PRDM16 (PR domain containing 16)

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PRDM16 (PR domain containing 16)

Written	2004-04	Jean-Loup Huret, Sylvie Senon
		Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias_names	PR domain containing 16
	PR domain 16
Alias_symbol (synonym)	MEL1
	PFM13
	KIAA1675
	MGC166915
	KMT8F
Other alias	MEL1 (MDS1/EVI1-like gene)
	PR-domain zinc finger protein 16
HGNC (Hugo)	PRDM16
LocusID (NCBI)	63976
Atlas_Id	408
Location	1p36.32 [Link to chromosome band 1p36]
Location_base_pair	Starts at 3069178 and ends at 3438621 bp from pter ( according to hg19-Feb_2009) [Mapping PRDM16.png]


	Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics

Fusion genes
(updated 2017)

Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

DUSP10 (1q41) / PRDM16 (1p36.32)	ETV6 (12p13.2) / PRDM16 (1p36.32)	IGL (22q11.22) / PRDM16 (1p36.32)
IKZF1 (7p12.2) / PRDM16 (1p36.32)	MECOM (3q26.2) / PRDM16 (1p36.32)	PRDM16 (1p36.32) / BBX (3q13.12)
PRDM16 (1p36.32) / MECOM (3q26.2)	PRDM16 (1p36.32) / SKI (1p36.33)	PRDM16 (1p36.32) / UMODL1 (21q22.3)
PSMD2 (3q27.1) / PRDM16 (1p36.32)	RPN1 (3q21.3) / PRDM16 (1p36.32)	RUNX1 (21q22.12) / PRDM16 (1p36.32)
SPOP (17q21.33) / PRDM16 (1p36.32)	UMODL1 (21q22.3) / PRDM16 (1p36.32)

Note	orientation plus strand

DNA/RNA

Description	spans 369 kb; 17exons; 3827 bp coding sequence.
Transcription	alternative transcripts MEL1 and MEL1S (MEL1 short)

Protein

Description	17O kDa (MEL1) and 150 Da (MEL1S); like MDS1/EVI1, The MEL1contains a PR domain (homologous to the SET domain present in MLL ) in the N term, two DNA binding domains (made of 7 and 3 zing fingers) separated by a repression domain, and an acidic domain at the C-term. MEL1S lacks the PR domain, like EVI1 alone. MEL1 and MEL1S, in a "yin-yang fashion", are hypothezised to display antagonistic properties; the PR domain may act as an inhibitor of tumorigenesis.
Expression	wide, contrarily to what was previously found
Localisation	nuclear
Homology	63% homology with MDS1/EVI1; both are members of the PR domain family

Implicated in

Note

Entity	t(1;3)(p36;q21) myeloid leukemias --> involving RPN1 and PRDM16
Disease	myelodysplastic syndromes (MDS), acute non lymphoblastic leukemias (AML), therapy-related leukemias and myeloprolifrative syndromes; with features similar to those of the 3q21q26 syndrome, including megakaryocytic dysplasia (see also 3q rearrangements in myeloid malignancies).
Prognosis	very poor
Hybrid/Mutated Gene	juxtaposition of the enhancer of the constitutively expressed housekeeping gene RPN1, normally sitting in 3q21, in 5' of MEL1 on der(1); both genes are orientated telomere to centromere; the same situation occurs between RPN1 in 5' of EVI1 in the t(3;3)(q21;q26) )
Oncogenesis	the translocation results in either an ectopic expression of MEL1 driven by RPN1or by disruption of its PR domain; this probable heterogenity may be associated with different clinical features. The short form, MEL1S, is mainly expressed

Bibliography

Molecular characterization of a t(1;3)(p36;q21) in a patient with MDS. MEL1 is widely expressed in normal tissues, including bone marrow, and it is not overexpressed in the t(1;3) cells.

Lahortiga I, Agirre X, Belloni E, V´zquez I, Larrayoz MJ, Gasparini P, Lo Coco F, Pelicci PG, Calasanz MJ, Odero MD

Oncogene. 2004 ; 23 (1) : 311-316.

PMID 14712237

A novel gene, MEL1, mapped to 1p36.3 is highly homologous to the MDS1/EVI1 gene and is transcriptionally activated in t(1;3)(p36;q21)-positive leukemia cells.

Mochizuki N, Shimizu S, Nagasawa T, Tanaka H, Taniwaki M, Yokota J, Morishita K

Blood. 2000 ; 96 (9) : 3209-3214.

PMID 11050005

A novel EVI1 gene family, MEL1, lacking a PR domain (MEL1S) is expressed mainly in t(1;3)(p36;q21)-positive AML and blocks G-CSF-induced myeloid differentiation.

