Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
8242
Gene name Gene Name - the full gene name approved by the HGNC.
Lysine demethylase 5C
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
KDM5C
Synonyms (NCBI Gene) Gene synonyms aliases
DXS1272E, JARID1C, MRX13, MRXJ, MRXS16, MRXSCJ, MRXSJ, SMCX, XE169
Chromosome Chromosome number
X
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
Xp11.22
Summary Summary of gene provided in NCBI Entrez Gene.
This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chr
SNPs SNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs35353912 G>A,C Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance, benign Coding sequence variant, non coding transcript variant, synonymous variant
rs138520224 G>A Conflicting-interpretations-of-pathogenicity Coding sequence variant, non coding transcript variant, synonymous variant
rs199422235 C>G Likely-pathogenic, pathogenic Non coding transcript variant, coding sequence variant, missense variant
rs199422237 G>A,C Pathogenic Synonymous variant, non coding transcript variant, coding sequence variant, missense variant
rs199422239 C>T Pathogenic Missense variant, non coding transcript variant, coding sequence variant, intron variant
miRNA miRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT050192 hsa-miR-26a-5p CLASH 23622248
MIRT044496 hsa-miR-320a CLASH 23622248
MIRT043887 hsa-miR-378a-3p CLASH 23622248
MIRT042989 hsa-miR-324-3p CLASH 23622248
MIRT042424 hsa-miR-425-3p CLASH 23622248
Transcription factors
Transcription factor Regulation Reference
ARX Unknown 23246292
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin IBA
GO:0003677 Function DNA binding IEA
GO:0005515 Function Protein binding IPI 17468742, 20133580
GO:0005634 Component Nucleus IBA
GO:0005634 Component Nucleus IDA 18078810
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
314690 11114 ENSG00000126012
Protein
UniProt ID P41229
Protein name Lysine-specific demethylase 5C (EC 1.14.11.67) (Histone demethylase JARID1C) (Jumonji/ARID domain-containing protein 1C) (Protein SmcX) (Protein Xe169) ([histone H3]-trimethyl-L-lysine(4) demethylase 5C)
Protein function Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:28262558). Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylat
PDB 2JRZ , 5FWJ
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF02375 JmjN 15 48 jmjN domain Family
PF01388 ARID 81 165 ARID/BRIGHT DNA binding domain Domain
PF00628 PHD 326 374 PHD-finger Domain
PF02373 JmjC 501 617 JmjC domain, hydroxylase Domain
PF02928 zf-C5HC2 707 759 C5HC2 zinc finger Domain
PF08429 PLU-1 772 1100 PLU-1-like protein Family
Tissue specificity TISSUE SPECIFICITY: Expressed in all tissues examined. Highest levels found in brain and skeletal muscle. {ECO:0000269|PubMed:15586325}.
