| Entity | t(11;12)(p15;p13) in Acute megakaryoblastic leukemia (AML -M7) --> NUP98/JARID1A |
| Note | Only one case to date, a 1- year-old boy |
| Prognosis | Patient reached complete remission and remains in complete remission (CR) for at least 5 years |
| Cytogenetics | complex/variant t(11;12)(p15;p13); i.e. t(11;21;12)(p15;p13;p13), but misdiagnosed as add(11)(p15) and der(21)t(11;21)(p15;p13). Chromosome 12 was cytogenetically normal by conventional banding techniques and only identified as a partner in this translocation after FISH. |
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| Hybrid/Mutated Gene | 5' NUP98 - 3' JARID1A, including the first 13 exons of NUP98 and exons 28-31 of JARID1A |
| Abnormal Protein | The NUP98-JARID1A fusion protein contains the Phe-Gly (FG) repeats of the N-terminal part of NUP98. The JARID1A sequence starting with exon 28 still contains the sequence encoding the C-terminal PHD domain. |
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| Nomenclature | | HGNC (Hugo) | KDM5A 9886 |
| Entrez_Gene (NCBI) | KDM5A 5927 lysine (K)-specific demethylase 5A |
| Cards | | Atlas | JARID1AID41033ch12p13 |
| GeneCards (Weizmann) | KDM5A |
| Ensembl (Hinxton) | ENSG00000073614 [Gene_View] chr12:389223-498620 [Contig_View] KDM5A [Vega] |
| AceView (NCBI) | KDM5A |
| Genatlas (Paris) | KDM5A |
| euGene (Indiana) | 5927 |
| SOURCE (Stanford) | NM_001042603 NM_005056 |
| Genomic and cartography | | GoldenPath (UCSC) | KDM5A - 12p13 chr12:389223-498620 - 12p11 [Description] (hg19-Feb_2009) |
| Ensembl | KDM5A - 12p11 [CytoView] |
| Mapping of homologs : NCBI | KDM5A [Mapview] |
| OMIM | 180202 |
| Gene and transcription |
| Genbank (Entrez) | AA101935 AB209999 AF007135 AK057703 AK225060 |
| RefSeq transcript (SRS) | NM_001042603 NM_005056 |
| RefSeq transcript (Entrez) | NM_001042603 NM_005056 |
| RefSeq genomic (SRS) | AC_000144 NC_000012 NT_009759 NW_001838049 |
| RefSeq genomic (Entrez) | AC_000144 NC_000012 NT_009759 NW_001838049 |
| Consensus coding sequences : CCDS (NCBI) | KDM5A |
| Cluster EST : Unigene | Hs.76272 [ SRS ] Hs.76272 [ NCBI ] |
| Alternative Splicing : Fast-db (Paris) | 258 |
| Alternative Splicing Gallery | ENSG00000073614 |
| Gene Expression | KDM5A [ NCBI-GEO ] KDM5A [ EBI - ARRAY_EXPRESS ] |
| Protein : pattern, domain, 3D structure |
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| UniProt/SwissProt | P29375 (SRS) P29375 (Uniprot) |
| With graphics : InterPro | P29375 |
| Splice isoforms : SwissVar | P29375(Swissvar) |
| Domaine pattern : Prosite (SRS) | ARID (PS51011) JMJC (PS51184) JMJN (PS51183) ZF_PHD_1 (PS01359) ZF_PHD_2 (PS50016) |
| Domaine pattern : Prosite (Expaxy) | ARID (PS51011) JMJC (PS51184) JMJN (PS51183) ZF_PHD_1 (PS01359) ZF_PHD_2 (PS50016) |
| Domains : Interpro (SRS) | ARID/BRIGHT_DNA-bd Lys_sp_deMease_like_dom TF_JmjC TF_JmjC_AAH TF_JmjN Zinc_finger_PHD-type_CS Znf_C5HC2 Znf_FYVE_PHD Znf_PHD Znf_PHD-finger Znf_RING/FYVE/PHD |
| Domains : Interpro (EBI) | ARID/BRIGHT_DNA-bd Lys_sp_deMease_like_dom TF_JmjC TF_JmjC_AAH TF_JmjN Zinc_finger_PHD-type_CS Znf_C5HC2 Znf_FYVE_PHD Znf_PHD Znf_PHD-finger Znf_RING/FYVE/PHD |
| Related proteins : CluSTr | P29375 |
| Domain families : Pfam (SRS) | ARID (PF01388) JmjC (PF02373) JmjN (PF02375) PHD (PF00628) PLU-1 (PF08429) zf-C5HC2 (PF02928) |
| Domain families : Pfam (Sanger) | ARID (PF01388) JmjC (PF02373) JmjN (PF02375) PHD (PF00628) PLU-1 (PF08429) zf-C5HC2 (PF02928) |
| Domain families : Pfam (NCBI) | pfam01388 pfam02373 pfam02375 pfam00628 pfam08429 pfam02928 |
| Domain families : Smart (EMBL) | BRIGHT (SM00501) JmjC (SM00558) JmjN (SM00545) PHD (SM00249) |
| Blocks (Seattle) | P29375 |
| PDB (SRS) | 2JXJ 2KGG 2KGI 3GL6 |
| PDB (PDBSum) | 2JXJ 2KGG 2KGI 3GL6 |
| PDB (IMB) | 2JXJ 2KGG 2KGI 3GL6 |
| PDB (RSDB) | 2JXJ 2KGG 2KGI 3GL6 |
| Human Protein Atlas | ENSG00000073614 |