Nishikata I, Sasaki H, Iga M, Tateno Y, Imayoshi S, Asou N, Nakamura T, Morishita K

Blood. 2003 ; 102 (9) : 3323-3332.

PMID 12816872

Fusion of the transcription factor TFE3 gene to a novel gene, PRCC, in t(X;1)(p11;q21)-positive papillary renal cell carcinomas.

Weterman MA, Wilbrink M, Geurts van Kessel A

Proceedings of the National Academy of Sciences of the United States of America. 1996 ; 93 (26) : 15294-15298.

PMID 8986805

Breakpoints at 1p36.3 in three MDS/AML(M4) patients with t(1;3)(p36;q21) occur in the first intron and in the 5' region of MEL1.

Xinh PT, Tri NK, Nagao H, Nakazato H, Taketazu F, Fujisawa S, Yagasaki F, Chen YZ, Hayashi Y, Toyoda A, Hattori M, Sakaki Y, Tokunaga K, Sato Y

Genes, chromosomes & cancer. 2003 ; 36 (3) : 313-316.

PMID 12557231

Citation

This paper should be referenced as such :

Huret, JL ; Senon, S

PRDM16 (PR domain containing 16)

Atlas Genet Cytogenet Oncol Haematol. 2004;8(2):76-77.

Free journal version : [ pdf ] [ DOI ]

On line version : http://AtlasGeneticsOncology.org/Genes/PRDM16MEL1ID408.html

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 9 ]

t(1;1)(p36;p36) PRDM16/SKI
t(1;1)(p36;q41) DUSP10/PRDM16
t(1;2)(p36;p21) THADA/PRDM16
t(1;3)(p36;q21) RPN1/PRDM16
t(1;7)(p36;p12) IKZF1/PRDM16
t(1;12)(p36;p13) ETV6/PRDM16
t(1;17)(p36;q21) WNT3 or NSF/PRDM16
t(1;21)(p36;q22) RUNX1/PRDM16
t(1;22)(p36;q11) IGL/PRDM16

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]

Breast: carcinoma with t(1;3)(p36;q13) PRDM16/BBX
Nervous system: Astrocytoma with t(1;17)(p36;q21) SPOP/PRDM16