Sequence
MEPGSDDFLPPPECPVFEPSWAEFRDPLGYIAKIRPIAEKSGICKIRPPADWQPPFAVEV
DNFRFTPRIQRLNELEAQTRVKLNYLDQIAKFWEIQGSSLKIPNVERRILDLYSLSKIVV
EEGGYEAICKDRRWARVAQRLNYPPGKNIGSLLRSHYERIVYPYE
MYQSGANLVQCNTRP
FDNEEKDKEYKPHSIPLRQSVQPSKFNSYGRRAKRLQPDPEPTEEDIEKNPELKKLQIYG
AGPKMMGLGLMAKDKTLRKKDKEGPECPPTVVVKEELGGDVKVESTSPKTFLESKEELSH
SPEPCTKMTMRLRRNHSNAQFIESYVCRMCSRGDEDDKLLLCDGCDDNYHIFCLLPPLPE
IPKGVWRCPKCVMA
ECKRPPEAFGFEQATREYTLQSFGEMADSFKADYFNMPVHMVPTEL
VEKEFWRLVNSIEEDVTVEYGADIHSKEFGSGFPVSDSKRHLTPEEEEYATSGWNLNVMP
VLEQSVLCHINADISGMKVPWLYVGMVFSAFCWHIEDHWSYSINYLHWGEPKTWYGVPSL
AAEHLEEVMKKLTPELFDSQPDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRA
YHSGFNQGYNFAEAVNF
CTADWLPAGRQCIEHYRRLRRYCVFSHEELICKMAACPEKLDL
NLAAAVHKEMFIMVQEERRLRKALLEKGITEAEREAFELLPDDERQCIKCKTTCFLSALA
CYDCPDGLVCLSHINDLCKCSSSRQYLRYRYTLDELPAM
LHKLKVRAESFDTWANKVRVA
LEVEDGRKRSLEELRALESEARERRFPNSELLQQLKNCLSEAEACVSRALGLVSGQEAGP
HRVAGLQMTLTELRAFLDQMNNLPCAMHQIGDVKGVLEQVEAYQAEAREALASLPSSPGL
LQSLLERGRQLGVEVPEAQQLQRQVEQARWLDEVKRTLAPSARRGTLAVMRGLLVAGASV
APSPAVDKAQAELQELLTIAERWEEKAHLCLEARQKHPPATLEAIIREAENIPVHLPNIQ
ALKEALAKARAWIADVDEIQNGDHYPCLDDLEGLVAVGRDLPVGLEELRQLELQVLTAHS
WREKASKTFLKKNSCYTLLE
VLCPCADAGSDSTKRSRWMEKELGLYKSDTELLGLSAQDL
RDPGSVIVAFKEGEQKEKEGILQLRRTNSAKPSPLASSSTASSTTSICVCGQVLAGAGAL
QCDLCQDWFHGRCVSVPRLLSSPRPNPTSSPLLAWWEWDTKFLCPLCMRSRRPRLETILA
LLVALQRLPVRLPEGEALQCLTERAISWQGRARQALASEDVTALLGRLAELRQRLQAEPR
PEEPPNYPAAPASDPLREGSGKDMPKVQGLLENGDSVTSPEKVAPEEGSGKRDLELLSSL
LPQLTGPVLELPEATRAPLEELMMEGDLLEVTLDENHSIWQLLQAGQPPDLERIRTLLEL
EKAERHGSRARGRALERRRRRKVDRGGEGDDPAREELEPKRVRSSGPEAEEVQEEEELEE
ETGGEGPPAPIPTTGSPSTQENQNGLEPAEGTTSGPSAPFSTLTPRLHLPCPQQPPQQQL
Sequence length 1560
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    HDMs demethylate histones
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Mental retardation intellectual disability rs1602226289, rs878853141, rs878853151 N/A
Mental Retardation, X-Linked Syndromic X-linked intellectual disability Claes-Jensen type rs587780372, rs1556836399, rs1602231587, rs782246658, rs1556852362, rs2073058023, rs199422234, rs782600511, rs199422235, rs886037836, rs199422236, rs1057518697, rs1569278313, rs199422237, rs1602183619
View all (10 more)
N/A
Spastic Paraplegia spastic paraplegia rs1556840029, rs1569285562, rs1569274606, rs1057518697 N/A
Multiple myeloma multiple myeloma rs1602247047 N/A
Associations from Text Mining Disease associations identified through Pubtator
Disease Name Relationship Type References
Adrenocortical Carcinoma Associate 25078331
Ataxia Associate 34530748
Autism Spectrum Disorder Associate 34089235
Axenfeld Rieger syndrome Associate 36672956
Body Dysmorphic Disorders Associate 40346491
Breast Neoplasms Associate 33977073
Carcinogenesis Stimulate 33977073
Carcinoma Non Small Cell Lung Associate 33953726
Carcinoma Renal Cell Associate 20054297, 23036577, 23644518, 24029645, 25124064, 26484545, 26527083, 27556922, 28408295, 28779136, 29132830, 29754934, 30622286, 34439859, 35444164
View all (1 more)
Clear cell metastatic renal cell carcinoma Associate 27751729