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PRDM16 (PR domain containing 16)

Written2004-04Jean-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

Other namesMEL1 (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 2985742 and ends at 3355185 bp from pter ( according to hg19-Feb_2009)  [Mapping PRDM16.png]
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
Fusion genes
(updated 2016)
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 MEL1
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

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
 
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
 
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
 
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
 

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) [ 6 ]
  Classification of myelodysplastic syndromes 2015
t(1;1)(p36;q21) in Non Hodgkin Lymphoma
t(1;2)(p36;p21) PRDM16 and LINC00982/?
t(1;3)(p36;q21) PSMD2/PRDM16
t(1;21)(p36;q22) RUNX1/PRDM16
1q translocations (unbalanced) in myeloid malignancies

External links

Nomenclature
HGNC (Hugo)PRDM16   14000
Cards
AtlasPRDM16MEL1ID408
Entrez_Gene (NCBI)PRDM16  63976  PR domain 16
AliasesCMD1LL; LVNC8; MEL1; PFM13
GeneCards (Weizmann)PRDM16
Ensembl hg19 (Hinxton)ENSG00000142611 [Gene_View]  chr1:2985742-3355185 [Contig_View]  PRDM16 [Vega]
Ensembl hg38 (Hinxton)ENSG00000142611 [Gene_View]  chr1:2985742-3355185 [Contig_View]  PRDM16 [Vega]
ICGC DataPortalENSG00000142611
TCGA cBioPortalPRDM16
AceView (NCBI)PRDM16
Genatlas (Paris)PRDM16
WikiGenes63976
SOURCE (Princeton)PRDM16
Genomic and cartography
GoldenPath hg19 (UCSC)PRDM16  -     chr1:2985742-3355185 +  1p36.32   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PRDM16  -     1p36.32   [Description]    (hg38-Dec_2013)
EnsemblPRDM16 - 1p36.32 [CytoView hg19]  PRDM16 - 1p36.32 [CytoView hg38]
Mapping of homologs : NCBIPRDM16 [Mapview hg19]  PRDM16 [Mapview hg38]
OMIM605557   615373   
Gene and transcription
Genbank (Entrez)AB051462 AB078876 AF294278 AI623202 AK093853
RefSeq transcript (Entrez)NM_022114 NM_199454
RefSeq genomic (Entrez)NC_000001 NC_018912 NG_029576 NT_032977 NW_004929288
Consensus coding sequences : CCDS (NCBI)PRDM16
Cluster EST : UnigeneHs.99500 [ NCBI ]
CGAP (NCI)Hs.99500
Alternative Splicing GalleryENSG00000142611
Gene ExpressionPRDM16 [ 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]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)63976
GTEX Portal (Tissue expression)PRDM16
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9HAZ2 (Uniprot)
NextProtQ9HAZ2  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9HAZ2
Splice isoforms : SwissVarQ9HAZ2 (Swissvar)
PhosPhoSitePlusQ9HAZ2
Domaine pattern : Prosite (Expaxy)SET (PS50280)    ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domains : Interpro (EBI)Evi1/Prdm16    SET_dom    Znf_C2H2    Znf_C2H2-like    Znf_C2H2/integrase_DNA-bd   
Domain families : Pfam (Sanger)zf-C2H2 (PF00096)    zf-C2H2_6 (PF13912)   
Domain families : Pfam (NCBI)pfam00096    pfam13912   
Domain families : Smart (EMBL)SET (SM00317)  ZnF_C2H2 (SM00355)  
DMDM Disease mutations63976
Blocks (Seattle)PRDM16
SuperfamilyQ9HAZ2
Human Protein AtlasENSG00000142611
Peptide AtlasQ9HAZ2
HPRD16122
IPIIPI00289654   IPI00914925   IPI00642532   IPI00963982   IPI01013488   IPI00940111   IPI00964578   IPI00964904   
Protein Interaction databases
DIP (DOE-UCLA)Q9HAZ2
IntAct (EBI)Q9HAZ2
FunCoupENSG00000142611
BioGRIDPRDM16
STRING (EMBL)PRDM16
ZODIACPRDM16
Ontologies - Pathways
QuickGOQ9HAZ2
