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

    Gene ID: 63976, updated on 7-Sep-2023

    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; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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 H3K4me1 hESC enhancer GRCh37_chr1:2976872-2977417 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2984086-2984660 Neighboring gene opioid growth factor receptor pseudogene Neighboring gene actin related protein T2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:2989243-2990091 Neighboring gene PRDM16 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3011815-3012660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3023590-3024149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3030215-3030791 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3030792-3031367 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3041525-3042136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3042749-3043359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3044803-3045728 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3052001-3052522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3052523-3053044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3054481-3054980 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3062305-3063167 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3066095-3066595 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3070263-3070764 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3070765-3071264 Neighboring gene uncharacterized LOC105378606 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3080396-3081595 Neighboring gene microRNA 4251 Neighboring gene uncharacterized LOC107984909 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3105417-3105918 Neighboring gene uncharacterized LOC105378605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3133830-3134598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3135420-3135963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3135964-3136506 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3138135-3138677 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3138678-3139220 Neighboring gene Sharpr-MPRA regulatory region 1148 Neighboring gene collagen alpha-5(IV) chain-like Neighboring gene VISTA enhancer hs705 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3191818-3193017 Neighboring gene Sharpr-MPRA regulatory region 1987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3212462-3212962 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:3215870-3217069 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3220731-3221288 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3229262-3230461 Neighboring gene uncharacterized LOC105378604 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:3231799-3232358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3236197-3236696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3235695-3236196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3237397-3238015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3246879-3247556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3255514-3256329 Neighboring gene VISTA enhancer hs1912 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3268668-3269642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3269643-3270616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3272921-3273812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3273813-3274702 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3277409-3277908 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:3285513-3286094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3303704-3304204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3304205-3304705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3307961-3308462 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3311898-3312581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3312582-3313264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3320127-3320627 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3325025-3325602 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3331680-3332376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3332377-3333072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3337228-3337728 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3350015-3350524 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3357159-3357921 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3369311-3370063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3373825-3374576 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3388131-3388756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3399659-3400494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3400495-3401329 Neighboring gene Rho guanine nucleotide exchange factor 16 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3408710-3409234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3408184-3408709 Neighboring gene MEGF6 intron CAGE-defined mid-level expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3439723-3440262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3445841-3446528 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3447217-3447902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3449965-3450651 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3459643-3460294 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3460295-3460948 Neighboring gene multiple EGF like domains 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3463961-3464599 Neighboring gene uncharacterized LOC105378608

    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

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 H3 methyltransferase activity TAS
    Traceable Author Statement
    more info
     
    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 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 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

    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)

    NEW Try the new Transcript table

    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
      A6NHQ8, B1AJP7, B1AJP8, B1AJP9, B1WB48, Q8WYJ9, Q9C0I8, Q9HAZ2
      UniProtKB/TrEMBL
      D6RDW0
      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
      UniProtKB/TrEMBL
      D6RDW0
      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: 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)