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KDM5C (lysine demethylase 5C)

Identity

Alias_namesSMCX
JARID1C
MRX13
Jumonji, AT rich interactive domain 1C (RBP2-like)
Smcy homolog, X-linked (mouse)
jumonji, AT rich interactive domain 1C
mental retardation, X-linked 13
lysine (K)-specific demethylase 5C
Alias_symbol (synonym)DXS1272E
XE169
Other aliasMRXJ
MRXSCJ
MRXSJ
HGNC (Hugo) KDM5C
LocusID (NCBI) 8242
Atlas_Id 50851
Location Xp11.22  [Link to chromosome band Xp11]
Location_base_pair Starts at 53191321 and ends at 53225422 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)
GUK1 (1q42.13) / KDM5C (Xp11.22)KDM5C (Xp11.22) / C1QBP (17p13.2)KDM5C (Xp11.22) / CCDC124 (19p13.11)
KDM5C (Xp11.22) / COLGALT1 (19p13.11)KDM5C (Xp11.22) / EPHA6 (3q11.2)KDM5C (Xp11.22) / KDM5C (Xp11.22)
KDM5C (Xp11.22) / PPP4R1 (18p11.22)KDM5C (Xp11.22) / PSMB7 (9q33.3)KDM5C (Xp11.22) / PTPMT1 (11p11.2)
KDM5C (Xp11.22) / UBTD2 (5q35.1)RPL11 (1p36.11) / KDM5C (Xp11.22)KDM5C Xp11.22 / PPP4R1 18p11.22

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

 


