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KDM5A (Jumonji, AT rich interactive domain 1A (RBBP2-like))

Written2006-04Laura J.C.M. van Zutven, Anne R.M. von Bergh
Afdeling Klinische Genetica, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands

(Note : for Links provided by Atlas : click)

Identity

Alias_namesRBBP2
JARID1A
retinoblastoma-binding protein 2
Jumonji, AT rich interactive domain 1A (RBBP2-like)
jumonji, AT rich interactive domain 1A
lysine (K)-specific demethylase 5A
HGNC (Hugo) KDM5A
LocusID (NCBI) 5927
Atlas_Id 41033
Location 12p13.33  [Link to chromosome band 12p13]
Location_base_pair Starts at 389223 and ends at 498621 bp from pter ( according to hg19-Feb_2009)  [Mapping KDM5A.png]
Local_order very telomeric side of 12p13
Fusion genes
(updated 2016)
BDP1 (5q13.2) / KDM5A (12p13.33)CGA (6q14.3) / KDM5A (12p13.33)IQSEC3 (12p13.33) / KDM5A (12p13.33)
KDM5A (12p13.33) / ANO2 (12p13.31)KDM5A (12p13.33) / CCDC77 (12p13.33)KDM5A (12p13.33) / MBP (18q23)
KDM5A (12p13.33) / MED11 (17p13.2)KDM5A (12p13.33) / NINJ2 (12p13.33)KDM5A (12p13.33) / NUP98 (11p15.4)
KDM5A (12p13.33) / PDXDC1 (16p13.11)KDM5A (12p13.33) / RAE1 (20q13.31)KDM5A (12p13.33) / TUBB4A (19p13.3)
NUP98 (11p15.4) / KDM5A (12p13.33)PBX3 (9q33.3) / KDM5A (12p13.33)TSKU (11q13.5) / KDM5A (12p13.33)
WNK1 (12p13.33) / KDM5A (12p13.33)

DNA/RNA

Description 31 exons over 105 kb
Transcription from centromere to telomere, yielding mRNA of 6,5 kb

Protein

 
Description JARID1A (Jumonji, AT-rich interactive domain 1A) encodes the 196 kDa retinoblastoma binding protein 2 (1722 amino acids). It contains several motifs, including a leucine-X-cysteine-X-glutamic acid (LXCXE) motif, which is important for association with the T/E1A pocket domain of the retinoblastoma protein. Additionally, the protein contains ARID, Jumonji, and 3 PHD (LAP) domains, which are frequent in proteins regulating transcription through changes in chromatin structure.
Expression Widely expressed
Localisation Nuclear
Function Probably in regulating transcription through changes in chromatin structure
Homology RBP2 homologue 1 (RBP2-H1)

Implicated in

Note
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.
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.
  

Bibliography

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
 
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
 
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
 

Citation

This paper should be referenced as such :
van Zutven, LJCM ; von Bergh, ARM
JARID1A (jumonji, AT rich interactive domain 1A (RBBP2-like))
Atlas Genet Cytogenet Oncol Haematol. 2006;10(4):214-215.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/JARID1AID41033ch12p13.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(11;12)(p15;p13) NUP98/KDM5A