| HPRD | 08915 |
| IPI | IPI01014284 IPI00872073 IPI01018722 IPI00021363 IPI00909864 IPI01011106 IPI01011614 |
| Protein Interaction databases |
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| DIP (DOE-UCLA) | P29375 |
| IntAct (EBI) | P29375 |
| FunCoup | ENSG00000073614 |
| REACTOME | KDM5A |
| BioGRID | KDM5A |
| InParanoid | P29375 |
| Interologous Interaction database | P29375 |
| Polymorphism : SNP, mutations, diseases | | SNP Single Nucleotide Polymorphism (NCBI) | KDM5A |
| SNP (GeneSNP Utah) | KDM5A |
| SNP : HGBase | KDM5A |
| Genetic variants : HAPMAP | KDM5A |
| Cancer Gene: Census | KDM5A |
| Somatic Mutations in Cancer : COSMIC | KDM5A |
| CONAN: Copy Number Analysis | KDM5A |
| Translocation Breakpoints in Cancer : TICdb | KDM5A |
| Mutations and Diseases : HGMD | KDM5A |
| OMIM | 180202 |
| GENETests | 180202 |
| Disease Genetic Association | KDM5A |
| Huge Navigator |
KDM5A [HugePedia] KDM5A [HugeCancerGEM] |
| Genomic Variants | KDM5A |
| snp3D : Map Gene to Disease | 5927 |
| General knowledge |
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| Homologs : HomoloGene | KDM5A |
| Homology/Alignments : Family Browser (UCSC) | KDM5A |
| Phylogenetic Trees/Animal Genes : TreeFam | KDM5A |
| Catalytic activity : Enzyme | 1.14.11.- [ Enzyme-Expasy ] 1.14.11.- [ Enzyme-SRS ] 1.14.11.- [ IntEnz-EBI ] 1.14.11.- [ BRENDA ] 1.14.11.- [ KEGG ] |
| Chemical/Protein Interactions : CTD | 5927 |
| Chemical/Pharm GKB Gene | PA34250 |
| Clinical trial | KDM5A |
| Cancer Resource (Charite) | ENSG00000073614 |
| Ontology : AmiGO | DNA binding chromatin binding sequence-specific DNA binding transcription factor activity intracellular nucleus nucleolus cytoplasm regulation of transcription, DNA-dependent transcription from RNA polymerase II promoter multicellular organismal development zinc ion binding oxidoreductase activity chromatin modification oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors cyclin-dependent protein kinase activating kinase holoenzyme complex positive regulation of transcription, DNA-dependent metal ion binding |
| Ontology : EGO-EBI | DNA binding chromatin binding sequence-specific DNA binding transcription factor activity intracellular nucleus nucleolus cytoplasm regulation of transcription, DNA-dependent transcription from RNA polymerase II promoter multicellular organismal development zinc ion binding oxidoreductase activity chromatin modification oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors cyclin-dependent protein kinase activating kinase holoenzyme complex positive regulation of transcription, DNA-dependent metal ion binding |
| Other databases |
| Probes |
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| Probes : Imagenes | JARID1A Related clones (RZPD - Berlin) |
| Litterature |
| PubMed | 36 Pubmed reference(s) in Entrez |
| PubGene | KDM5A |
| iHOP | KDM5A |
| Differential specificity for binding of retinoblastoma binding protein 2 to RB, p107, and TATA-binding protein. |
| Kim YW, Otterson GA, Kratzke RA, Coxon AB, Kaye FJ |
| Molecular and cellular biology. 1994 ; 14 (11) : 7256-7264. |
| PMID 7935440 |
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| Binding of pRB to the PHD protein RBP2 promotes cellular differentiation. |
| Benevolenskaya EV, Murray HL, Branton P, Young RA, Kaelin WG Jr |
| Molecular cell. 2005 ; 18 (6) : 623-635. |
| PMID 15949438 |
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| Identification of NUP98 abnormalities in acute leukemia: JARID1A (12p13) as a new partner gene. |
| van Zutven LJ, Onen E, Velthuizen SC, van Drunen E, von Bergh AR, van den Heuvel-Eibrink MM, Veronese A, Mecucci C, Negrini M, de Greef GE, Beverloo HB |
| Genes, chromosomes & cancer. 2006 ; 45 (5) : 437-446. |
| PMID 16419055 |
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