Atlas of Genetics and Cytogenetics in Oncology and Haematology

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KDM2A (lysine demethylase 2A)

Identity

Alias_namesFBXL11
F-box and leucine-rich repeat protein 11
lysine (K)-specific demethylase 2A
Alias_symbol (synonym)KIAA1004
FBL11
LILINA
DKFZP434M1735
FBL7
FLJ00115
CXXC8
JHDM1A
Other alias
HGNC (Hugo) KDM2A
LocusID (NCBI) 22992
Atlas_Id 40540
Location 6p22.3  [Link to chromosome band 6p22]
Location_base_pair Starts at 67119269 and ends at 67258079 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
AAAS (12q13.13) / KDM2A (11q13.2)IGSF3 (1p13.1) / KDM2A (11q13.2)KDM2A (11q13.2) / C11orf80 (11q13.2)
KDM2A (11q13.2) / DDR2 (1q23.3)KDM2A (11q13.2) / FBXO3 (11p13)KDM2A (11q13.2) / GLB1L2 (11q25)
KDM2A (11q13.2) / GRIP1 (12q14.3)KDM2A (11q13.2) / KDM2A (11q13.2)KDM2A (11q13.2) / MAP3K3 (17q23.3)
KDM2A (11q13.2) / PACS1 (11q13.1)KDM2A (11q13.2) / PPP6R3 (11q13.2)KDM2A (11q13.2) / RHOD (11q13.2)
KDM2A (11q13.2) / SLC6A19 (5p15.33)KDM2A (11q13.2) / SYT12 (11q13.2)KDM2A (11q13.2) / TMEM71 (8q24.22)
PACS1 (11q13.1) / KDM2A (11q13.2)PCF11 (11q14.1) / KDM2A (11q13.2)PPP2R5B (11q13.1) / KDM2A (11q13.2)
RPS6KB2 (11q13.2) / KDM2A (11q13.2)SLC44A1 (9q31.1) / KDM2A (11q13.2)IGSF3 1p13.1 / KDM2A 11q13.2
KDM2A 11q13.2 / C11orf80 11q13.2KDM2A 11q13.2 / DDR2 1q23.3KDM2A 11q13.2 / FBXO3 11p13
KDM2A 11q13.2 / GRIP1 12q14.3KDM2A 11q13.2 / MAP3K3 17q23.3KDM2A 11q13.2 / PACS1 11q13.1
KDM2A 11q13.2 / PPP6R3 11q13.2KDM2A 11q13.2 / RHOD 11q13.2KDM2A 11q13.2 / SYT12 11q13.2
PCF11 11q14.1 / KDM2A 11q13.2PPP2R5B 11q13.1 / KDM2A 11q13.2

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 15 ]
  t(1;11)(p13;q13) IGSF3/KDM2A
t(1;11)(q23;q13) KDM2A/DDR2
t(3;11)(q25;q13) KDM2A/WWTR1
t(11;11)(p13;q13) KDM2A/FBXO3
KDM2A/C11orf80 (11q13)
KDM2A/PACS1 (11q13)
KDM2A/PPP6R3 (11q13)
KDM2A/RHOD (11q13)
KDM2A/SYT12 (11q13)
PACS1/KDM2A (11q13)
PPP2R5B/KDM2A (11q13)
t(11;11)(q13;q14) PCF11/KDM2A
t(11;11)(q13;q25) KDM2A/GLB1L2
t(11;12)(q13;q14) KDM2A/GRIP1
t(11;17)(q13;q23) KDM2A/MAP3K3