External links

Nomenclature
HGNC (Hugo)KDM5A   9886
Cards
AtlasJARID1AID41033ch12p13
Entrez_Gene (NCBI)KDM5A  5927  lysine demethylase 5A
AliasesRBBP-2; RBBP2; RBP2
GeneCards (Weizmann)KDM5A
Ensembl hg19 (Hinxton)ENSG00000073614 [Gene_View]  chr12:389223-498621 [Contig_View]  KDM5A [Vega]
Ensembl hg38 (Hinxton)ENSG00000073614 [Gene_View]  chr12:389223-498621 [Contig_View]  KDM5A [Vega]
ICGC DataPortalENSG00000073614
TCGA cBioPortalKDM5A
AceView (NCBI)KDM5A
Genatlas (Paris)KDM5A
WikiGenes5927
SOURCE (Princeton)KDM5A
Genetics Home Reference (NIH)KDM5A
Genomic and cartography
GoldenPath hg19 (UCSC)KDM5A  -     chr12:389223-498621 -  12p13.33   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)KDM5A  -     12p13.33   [Description]    (hg38-Dec_2013)
EnsemblKDM5A - 12p13.33 [CytoView hg19]  KDM5A - 12p13.33 [CytoView hg38]
Mapping of homologs : NCBIKDM5A [Mapview hg19]  KDM5A [Mapview hg38]
OMIM180202   
Gene and transcription
Genbank (Entrez)AA101935 AB209999 AF007135 AK057703 AK225060
RefSeq transcript (Entrez)NM_001042603 NM_005056
RefSeq genomic (Entrez)NC_000012 NC_018923 NT_009759 NW_004929382
Consensus coding sequences : CCDS (NCBI)KDM5A
Cluster EST : UnigeneHs.76272 [ NCBI ]
CGAP (NCI)Hs.76272
Alternative Splicing GalleryENSG00000073614
Gene ExpressionKDM5A [ NCBI-GEO ]   KDM5A [ EBI - ARRAY_EXPRESS ]   KDM5A [ SEEK ]   KDM5A [ MEM ]
Gene Expression Viewer (FireBrowse)KDM5A [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5927
GTEX Portal (Tissue expression)KDM5A
Protein : pattern, domain, 3D structure
UniProt/SwissProtP29375   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP29375  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP29375
Splice isoforms : SwissVarP29375
Catalytic activity : Enzyme1.14.11.- [ Enzyme-Expasy ]   1.14.11.-1.14.11.- [ IntEnz-EBI ]   1.14.11.- [ BRENDA ]   1.14.11.- [ KEGG ]   
PhosPhoSitePlusP29375
Domaine pattern : Prosite (Expaxy)ARID (PS51011)    JMJC (PS51184)    JMJN (PS51183)    ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domains : Interpro (EBI)ARID_dom    JmjC_dom    JmjN    Lys_sp_deMease-like_dom    Zinc_finger_PHD-type_CS    Znf_C5HC2    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING/FYVE/PHD   
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)  
Conserved Domain (NCBI)KDM5A
DMDM Disease mutations5927
Blocks (Seattle)KDM5A
PDB (SRS)2JXJ    2KGG    2KGI    3GL6    5C11    5E6H   
PDB (PDBSum)2JXJ    2KGG    2KGI    3GL6    5C11    5E6H   
PDB (IMB)2JXJ    2KGG    2KGI    3GL6    5C11    5E6H   
PDB (RSDB)2JXJ    2KGG    2KGI    3GL6    5C11    5E6H   
Structural Biology KnowledgeBase2JXJ    2KGG    2KGI    3GL6    5C11    5E6H   
SCOP (Structural Classification of Proteins)2JXJ    2KGG    2KGI    3GL6    5C11    5E6H   
CATH (Classification of proteins structures)2JXJ    2KGG    2KGI    3GL6    5C11    5E6H   
SuperfamilyP29375
Human Protein AtlasENSG00000073614
Peptide AtlasP29375
HPRD08915
IPIIPI01014284   IPI00872073   IPI01018722   IPI00021363   IPI00909864   IPI01011106   IPI01011614   
Protein Interaction databases
DIP (DOE-UCLA)P29375
IntAct (EBI)P29375
FunCoupENSG00000073614
BioGRIDKDM5A
STRING (EMBL)KDM5A
ZODIACKDM5A
Ontologies - Pathways
QuickGOP29375
