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KDM5C (lysine demethylase 5C)

Identity

Alias (NCBI)DXS1272E
JARID1C
MRX13
MRXJ
MRXSCJ
MRXSJ
SMCX
XE169
HGNC (Hugo) KDM5C
HGNC Alias symbDXS1272E
XE169
HGNC Previous nameSMCX
 JARID1C
 MRX13
HGNC Previous nameJumonji, 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
LocusID (NCBI) 8242
Atlas_Id 50851
Location Xp11.22  [Link to chromosome band Xp11]
Location_base_pair Starts at 53192159 and ends at 53225207 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    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]  ENSG00000126012 [Sequence]  chrX:53192159-53225207 [Contig_View]  KDM5C [Vega]
ICGC DataPortalENSG00000126012
TCGA cBioPortalKDM5C
AceView (NCBI)KDM5C
Genatlas (Paris)KDM5C
SOURCE (Princeton)KDM5C
Genetics Home Reference (NIH)KDM5C
Genomic and cartography
GoldenPath hg38 (UCSC)KDM5C  -     chrX:53192159-53225207 -  Xp11.22   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)KDM5C  -     Xp11.22   [Description]    (hg19-Feb_2009)
GoldenPathKDM5C - Xp11.22 [CytoView hg19]  KDM5C - Xp11.22 [CytoView hg38]
ImmunoBaseENSG00000126012
Genome Data Viewer NCBIKDM5C [Mapview hg19]  
OMIM300534   314690   
Gene and transcription
Genbank (Entrez)AI221739 AK304732 AK308077 BC047751 BC054499
RefSeq transcript (Entrez)NM_001146702 NM_001282622 NM_001353978 NM_001353979 NM_001353981 NM_001353982 NM_001353984 NM_004187
Consensus coding sequences : CCDS (NCBI)KDM5C
Gene ExpressionKDM5C [ NCBI-GEO ]   KDM5C [ EBI - ARRAY_EXPRESS ]   KDM5C [ SEEK ]   KDM5C [ MEM ]
Gene Expression Viewer (FireBrowse)KDM5C [ Firebrowse - Broad ]
GenevisibleExpression of KDM5C 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
PhosPhoSitePlusP41229
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)KDM5C
PDB (RSDB)2JRZ    5FWJ   
PDB Europe2JRZ    5FWJ   
PDB (PDBSum)2JRZ    5FWJ   
PDB (IMB)2JRZ    5FWJ   
Structural Biology KnowledgeBase2JRZ    5FWJ   
SCOP (Structural Classification of Proteins)2JRZ    5FWJ   
CATH (Classification of proteins structures)2JRZ    5FWJ   
SuperfamilyP41229
AlphaFold pdb e-kbP41229   
Human Protein Atlas [tissue]ENSG00000126012-KDM5C [tissue]
HPRD02442
Protein Interaction databases
DIP (DOE-UCLA)P41229
IntAct (EBI)P41229
BioGRIDKDM5C
STRING (EMBL)KDM5C
ZODIACKDM5C
Ontologies - Pathways
QuickGOP41229
Ontology : AmiGODNA binding  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytosol  chromatin remodeling  zinc ion binding  response to toxic substance  histone demethylase activity  histone demethylase activity (H3-K4 specific)  histone demethylase activity (H3-K4 specific)  histone demethylase activity (H3-trimethyl-K4 specific)  histone H3-K4 demethylation  histone H3-K4 demethylation  histone H3-K4 demethylation, trimethyl-H3-K4-specific  negative regulation of transcription, DNA-templated  rhythmic process  dioxygenase activity  
Ontology : EGO-EBIDNA binding  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytosol  chromatin remodeling  zinc ion binding  response to toxic substance  histone demethylase activity  histone demethylase activity (H3-K4 specific)  histone demethylase activity (H3-K4 specific)  histone demethylase activity (H3-trimethyl-K4 specific)  histone H3-K4 demethylation  histone H3-K4 demethylation  histone H3-K4 demethylation, trimethyl-H3-K4-specific  negative regulation of transcription, DNA-templated  rhythmic process  dioxygenase activity  
NDEx NetworkKDM5C
Atlas of Cancer Signalling NetworkKDM5C
Wikipedia pathwaysKDM5C
Orthology - Evolution
OrthoDB8242
GeneTree (enSembl)ENSG00000126012
Phylogenetic Trees/Animal Genes : TreeFamKDM5C
Homologs : HomoloGeneKDM5C
Homology/Alignments : Family Browser (UCSC)KDM5C
Gene fusions - Rearrangements
Fusion : MitelmanKDM5C/PPP4R1 [Xp11.22/18p11.22]  
Fusion : QuiverKDM5C
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerKDM5C [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)KDM5C
dbVarKDM5C
ClinVarKDM5C
MonarchKDM5C
1000_GenomesKDM5C 
Exome Variant ServerKDM5C
GNOMAD BrowserENSG00000126012
Varsome BrowserKDM5C
ACMGKDM5C variants
VarityP41229
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]  
Somatic Mutations in Cancer : COSMIC3DKDM5C
Mutations and Diseases : HGMDKDM5C
intOGen PortalKDM5C
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaKDM5C
DgiDB (Drug Gene Interaction Database)KDM5C
DoCM (Curated mutations)KDM5C
CIViC (Clinical Interpretations of Variants in Cancer)KDM5C
Cancer3DKDM5C
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM300534    314690   
Orphanet11669   
DisGeNETKDM5C
MedgenKDM5C
Genetic Testing Registry KDM5C
NextProtP41229 [Medical]
GENETestsKDM5C
Target ValidationKDM5C
Huge Navigator KDM5C [HugePedia]
ClinGenKDM5C (curated)
Clinical trials, drugs, therapy
MyCancerGenomeKDM5C
Protein Interactions : CTDKDM5C
Pharm GKB GenePA35964
PharosP41229
Drug Sensitivity KDM5C
Clinical trialKDM5C
Miscellaneous
canSAR (ICR)KDM5C
HarmonizomeKDM5C
DataMed IndexKDM5C
Probes
Litterature
PubMed79 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXKDM5C
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 4 15:14:52 CEST 2021

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