External links

	Nomenclature
HGNC (Hugo)	PRDM16 14000
	Cards
Atlas	PRDM16MEL1ID408
Entrez_Gene (NCBI)	PRDM16 63976 PR/SET domain 16
Aliases	CMD1LL; KMT8F; LVNC8; MEL1;
	PFM13
GeneCards (Weizmann)	PRDM16
Ensembl hg19 (Hinxton)	ENSG00000142611 [Gene_View]
Ensembl hg38 (Hinxton)	ENSG00000142611 [Gene_View] ENSG00000142611 [Sequence] chr1:3069178-3438621 [Contig_View] PRDM16 [Vega]
ICGC DataPortal	ENSG00000142611
TCGA cBioPortal	PRDM16
AceView (NCBI)	PRDM16
Genatlas (Paris)	PRDM16
WikiGenes	63976
SOURCE (Princeton)	PRDM16
Genetics Home Reference (NIH)	PRDM16
	Genomic and cartography
GoldenPath hg38 (UCSC)	PRDM16 - chr1:3069178-3438621 + 1p36.32 [Description] (hg38-Dec_2013)
GoldenPath hg19 (UCSC)	PRDM16 - 1p36.32 [Description] (hg19-Feb_2009)
GoldenPath	PRDM16 - 1p36.32 [CytoView hg19] PRDM16 - 1p36.32 [CytoView hg38]
ImmunoBase	ENSG00000142611
Mapping of homologs : NCBI	PRDM16 [Mapview hg19] PRDM16 [Mapview hg38]
OMIM	605557 615373
	Gene and transcription
Genbank (Entrez)	AB051462 AB078876 AF294278 AI623202 AK093853
RefSeq transcript (Entrez)	NM_022114 NM_199454
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)	PRDM16
Cluster EST : Unigene	Hs.99500 [ NCBI ]
CGAP (NCI)	Hs.99500
Alternative Splicing Gallery	ENSG00000142611
Gene Expression	PRDM16 [ NCBI-GEO ] PRDM16 [ EBI - ARRAY_EXPRESS ] PRDM16 [ SEEK ] PRDM16 [ MEM ]
Gene Expression Viewer (FireBrowse)	PRDM16 [ Firebrowse - Broad ]
SOURCE (Princeton)	Expression in : [Datasets] [Normal Tissue Atlas] [carcinoma Classsification] [NCI60]
Genevestigator	Expression in : [tissues] [cell-lines] [cancer] [perturbations]
BioGPS (Tissue expression)	63976
GTEX Portal (Tissue expression)	PRDM16
Human Protein Atlas	ENSG00000142611-PRDM16 [pathology] [cell] [tissue]
	Protein : pattern, domain, 3D structure
UniProt/SwissProt	Q9HAZ2 [function] [subcellular_location] [family_and_domains] [pathology_and_biotech] [ptm_processing] [expression] [interaction]
NextProt	Q9HAZ2 [Sequence] [Exons] [Medical] [Publications]
With graphics : InterPro	Q9HAZ2
Splice isoforms : SwissVar	Q9HAZ2
PhosPhoSitePlus	Q9HAZ2
Domaine pattern : Prosite (Expaxy)	SET (PS50280) ZINC_FINGER_C2H2_1 (PS00028) ZINC_FINGER_C2H2_2 (PS50157)
Domains : Interpro (EBI)	PRDM16 SET_dom Znf_C2H2_sf Znf_C2H2_type
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Domain families : Smart (EMBL)	SET (SM00317) ZnF_C2H2 (SM00355)
Conserved Domain (NCBI)	PRDM16
DMDM Disease mutations	63976
Blocks (Seattle)	PRDM16
PDB (RSDB)	2N1I 6BW4
PDB Europe	2N1I 6BW4
PDB (PDBSum)	2N1I 6BW4
PDB (IMB)	2N1I 6BW4
Structural Biology KnowledgeBase	2N1I 6BW4
SCOP (Structural Classification of Proteins)	2N1I 6BW4
CATH (Classification of proteins structures)	2N1I 6BW4
Superfamily	Q9HAZ2
Human Protein Atlas [tissue]	ENSG00000142611-PRDM16 [tissue]
Peptide Atlas	Q9HAZ2
HPRD	16122
IPI	IPI00289654 IPI00914925 IPI00642532 IPI00963982 IPI01013488 IPI00940111 IPI00964578 IPI00964904
	Protein Interaction databases
DIP (DOE-UCLA)	Q9HAZ2
IntAct (EBI)	Q9HAZ2
FunCoup	ENSG00000142611
BioGRID	PRDM16
STRING (EMBL)	PRDM16
ZODIAC	PRDM16
	Ontologies - Pathways
QuickGO	Q9HAZ2
Ontology : AmiGO	negative regulation of transcription by RNA polymerase II DNA-binding transcription factor activity, RNA polymerase II-specific transcription coactivator activity protein binding nucleus nucleoplasm cytosol cytosol aggresome transcriptional repressor complex neurogenesis negative regulation of transforming growth factor beta receptor signaling pathway negative regulation of transforming growth factor beta receptor signaling pathway activating transcription factor binding somatic stem cell population maintenance regulation of cellular respiration sequence-specific DNA binding tongue development negative regulation of transcription, DNA-templated negative regulation of transcription, DNA-templated positive regulation of transcription, DNA-templated positive regulation of transcription, DNA-templated SMAD binding metal ion binding histone methyltransferase activity (H3-K9 specific) white fat cell differentiation brown fat cell differentiation histone H3-K9 methylation roof of mouth development heterochromatin organization positive regulation of brown fat cell differentiation positive regulation of cold-induced thermogenesis