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  transcription coactivator activity  protein binding  nucleus  cytosol  transcription, DNA-templated  transcriptional repressor complex  histone-lysine N-methyltransferase activity  neurogenesis  negative regulation of transforming growth factor beta receptor signaling pathway  negative regulation of transforming growth factor beta receptor signaling pathway  negative regulation of transforming growth factor beta receptor signaling pathway  negative regulation of granulocyte differentiation  activating transcription factor binding  histone lysine methylation  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  white fat cell differentiation  brown fat cell differentiation  palate development  positive regulation of brown fat cell differentiation  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  transcription coactivator activity  protein binding  nucleus  cytosol  transcription, DNA-templated  transcriptional repressor complex  histone-lysine N-methyltransferase activity  neurogenesis  negative regulation of transforming growth factor beta receptor signaling pathway  negative regulation of transforming growth factor beta receptor signaling pathway  negative regulation of transforming growth factor beta receptor signaling pathway  negative regulation of granulocyte differentiation  activating transcription factor binding  histone lysine methylation  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  white fat cell differentiation  brown fat cell differentiation  palate development  positive regulation of brown fat cell differentiation  
NDEx Network
Atlas of Cancer Signalling NetworkPRDM16
Wikipedia pathwaysPRDM16
Orthology - Evolution
OrthoDB63976
GeneTree (enSembl)ENSG00000142611
Phylogenetic Trees/Animal Genes : TreeFamPRDM16
Homologs : HomoloGenePRDM16
Homology/Alignments : Family Browser (UCSC)PRDM16
Gene fusions - Rearrangements
Fusion : MitelmanDUSP10/PRDM16 [1q41/1p36.32]  [t(1;1)(p36;q41)]  
Fusion : MitelmanETV6/PRDM16 [12p13.2/1p36.32]  [t(1;12)(p36;p13)]  
Fusion : MitelmanIGL/PRDM16 [22q11.22/1p36.32]  [t(1;22)(p36;q11)]  
Fusion : MitelmanIKZF1/PRDM16 [7p12.2/1p36.32]  [t(1;7)(p36;p12)]  
Fusion : MitelmanPRDM16/BBX [1p36.32/3q13.12]  [t(1;3)(p36;q13)]  
Fusion : MitelmanPRDM16/SKI [1p36.32/1p36.33]  [t(1;1)(p36;p36)]  
Fusion : MitelmanRPN1/PRDM16 [3q21.3/1p36.32]  [t(1;3)(p36;q21)]  
Fusion : MitelmanRUNX1/PRDM16 [21q22.12/1p36.32]  [t(1;21)(p36;q22)]  
Fusion : MitelmanSPOP/PRDM16 [17q21.33/1p36.32]  [t(1;17)(p36;q21)]  
Fusion: TCGAPRDM16 1p36.32 BBX 3q13.12 BRCA
Fusion: TCGASPOP 17q21.33 PRDM16 1p36.32 LGG
Fusion : TICdbETV6 [12p13.2]  -  PRDM16 [1p36.32]
Polymorphisms : SNP, variants
NCBI Variation ViewerPRDM16 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PRDM16
dbVarPRDM16
ClinVarPRDM16
1000_GenomesPRDM16 
Exome Variant ServerPRDM16
ExAC (Exome Aggregation Consortium)PRDM16 (select the gene name)
Genetic variants : HAPMAP63976
Genomic Variants (DGV)PRDM16 [DGVbeta]
Mutations
ICGC Data PortalPRDM16 
TCGA Data PortalPRDM16 
Broad Tumor PortalPRDM16
OASIS PortalPRDM16 [ Somatic mutations - Copy number]
Cancer Gene: CensusPRDM16 
Somatic Mutations in Cancer : COSMICPRDM16 
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
BioMutasearch 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)
intoGenPRDM16
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)1:2985742-3355185  ENSG00000142611
CONAN: Copy Number AnalysisPRDM16 
Mutations and Diseases : HGMDPRDM16
OMIM605557    615373   
MedgenPRDM16
Genetic Testing Registry PRDM16
NextProtQ9HAZ2 [Medical]
TSGene63976
GENETestsPRDM16
Huge Navigator PRDM16 [HugePedia]
snp3D : Map Gene to Disease63976
BioCentury BCIQPRDM16
ClinGenPRDM16
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD63976
Chemical/Pharm GKB GenePA33714
Clinical trialPRDM16
Miscellaneous
canSAR (ICR)PRDM16 (select the gene name)
Probes
Litterature
PubMed50 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePRDM16
EVEXPRDM16
GoPubMedPRDM16
iHOPPRDM16
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat Jun 11 13:04:11 CEST 2016

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