| | 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 | |
| | |
| 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 |
| | |
| 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 |
| |
| 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) |
| Ensembl | PRDM16 - 1p36.32 [CytoView hg19] PRDM16 - 1p36.32 [CytoView hg38] |
| 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 (SRS) | 2N1I 6BW4 |
| PDB (PDBSum) | 2N1I 6BW4 |
| PDB (IMB) | 2N1I 6BW4 |
| PDB (RSDB) | 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 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 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 roof of mouth development 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 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 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 roof of mouth development 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 |
| HOVERGEN | Q9HAZ2 |
| 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 : 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] |
| Cancer Gene: Census | PRDM16 |
| Somatic Mutations in Cancer : COSMIC | PRDM16 [overview] [genome browser] [tissue] [distribution] |
| 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) |
| Probes |
|---|
| Litterature |
|---|
| PubMed | 63 Pubmed reference(s) in Entrez |
| GeneRIFs | Gene References Into Functions (Entrez) |
| CoreMine | PRDM16 |
| EVEX | PRDM16 |
| GoPubMed | PRDM16 |
| iHOP | PRDM16 |
