Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

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 (NCBI)JARID1A
RBBP2
RBP2
HGNC (Hugo) KDM5A
HGNC Previous nameRBBP2
 JARID1A
HGNC Previous nameretinoblastoma-binding protein 2
 Jumonji, AT rich interactive domain 1A (RBBP2-like)
 jumonji, AT rich interactive domain 1A
 lysine (K)-specific demethylase 5A
LocusID (NCBI) 5927
Atlas_Id 41033
Location 12p13.33  [Link to chromosome band 12p13]
Location_base_pair Starts at 280057 and ends at 389320 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping KDM5A.png]
Local_order very telomeric side of 12p13
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
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 in --> NUP98/KDM5A
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 ]


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(11;12)(p15;p13) NUP98::KDM5A
inv(12)(p13p13) IQSEC3::KDM5A


External links

 

Nomenclature
HGNC (Hugo)KDM5A   9886
Cards
AtlasJARID1AID41033ch12p13
Entrez_Gene (NCBI)KDM5A    lysine demethylase 5A
AliasesRBBP-2; RBBP2; RBP2
GeneCards (Weizmann)KDM5A
Ensembl hg19 (Hinxton)ENSG00000073614 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000073614 [Gene_View]  ENSG00000073614 [Sequence]  chr12:280057-389320 [Contig_View]  KDM5A [Vega]
ICGC DataPortalENSG00000073614
TCGA cBioPortalKDM5A
AceView (NCBI)KDM5A
Genatlas (Paris)KDM5A
SOURCE (Princeton)KDM5A
Genetics Home Reference (NIH)KDM5A
Genomic and cartography
GoldenPath hg38 (UCSC)KDM5A  -     chr12:280057-389320 -  12p13.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM5A  -     12p13.33   [Description]    (hg19-Feb_2009)
GoldenPathKDM5A - 12p13.33 [CytoView hg19]  KDM5A - 12p13.33 [CytoView hg38]
ImmunoBaseENSG00000073614
Genome Data Viewer NCBIKDM5A [Mapview hg19]  
OMIM180202   
Gene and transcription
Genbank (Entrez)AA101935 AB209999 AF007135 AK057703 AK225060
RefSeq transcript (Entrez)NM_001042603 NM_005056
Consensus coding sequences : CCDS (NCBI)KDM5A
Gene ExpressionKDM5A [ NCBI-GEO ]   KDM5A [ EBI - ARRAY_EXPRESS ]   KDM5A [ SEEK ]   KDM5A [ MEM ]
Gene Expression Viewer (FireBrowse)KDM5A [ Firebrowse - Broad ]
GenevisibleExpression of KDM5A in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5927
GTEX Portal (Tissue expression)KDM5A
Human Protein AtlasENSG00000073614-KDM5A [pathology]   [cell]   [tissue]
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
PhosPhoSitePlusP29375
Domaine pattern : Prosite (Expaxy)ARID (PS51011)    JMJC (PS51184)    JMJN (PS51183)    ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domains : Interpro (EBI)ARID_dom    ARID_dom_sf    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
PDB (RSDB)2JXJ    2KGG    2KGI    3GL6    5C11    5CEH    5E6H    5ISL    5IVB    5IVC    5IVE    5IVF    5IVJ    5IVV    5IVY    5IW0    5IWF    5K4L    5V9P    5V9T    6BGU    6BGV    6BGW    6BGX    6BGY    6BGZ    6BH0    6BH1    6BH2    6BH3    6BH4    6BH5    6DQ4    6DQ5    6DQ6    6DQ7    6DQ8    6DQ9    6DQA    6DQB    6DQC    6DQD    6DQE    6DQF   