External links

Nomenclature
HGNC (Hugo)KDM2A   13606
Cards
Entrez_Gene (NCBI)KDM2A  22992  lysine demethylase 2A
AliasesCXXC8; FBL11; FBL7; FBXL11; 
JHDM1A; LILINA
GeneCards (Weizmann)KDM2A
Ensembl hg19 (Hinxton)ENSG00000173120 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000173120 [Gene_View]  ENSG00000173120 [Sequence]  chr11:67119269-67258079 [Contig_View]  KDM2A [Vega]
ICGC DataPortalENSG00000173120
TCGA cBioPortalKDM2A
AceView (NCBI)KDM2A
Genatlas (Paris)KDM2A
WikiGenes22992
SOURCE (Princeton)KDM2A
Genetics Home Reference (NIH)KDM2A
Genomic and cartography
GoldenPath hg38 (UCSC)KDM2A  -     chr11:67119269-67258079 +  6p22.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM2A  -     6p22.3   [Description]    (hg19-Feb_2009)
EnsemblKDM2A - 6p22.3 [CytoView hg19]  KDM2A - 6p22.3 [CytoView hg38]
Mapping of homologs : NCBIKDM2A [Mapview hg19]  KDM2A [Mapview hg38]
OMIM605657   
Gene and transcription
Genbank (Entrez)AB023221 AB490246 AF179221 AI185920 AK022684
RefSeq transcript (Entrez)NM_001256405 NM_012308
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)KDM2A
Cluster EST : UnigeneHs.124147 [ NCBI ]
CGAP (NCI)Hs.124147
Alternative Splicing GalleryENSG00000173120
Gene ExpressionKDM2A [ NCBI-GEO ]   KDM2A [ EBI - ARRAY_EXPRESS ]   KDM2A [ SEEK ]   KDM2A [ MEM ]
Gene Expression Viewer (FireBrowse)KDM2A [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)22992
GTEX Portal (Tissue expression)KDM2A
Human Protein AtlasENSG00000173120-KDM2A [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9Y2K7   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9Y2K7  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9Y2K7
Splice isoforms : SwissVarQ9Y2K7
PhosPhoSitePlusQ9Y2K7
Domaine pattern : Prosite (Expaxy)JMJC (PS51184)    ZF_CXXC (PS51058)    ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domains : Interpro (EBI)F-box_dom    JmjC_dom    Leu-rich_rpt_Cys-con_subtyp    LRR_dom_sf    Zinc_finger_PHD-type_CS    Znf_CXXC    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)F-box (PF00646)    JmjC (PF02373)    PHD_4 (PF16866)    zf-CXXC (PF02008)   
Domain families : Pfam (NCBI)pfam00646    pfam02373    pfam16866    pfam02008   
Domain families : Smart (EMBL)JmjC (SM00558)  LRR_CC (SM00367)  PHD (SM00249)  
Conserved Domain (NCBI)KDM2A
DMDM Disease mutations22992
Blocks (Seattle)KDM2A
PDB (SRS)2YU1    2YU2    4BBQ   
PDB (PDBSum)2YU1    2YU2    4BBQ   
PDB (IMB)2YU1    2YU2    4BBQ   
PDB (RSDB)2YU1    2YU2    4BBQ   
Structural Biology KnowledgeBase2YU1    2YU2    4BBQ   
SCOP (Structural Classification of Proteins)2YU1    2YU2    4BBQ   
CATH (Classification of proteins structures)2YU1    2YU2    4BBQ   
SuperfamilyQ9Y2K7
Human Protein Atlas [tissue]ENSG00000173120-KDM2A [tissue]
Peptide AtlasQ9Y2K7
HPRD05741
IPIIPI00166009   IPI00739880   IPI00737083   IPI00908626   IPI00975919   
Protein Interaction databases
DIP (DOE-UCLA)Q9Y2K7
IntAct (EBI)Q9Y2K7
FunCoupENSG00000173120
BioGRIDKDM2A
STRING (EMBL)KDM2A
ZODIACKDM2A
Ontologies - Pathways
QuickGOQ9Y2K7
Ontology : AmiGORNA polymerase II transcription factor activity, sequence-specific DNA binding  DNA binding  protein binding  nucleoplasm  double-strand break repair via nonhomologous end joining  transcription, DNA-templated  regulation of transcription by RNA polymerase II  zinc ion binding  histone demethylase activity  histone demethylase activity (H3-K36 specific)  oxidation-reduction process  histone H3-K36 demethylation  
