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

Gene ID: 63976, updated on 2-May-2024

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
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Genomic context

See PRDM16 in Genome Data Viewer
Location:
1p36.32
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (3069203..3438621)
RS_2023_10 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 Neanderthal introgressed variant-containing enhancer experimental_6552 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 ReSE screen-validated silencer GRCh37_chr1:3008649-3008795 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 Neanderthal introgressed variant-containing enhancer experimental_6604 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 Neanderthal introgressed variant-containing enhancer experimental_6702 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 Neanderthal introgressed variant-containing enhancer experimental_6721 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:3220731-3221288 Neighboring gene uncharacterized LOC105378604 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:3229262-3230461 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_chr1:3304205-3304705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:3303704-3304204 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 Neanderthal introgressed variant-containing enhancer experimental_7120 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 ATAC-STARR-seq lymphoblastoid silent region 120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 119 Neighboring gene MEGF6 intron CAGE-defined mid-level expression enhancer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7326 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 MPRA-validated peak19 silencer 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
 
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
 
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
 
Process Evidence Code Pubs
involved_in brown fat cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
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
 
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
 
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/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_10

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)