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  DNA binding  transcription factor activity, sequence-specific DNA binding  transcription coactivator activity  protein binding  nucleus  nucleoplasm  nucleolus  cytoplasm  transcription from RNA polymerase II promoter  spermatogenesis  zinc ion binding  male gonad development  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  chromatin DNA binding  histone demethylase activity  circadian regulation of gene expression  protein-DNA complex  histone H3-K4 demethylation  positive regulation of transcription, DNA-templated  oxidation-reduction process  negative regulation of histone deacetylase activity  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  DNA binding  transcription factor activity, sequence-specific DNA binding  transcription coactivator activity  protein binding  nucleus  nucleoplasm  nucleolus  cytoplasm  transcription from RNA polymerase II promoter  spermatogenesis  zinc ion binding  male gonad development  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  chromatin DNA binding  histone demethylase activity  circadian regulation of gene expression  protein-DNA complex  histone H3-K4 demethylation  positive regulation of transcription, DNA-templated  oxidation-reduction process  negative regulation of histone deacetylase activity  
REACTOMEP29375 [protein]
REACTOME PathwaysR-HSA-3214842 HDMs demethylate histones [pathway]
NDEx NetworkKDM5A
Atlas of Cancer Signalling NetworkKDM5A
Wikipedia pathwaysKDM5A
Orthology - Evolution
OrthoDB5927
GeneTree (enSembl)ENSG00000073614
Phylogenetic Trees/Animal Genes : TreeFamKDM5A
HOVERGENP29375
HOGENOMP29375
Homologs : HomoloGeneKDM5A
Homology/Alignments : Family Browser (UCSC)KDM5A
Gene fusions - Rearrangements
Fusion : MitelmanIQSEC3/KDM5A [12p13.33/12p13.33]  [inv(12)(p13p13)]  
Fusion : MitelmanKDM5A/ANO2 [12p13.33/12p13.31]  [t(12;12)(p13;p13)]  
Fusion : MitelmanKDM5A/CCDC77 [12p13.33/12p13.33]  [t(12;12)(p13;p13)]  
Fusion : MitelmanKDM5A/NINJ2 [12p13.33/12p13.33]  [t(12;12)(p13;p13)]  
Fusion : MitelmanKDM5A/RAE1 [12p13.33/20q13.31]  [t(12;20)(p13;q13)]  
Fusion : MitelmanNUP98/KDM5A [11p15.4/12p13.33]  [t(11;12)(p15;p13)]  [t(11;21;12)(p15;p13;p13)]  
Fusion : MitelmanWNK1/KDM5A [12p13.33/12p13.33]  [t(12;12)(p13;p13)]  
Fusion : COSMICNUP98 [11p15.4]  -  KDM5A [12p13.33]  [fusion_2291]  [fusion_2292]  [fusion_2294]  
Fusion: TCGAKDM5A 12p13.33 ANO2 12p13.31 BRCA
Fusion: TCGAKDM5A 12p13.33 NINJ2 12p13.33 BRCA
Fusion: TCGAKDM5A 12p13.33 RAE1 20q13.31 LUAD
Fusion: TCGAWNK1 12p13.33 KDM5A 12p13.33 BRCA
Fusion : TICdbNUP98 [11p15.4]  -  KDM5A [12p13.33]
Fusion Cancer (Beijing)KDM5A [12p13.33]  -  PDXDC1 [16p13.11]  [FUSC002421]  [FUSC002421]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM5A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM5A
dbVarKDM5A
ClinVarKDM5A
1000_GenomesKDM5A 
Exome Variant ServerKDM5A
ExAC (Exome Aggregation Consortium)KDM5A (select the gene name)
Genetic variants : HAPMAP5927
Genomic Variants (DGV)KDM5A [DGVbeta]
DECIPHER (Syndromes)12:389223-498621  ENSG00000073614
CONAN: Copy Number AnalysisKDM5A 
Mutations
ICGC Data PortalKDM5A 
TCGA Data PortalKDM5A 
Broad Tumor PortalKDM5A
OASIS PortalKDM5A [ Somatic mutations - Copy number]
Cancer Gene: CensusKDM5A 
Somatic Mutations in Cancer : COSMICKDM5A  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDKDM5A
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
BioMutasearch KDM5A
DgiDB (Drug Gene Interaction Database)KDM5A
DoCM (Curated mutations)KDM5A (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM5A (select a term)
intoGenKDM5A
NCG5 (London)KDM5A
Cancer3DKDM5A(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM180202   
Orphanet
MedgenKDM5A
Genetic Testing Registry KDM5A
NextProtP29375 [Medical]
TSGene5927
GENETestsKDM5A
Huge Navigator KDM5A [HugePedia]
snp3D : Map Gene to Disease5927
BioCentury BCIQKDM5A
ClinGenKDM5A
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5927
Chemical/Pharm GKB GenePA34250
Clinical trialKDM5A
Miscellaneous
canSAR (ICR)KDM5A (select the gene name)
Probes
Litterature
PubMed56 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM5A
EVEXKDM5A
GoPubMedKDM5A
iHOPKDM5A
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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