PDB Europe2JXJ    2KGG    2KGI    3GL6    5C11    5CEH    5E6H    5ISL    5IVB    5IVC    5IVE    5IVF    5IVJ    5IVV    5IVY    5IW0    5IWF    5K4L    5V9P    5V9T    6BGU    6BGV    6BGW    6BGX    6BGY    6BGZ    6BH0    6BH1    6BH2    6BH3    6BH4    6BH5    6DQ4    6DQ5    6DQ6    6DQ7    6DQ8    6DQ9    6DQA    6DQB    6DQC    6DQD    6DQE    6DQF   
PDB (PDBSum)2JXJ    2KGG    2KGI    3GL6    5C11    5CEH    5E6H    5ISL    5IVB    5IVC    5IVE    5IVF    5IVJ    5IVV    5IVY    5IW0    5IWF    5K4L    5V9P    5V9T    6BGU    6BGV    6BGW    6BGX    6BGY    6BGZ    6BH0    6BH1    6BH2    6BH3    6BH4    6BH5    6DQ4    6DQ5    6DQ6    6DQ7    6DQ8    6DQ9    6DQA    6DQB    6DQC    6DQD    6DQE    6DQF   
PDB (IMB)2JXJ    2KGG    2KGI    3GL6    5C11    5CEH    5E6H    5ISL    5IVB    5IVC    5IVE    5IVF    5IVJ    5IVV    5IVY    5IW0    5IWF    5K4L    5V9P    5V9T    6BGU    6BGV    6BGW    6BGX    6BGY    6BGZ    6BH0    6BH1    6BH2    6BH3    6BH4    6BH5    6DQ4    6DQ5    6DQ6    6DQ7    6DQ8    6DQ9    6DQA    6DQB    6DQC    6DQD    6DQE    6DQF   
Structural Biology KnowledgeBase2JXJ    2KGG    2KGI    3GL6    5C11    5CEH    5E6H    5ISL    5IVB    5IVC    5IVE    5IVF    5IVJ    5IVV    5IVY    5IW0    5IWF    5K4L    5V9P    5V9T    6BGU    6BGV    6BGW    6BGX    6BGY    6BGZ    6BH0    6BH1    6BH2    6BH3    6BH4    6BH5    6DQ4    6DQ5    6DQ6    6DQ7    6DQ8    6DQ9    6DQA    6DQB    6DQC    6DQD    6DQE    6DQF   
SCOP (Structural Classification of Proteins)2JXJ    2KGG    2KGI    3GL6    5C11    5CEH    5E6H    5ISL    5IVB    5IVC    5IVE    5IVF    5IVJ    5IVV    5IVY    5IW0    5IWF    5K4L    5V9P    5V9T    6BGU    6BGV    6BGW    6BGX    6BGY    6BGZ    6BH0    6BH1    6BH2    6BH3    6BH4    6BH5    6DQ4    6DQ5    6DQ6    6DQ7    6DQ8    6DQ9    6DQA    6DQB    6DQC    6DQD    6DQE    6DQF   
CATH (Classification of proteins structures)2JXJ    2KGG    2KGI    3GL6    5C11    5CEH    5E6H    5ISL    5IVB    5IVC    5IVE    5IVF    5IVJ    5IVV    5IVY    5IW0    5IWF    5K4L    5V9P    5V9T    6BGU    6BGV    6BGW    6BGX    6BGY    6BGZ    6BH0    6BH1    6BH2    6BH3    6BH4    6BH5    6DQ4    6DQ5    6DQ6    6DQ7    6DQ8    6DQ9    6DQA    6DQB    6DQC    6DQD    6DQE    6DQF   
SuperfamilyP29375
AlphaFold pdb e-kbP29375   
Human Protein Atlas [tissue]ENSG00000073614-KDM5A [tissue]
HPRD08915
Protein Interaction databases
DIP (DOE-UCLA)P29375
IntAct (EBI)P29375
BioGRIDKDM5A
STRING (EMBL)KDM5A
ZODIACKDM5A
Ontologies - Pathways
QuickGOP29375
Ontology : AmiGOtranscription cis-regulatory region binding  DNA binding  transcription coactivator activity  protein binding  nucleus  nucleus  nucleoplasm  nucleolus  chromatin remodeling  spermatogenesis  zinc ion binding  male gonad development  histone demethylase activity  circadian regulation of gene expression  histone demethylase activity (H3-trimethyl-K4 specific)  histone demethylase activity (H3-trimethyl-K4 specific)  histone demethylase activity (H3-dimethyl-K4 specific)  histone H3-K4 demethylation  histone H3-K4 demethylation, trimethyl-H3-K4-specific  methylated histone binding  histone binding  positive regulation of transcription, DNA-templated  regulation of DNA-binding transcription factor activity  dioxygenase activity  negative regulation of histone deacetylase activity  