Ontology : EGO-EBI	negative regulation of transcription by RNA polymerase II DNA-binding transcription factor activity, RNA polymerase II-specific transcription coactivator activity protein binding nucleus nucleoplasm cytosol cytosol aggresome transcriptional repressor complex neurogenesis negative regulation of transforming growth factor beta receptor signaling pathway negative regulation of transforming growth factor beta receptor signaling pathway activating transcription factor binding somatic stem cell population maintenance regulation of cellular respiration sequence-specific DNA binding tongue development negative regulation of transcription, DNA-templated negative regulation of transcription, DNA-templated positive regulation of transcription, DNA-templated positive regulation of transcription, DNA-templated SMAD binding metal ion binding histone methyltransferase activity (H3-K9 specific) white fat cell differentiation brown fat cell differentiation histone H3-K9 methylation roof of mouth development heterochromatin organization positive regulation of brown fat cell differentiation positive regulation of cold-induced thermogenesis
NDEx Network	PRDM16
Atlas of Cancer Signalling Network	PRDM16
Wikipedia pathways	PRDM16
	Orthology - Evolution
OrthoDB	63976
GeneTree (enSembl)	ENSG00000142611
Phylogenetic Trees/Animal Genes : TreeFam	PRDM16
HOGENOM	Q9HAZ2
Homologs : HomoloGene	PRDM16
Homology/Alignments : Family Browser (UCSC)	PRDM16
	Gene fusions - Rearrangements
Fusion : Mitelman	DUSP10/PRDM16 [1q41/1p36.32] [t(1;1)(p36;q41)]
Fusion : Mitelman	ETV6/PRDM16 [12p13.2/1p36.32] [t(1;12)(p36;p13)]
Fusion : Mitelman	IGL/PRDM16 [22q11.22/1p36.32] [t(1;22)(p36;q11)]
Fusion : Mitelman	IKZF1/PRDM16 [7p12.2/1p36.32] [t(1;7)(p36;p12)]
Fusion : Mitelman	PRDM16/BBX [1p36.32/3q13.12] [t(1;3)(p36;q13)]
Fusion : Mitelman	PRDM16/SKI [1p36.32/1p36.33] [t(1;1)(p36;p36)]
Fusion : Mitelman	RPN1/PRDM16 [3q21.3/1p36.32] [t(1;3)(p36;q21)]
Fusion : Mitelman	RUNX1/PRDM16 [21q22.12/1p36.32] [t(1;21)(p36;q22)]
Fusion : Mitelman	SPOP/PRDM16 [17q21.33/1p36.32] [t(1;17)(p36;q21)]
Fusion Portal	PRDM16 1p36.32 BBX 3q13.12 BRCA
Fusion Portal	SPOP 17q21.33 PRDM16 1p36.32 LGG
Fusion : TICdb	ETV6 [12p13.2] - PRDM16 [1p36.32]
Fusion : FusionGDB	12189 28596 28597 28598 31835 35758 40774 7240
Fusion : Fusion_Hub	CIITA--PRDM16 DUSP10--PRDM16 ETV6--PRDM16 EVI1--PRDM16 GBP1--PRDM16 IGL@--PRDM16 PANK4--PRDM16 PRDM16--ABL1 PRDM16--BBX PRDM16--CDC42 PRDM16--COL18A1 PRDM16--CSDE1 PRDM16--DENND3 PRDM16--FAM120B PRDM16--NARS2
	PRDM16--NFIL3 PRDM16--PRKCZ PRDM16--PSMD2 PRDM16--RPN1 PRDM16--RUNX1 PRDM16--SKI PRDM16--UBC PRDM16--UMODL1 PRDM16--ZBTB2 PSMD2--PRDM16 RPL22--PRDM16 RUNX1--PRDM16 SKI--PRDM16 SPOP--PRDM16 UMODL1--PRDM16
	ZFP36L2--PRDM16
Fusion : Quiver	PRDM16
	Polymorphisms : SNP and Copy number variants
NCBI Variation Viewer	PRDM16 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)	PRDM16
dbVar	PRDM16
ClinVar	PRDM16
1000_Genomes	PRDM16
Exome Variant Server	PRDM16
ExAC (Exome Aggregation Consortium)	ENSG00000142611
GNOMAD Browser	ENSG00000142611
Varsome Browser	PRDM16
Genetic variants : HAPMAP	63976
Genomic Variants (DGV)	PRDM16 [DGVbeta]
DECIPHER	PRDM16 [patients] [syndromes] [variants] [genes]
CONAN: Copy Number Analysis	PRDM16
	Mutations
ICGC Data Portal	PRDM16
TCGA Data Portal	PRDM16
Broad Tumor Portal	PRDM16
OASIS Portal	PRDM16 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMIC	PRDM16 [overview] [genome browser] [tissue] [distribution]
Somatic Mutations in Cancer : COSMIC3D	PRDM16
Mutations and Diseases : HGMD	PRDM16
LOVD (Leiden Open Variation Database)	Whole genome datasets
LOVD (Leiden Open Variation Database)	LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)	LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)	MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMuta	search PRDM16
DgiDB (Drug Gene Interaction Database)	PRDM16
DoCM (Curated mutations)	PRDM16 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)	PRDM16 (select a term)
intoGen	PRDM16
NCG5 (London)	PRDM16
Cancer3D	PRDM16(select the gene name)
Impact of mutations	[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
	Diseases
OMIM	605557 615373
Orphanet	635 1738 10750
DisGeNET	PRDM16
Medgen	PRDM16
Genetic Testing Registry	PRDM16
NextProt	Q9HAZ2 [Medical]
TSGene	63976
GENETests	PRDM16
Target Validation	PRDM16
Huge Navigator	PRDM16 [HugePedia]
snp3D : Map Gene to Disease	63976
BioCentury BCIQ	PRDM16
ClinGen	PRDM16
	Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD	63976
Chemical/Pharm GKB Gene	PA33714
Clinical trial	PRDM16
	Miscellaneous
canSAR (ICR)	PRDM16 (select the gene name)
DataMed Index	PRDM16
	Probes
	Litterature
PubMed	70 Pubmed reference(s) in Entrez
GeneRIFs	Gene References Into Functions (Entrez)
CoreMine	PRDM16
EVEX	PRDM16
GoPubMed	PRDM16
iHOP	PRDM16

REVIEW articles	automatic search in PubMed
Last year publications	automatic search in PubMed

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indexed on : Wed Nov 13 21:51:04 CET 2019

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