot:Q9HAZ2

Gene LinkOut

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

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