External links

Nomenclature
HGNC (Hugo)KDM5C   11114
Cards
Entrez_Gene (NCBI)KDM5C  8242  lysine demethylase 5C
AliasesDXS1272E; JARID1C; MRX13; MRXJ; 
MRXSCJ; MRXSJ; SMCX; XE169
GeneCards (Weizmann)KDM5C
Ensembl hg19 (Hinxton)ENSG00000126012 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000126012 [Gene_View]  chrX:53191321-53225422 [Contig_View]  KDM5C [Vega]
ICGC DataPortalENSG00000126012
TCGA cBioPortalKDM5C
AceView (NCBI)KDM5C
Genatlas (Paris)KDM5C
WikiGenes8242
SOURCE (Princeton)KDM5C
Genetics Home Reference (NIH)KDM5C
Genomic and cartography
GoldenPath hg38 (UCSC)KDM5C  -     chrX:53191321-53225422 -  Xp11.22   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM5C  -     Xp11.22   [Description]    (hg19-Feb_2009)
EnsemblKDM5C - Xp11.22 [CytoView hg19]  KDM5C - Xp11.22 [CytoView hg38]
Mapping of homologs : NCBIKDM5C [Mapview hg19]  KDM5C [Mapview hg38]
OMIM300534   314690   
Gene and transcription
Genbank (Entrez)AI221739 AK304732 AK308077 BC047751 BC054499
RefSeq transcript (Entrez)NM_001146702 NM_001282622 NM_004187
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)KDM5C
Cluster EST : UnigeneHs.631768 [ NCBI ]
CGAP (NCI)Hs.631768
Alternative Splicing GalleryENSG00000126012
Gene ExpressionKDM5C [ NCBI-GEO ]   KDM5C [ EBI - ARRAY_EXPRESS ]   KDM5C [ SEEK ]   KDM5C [ MEM ]
Gene Expression Viewer (FireBrowse)KDM5C [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8242
GTEX Portal (Tissue expression)KDM5C
Human Protein AtlasENSG00000126012-KDM5C [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP41229   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP41229  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP41229
Splice isoforms : SwissVarP41229
Catalytic activity : Enzyme1.14.11.- [ Enzyme-Expasy ]   1.14.11.-1.14.11.- [ IntEnz-EBI ]   1.14.11.- [ BRENDA ]   1.14.11.- [ KEGG ]   
PhosPhoSitePlusP41229
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)KDM5C
DMDM Disease mutations8242
Blocks (Seattle)KDM5C
PDB (SRS)2JRZ    5FWJ   
PDB (PDBSum)2JRZ    5FWJ   
PDB (IMB)2JRZ    5FWJ   
PDB (RSDB)2JRZ    5FWJ   
Structural Biology KnowledgeBase2JRZ    5FWJ   
SCOP (Structural Classification of Proteins)2JRZ    5FWJ   
CATH (Classification of proteins structures)2JRZ    5FWJ   
SuperfamilyP41229
Human Protein Atlas [tissue]ENSG00000126012-KDM5C [tissue]
Peptide AtlasP41229
HPRD02442
IPIIPI00013185   IPI00219412   IPI00640875   IPI01012687   IPI00879547   IPI00878406   IPI00872538   IPI00877741   
Protein Interaction databases
DIP (DOE-UCLA)P41229
IntAct (EBI)P41229
FunCoupENSG00000126012
BioGRIDKDM5C
STRING (EMBL)KDM5C
ZODIACKDM5C
Ontologies - Pathways
QuickGOP41229
Ontology : AmiGODNA binding  nucleus  nucleoplasm  nucleoplasm  cytosol  transcription, DNA-templated  zinc ion binding  response to toxic substance  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  histone demethylase activity  histone demethylase activity (H3-K4 specific)  histone H3-K4 demethylation  negative regulation of transcription, DNA-templated  rhythmic process  oxidation-reduction process  
Ontology : EGO-EBIDNA binding  nucleus  nucleoplasm  nucleoplasm  cytosol  transcription, DNA-templated  zinc ion binding  response to toxic substance  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  histone demethylase activity  histone demethylase activity (H3-K4 specific)  histone H3-K4 demethylation  negative regulation of transcription, DNA-templated  rhythmic process  oxidation-reduction process  
NDEx NetworkKDM5C
Atlas of Cancer Signalling NetworkKDM5C
Wikipedia pathwaysKDM5C
Orthology - Evolution
OrthoDB8242
GeneTree (enSembl)ENSG00000126012
Phylogenetic Trees/Animal Genes : TreeFamKDM5C
HOVERGENP41229
HOGENOMP41229
Homologs : HomoloGeneKDM5C
Homology/Alignments : Family Browser (UCSC)KDM5C
Gene fusions - Rearrangements
Fusion : MitelmanKDM5C/PPP4R1 [Xp11.22/18p11.22]  
Fusion: TCGA_MDACCKDM5C Xp11.22 PPP4R1 18p11.22 LUAD
Tumor Fusion PortalKDM5C
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM5C [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM5C
dbVarKDM5C
ClinVarKDM5C
1000_GenomesKDM5C 
Exome Variant ServerKDM5C
ExAC (Exome Aggregation Consortium)ENSG00000126012
GNOMAD BrowserENSG00000126012
Genetic variants : HAPMAP8242
Genomic Variants (DGV)KDM5C [DGVbeta]
DECIPHERKDM5C [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisKDM5C 
Mutations
ICGC Data PortalKDM5C 
TCGA Data PortalKDM5C 
Broad Tumor PortalKDM5C
OASIS PortalKDM5C [ Somatic mutations - Copy number]
Cancer Gene: CensusKDM5C 
Somatic Mutations in Cancer : COSMICKDM5C  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDKDM5C
intOGen PortalKDM5C
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 KDM5C
DgiDB (Drug Gene Interaction Database)KDM5C
DoCM (Curated mutations)KDM5C (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)KDM5C (select a term)
intoGenKDM5C
Cancer3DKDM5C(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM300534    314690   
Orphanet11669   
DisGeNETKDM5C
MedgenKDM5C
Genetic Testing Registry KDM5C
NextProtP41229 [Medical]
TSGene8242
GENETestsKDM5C
Target ValidationKDM5C
Huge Navigator KDM5C [HugePedia]
snp3D : Map Gene to Disease8242
BioCentury BCIQKDM5C
ClinGenKDM5C (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8242
Chemical/Pharm GKB GenePA35964
Drug Sensitivity KDM5C
Clinical trialKDM5C
Miscellaneous
canSAR (ICR)KDM5C (select the gene name)
Probes
Litterature
PubMed52 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineKDM5C
EVEXKDM5C
GoPubMedKDM5C
iHOPKDM5C
Genes in titleautomatic search in PubMed
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 : Tue Nov 21 14:18:46 CET 2017

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