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

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: mouse all
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nonsense Variant PRDM16-Q187X Causes Impaired Myocardial Development and TGF-beta Signaling Resulting in Noncompaction Cardiomyopathy in Humans and Mice.
Title: Nonsense Variant PRDM16-Q187X Causes Impaired Myocardial Development and TGF-β Signaling Resulting in Noncompaction Cardiomyopathy in Humans and Mice.
Discovery of PRDM16-Mediated TRPA1 Induction as the Mechanism for Low Tubulo-Interstitial Fibrosis in Diabetic Kidney Disease.
Title: Discovery of PRDM16-Mediated TRPA1 Induction as the Mechanism for Low Tubulo-Interstitial Fibrosis in Diabetic Kidney Disease.
Distinct response of adipocyte progenitors to glucocorticoids determines visceral obesity via the TEAD1-miR-27b-PRDM16 axis.
Title: Distinct response of adipocyte progenitors to glucocorticoids determines visceral obesity via the TEAD1-miR-27b-PRDM16 axis.
Long Noncoding RNA MAGI2-AS3 Represses Cell Progression in Clear Cell Renal Cell Carcinoma by Modulating the miR-629-5p/PRDM16 Axis.
Title: Long Noncoding RNA MAGI2-AS3 Represses Cell Progression in Clear Cell Renal Cell Carcinoma by Modulating the miR-629-5p/PRDM16 Axis.
PRDM16 Deletion Is Associated With Sex-dependent Cardiomyopathy and Cardiac Mortality: A Translational, Multi-Institutional Cohort Study.
Title: PRDM16 Deletion Is Associated With Sex-dependent Cardiomyopathy and Cardiac Mortality: A Translational, Multi-Institutional Cohort Study.
Androgen Receptor is a Negative Regulator of PRDM16 in Beige Adipocyte.
Title: Androgen Receptor is a Negative Regulator of PRDM16 in Beige Adipocyte.
The ALDH2, IGSF9, and PRDM16 Proteins as Predictive Biomarkers for Prognosis in Breast Cancer.
Title: The ALDH2, IGSF9, and PRDM16 Proteins as Predictive Biomarkers for Prognosis in Breast Cancer.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (68)

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	Compare labs

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-74091 (e-PCR)
- UniSTS:775

D1S1341 (e-PCR)
- UniSTS:149538

SHGC-146428 (e-PCR)
- UniSTS:175209

D1S1448 (e-PCR)
- UniSTS:149644

D1S1467 (e-PCR)
- UniSTS:149663

G65472 (e-PCR)
- UniSTS:166565

SHGC-147011 (e-PCR)
- UniSTS:175558

AL033971 (e-PCR)
- UniSTS:93383

SHGC-149994 (e-PCR)
- UniSTS:177356

RH120616 (e-PCR)
- UniSTS:132557

SHGC-111116 (e-PCR)
- UniSTS:168150

D1S1274 (e-PCR)
- UniSTS:149471

D1S1278 (e-PCR)
- UniSTS:149475

RH122382 (e-PCR)
- UniSTS:138479

SHGC-153745 (e-PCR)
- UniSTS:177914

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 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

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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

EC 2.1.1.367

NP_955533.2

EC 2.1.1.367

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

NG_029576.2 RefSeqGene

Range

5026..374444

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

A6NHQ8, B1AJP7, B1AJP8, B1AJP9, B1WB48, Q8WYJ9, Q9C0I8, Q9HAZ2

UniProtKB/TrEMBL

D6RDW0

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
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/TrEMBL

D6RDW0

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