Ontology : EGO-EBIRNA polymerase II transcription factor activity, sequence-specific DNA binding  DNA binding  protein binding  nucleoplasm  double-strand break repair via nonhomologous end joining  transcription, DNA-templated  regulation of transcription by RNA polymerase II  zinc ion binding  histone demethylase activity  histone demethylase activity (H3-K36 specific)  oxidation-reduction process  histone H3-K36 demethylation  
NDEx NetworkKDM2A
Atlas of Cancer Signalling NetworkKDM2A
Wikipedia pathwaysKDM2A
Orthology - Evolution
OrthoDB22992
GeneTree (enSembl)ENSG00000173120
Phylogenetic Trees/Animal Genes : TreeFamKDM2A
HOVERGENQ9Y2K7
HOGENOMQ9Y2K7
Homologs : HomoloGeneKDM2A
Homology/Alignments : Family Browser (UCSC)KDM2A
Gene fusions - Rearrangements
Fusion : MitelmanIGSF3/KDM2A [1p13.1/11q13.2]  [t(1;11)(p13;q13)]  
Fusion : MitelmanKDM2A/C11orf80 [11q13.2/11q13.2]  [t(11;11)(q13;q13)]  
Fusion : MitelmanKDM2A/DDR2 [11q13.2/1q23.3]  [t(1;11)(q23;q13)]  
Fusion : MitelmanKDM2A/FBXO3 [11q13.2/11p13]  [t(11;11)(p13;q13)]  
Fusion : MitelmanKDM2A/GRIP1 [11q13.2/12q14.3]  [t(11;12)(q13;q14)]  
Fusion : MitelmanKDM2A/MAP3K3 [11q13.2/17q23.3]  [t(11;17)(q13;q23)]  
Fusion : MitelmanKDM2A/PACS1 [11q13.2/11q13.1]  [t(11;11)(q13;q13)]  
Fusion : MitelmanKDM2A/PPP6R3 [11q13.2/11q13.2]  [t(11;11)(q13;q13)]  
Fusion : MitelmanKDM2A/RHOD [11q13.2/11q13.2]  [t(11;11)(q13;q13)]  
Fusion : MitelmanKDM2A/SYT12 [11q13.2/11q13.2]  [t(11;11)(q13;q13)]  
Fusion : MitelmanPCF11/KDM2A [11q14.1/11q13.2]  [t(11;11)(q13;q14)]  
Fusion : MitelmanPPP2R5B/KDM2A [11q13.1/11q13.2]  [t(11;11)(q13;q13)]  
Fusion PortalIGSF3 1p13.1 KDM2A 11q13.2 BRCA
Fusion PortalKDM2A 11q13.2 C11orf80 11q13.2 LUSC PRAD
Fusion PortalKDM2A 11q13.2 DDR2 1q23.3 LUAD
Fusion PortalKDM2A 11q13.2 FBXO3 11p13 BRCA
Fusion PortalKDM2A 11q13.2 GRIP1 12q14.3 BRCA
Fusion PortalKDM2A 11q13.2 MAP3K3 17q23.3 BRCA
Fusion PortalKDM2A 11q13.2 PACS1 11q13.1 KIRC LUAD
Fusion PortalKDM2A 11q13.2 PPP6R3 11q13.2 BRCA
Fusion PortalKDM2A 11q13.2 RHOD 11q13.2 BRCA LUSC
Fusion PortalKDM2A 11q13.2 SYT12 11q13.2 BRCA GBM
Fusion PortalPCF11 11q14.1 KDM2A 11q13.2 BRCA
Fusion PortalPPP2R5B 11q13.1 KDM2A 11q13.2 BRCA
Fusion : QuiverKDM2A
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM2A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM2A
dbVarKDM2A
ClinVarKDM2A
1000_GenomesKDM2A 
Exome Variant ServerKDM2A
ExAC (Exome Aggregation Consortium)ENSG00000173120
GNOMAD BrowserENSG00000173120
Varsome BrowserKDM2A
Genetic variants : HAPMAP22992
Genomic Variants (DGV)KDM2A [DGVbeta]
DECIPHERKDM2A [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisKDM2A 
Mutations
ICGC Data PortalKDM2A 
TCGA Data PortalKDM2A 
Broad Tumor PortalKDM2A
OASIS PortalKDM2A [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICKDM2A  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDKDM2A
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
BioMutasearch KDM2A
DgiDB (Drug Gene Interaction Database)KDM2A
DoCM (Curated mutations)KDM2A (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM2A (select a term)
intoGenKDM2A
Cancer3DKDM2A(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605657   
Orphanet
DisGeNETKDM2A
MedgenKDM2A
Genetic Testing Registry KDM2A
NextProtQ9Y2K7 [Medical]
TSGene22992
GENETestsKDM2A
Target ValidationKDM2A
Huge Navigator KDM2A [HugePedia]
snp3D : Map Gene to Disease22992
BioCentury BCIQKDM2A
ClinGenKDM2A
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD22992
Chemical/Pharm GKB GenePA164721195
Clinical trialKDM2A
Miscellaneous
canSAR (ICR)KDM2A (select the gene name)
Probes
Litterature
PubMed63 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM2A
EVEXKDM2A
GoPubMedKDM2A
iHOPKDM2A
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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