Ontology : EGO-EBItranscription cis-regulatory region binding  DNA binding  transcription coactivator activity  protein binding  nucleus  nucleus  nucleoplasm  nucleolus  chromatin remodeling  spermatogenesis  zinc ion binding  male gonad development  histone demethylase activity  circadian regulation of gene expression  histone demethylase activity (H3-trimethyl-K4 specific)  histone demethylase activity (H3-trimethyl-K4 specific)  histone demethylase activity (H3-dimethyl-K4 specific)  histone H3-K4 demethylation  histone H3-K4 demethylation, trimethyl-H3-K4-specific  methylated histone binding  histone binding  positive regulation of transcription, DNA-templated  regulation of DNA-binding transcription factor activity  dioxygenase activity  negative regulation of histone deacetylase activity  
NDEx NetworkKDM5A
Atlas of Cancer Signalling NetworkKDM5A
Wikipedia pathwaysKDM5A
Orthology - Evolution
OrthoDB5927
GeneTree (enSembl)ENSG00000073614
Phylogenetic Trees/Animal Genes : TreeFamKDM5A
Homologs : HomoloGeneKDM5A
Homology/Alignments : Family Browser (UCSC)KDM5A
Gene fusions - Rearrangements
Fusion : MitelmanIQSEC3::KDM5A [12p13.33/12p13.33]  
Fusion : MitelmanKDM5A::ANO2 [12p13.33/12p13.31]  
Fusion : MitelmanKDM5A::CCDC77 [12p13.33/12p13.33]  
Fusion : MitelmanKDM5A::NINJ2 [12p13.33/12p13.33]  
Fusion : MitelmanKDM5A::RAE1 [12p13.33/20q13.31]  
Fusion : MitelmanNUP98::KDM5A [11p15.4/12p13.33]  
Fusion : MitelmanWNK1::KDM5A [12p13.33/12p13.33]  
Fusion : COSMICNUP98 [11p15.4]  -  KDM5A [12p13.33]  [fusion_2291]  [fusion_2294]  
Fusion Cancer (Beijing)KDM5A [12p13.33]  -  PDXDC1 [16p13.11]  [FUSC002421]  [FUSC002421]
Fusion : QuiverKDM5A
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM5A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM5A
dbVarKDM5A
ClinVarKDM5A
MonarchKDM5A
1000_GenomesKDM5A 
Exome Variant ServerKDM5A
GNOMAD BrowserENSG00000073614
Varsome BrowserKDM5A
ACMGKDM5A variants
VarityP29375
Genomic Variants (DGV)KDM5A [DGVbeta]
DECIPHERKDM5A [patients]   [syndromes]   [variants]   [genes]  
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]  
Somatic Mutations in Cancer : COSMIC3DKDM5A
Mutations and Diseases : HGMDKDM5A
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaKDM5A
DgiDB (Drug Gene Interaction Database)KDM5A
DoCM (Curated mutations)KDM5A
CIViC (Clinical Interpretations of Variants in Cancer)KDM5A
OncoKBKDM5A
NCG (London)KDM5A
Cancer3DKDM5A
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM180202   
Orphanet
DisGeNETKDM5A
MedgenKDM5A
Genetic Testing Registry KDM5A
NextProtP29375 [Medical]
GENETestsKDM5A
Target ValidationKDM5A
Huge Navigator KDM5A [HugePedia]
ClinGenKDM5A
Clinical trials, drugs, therapy
MyCancerGenomeKDM5A
Protein Interactions : CTDKDM5A
Pharm GKB GenePA34250
PharosP29375
Clinical trialKDM5A
Miscellaneous
canSAR (ICR)KDM5A
HarmonizomeKDM5A
DataMed IndexKDM5A
Probes
Litterature
PubMed97 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXKDM5A
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri Oct 8 21:20:37 CEST 2021

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.