Seroatlas · Human Serome Atlas

KDM5C

Lysine-specific demethylase 5C

Also known as: DXS1272E, JARID1C, KDM5C_HUMAN, MRX13, SMCX, XE169

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: P41229
Gene: KDM5C
Ensembl: ENSG00000126012
Chromosome: X
Canonical length: 1560 aa
Protein class: Cancer-related genes, Disease related genes, Enzymes, Human disease related genes, Plasma proteins, Potential drug targets, Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoplasm,Cytosol

OverviewNCBI 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 chromatin remodeling. Mutations in this gene have been associated with X-linked cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

Canonical amino-acid sequenceUniProt

1560 residues, UniProt reviewed canonical sequence.

>P41229|KDM5C
     1  MEPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV
    61  DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERRIL DLYSLSKIVV
   121  EEGGYEAICK DRRWARVAQR LNYPPGKNIG SLLRSHYERI VYPYEMYQSG ANLVQCNTRP
   181  FDNEEKDKEY KPHSIPLRQS VQPSKFNSYG RRAKRLQPDP EPTEEDIEKN PELKKLQIYG
   241  AGPKMMGLGL MAKDKTLRKK DKEGPECPPT VVVKEELGGD VKVESTSPKT FLESKEELSH
   301  SPEPCTKMTM RLRRNHSNAQ FIESYVCRMC SRGDEDDKLL LCDGCDDNYH IFCLLPPLPE
   361  IPKGVWRCPK CVMAECKRPP EAFGFEQATR EYTLQSFGEM ADSFKADYFN MPVHMVPTEL
   421  VEKEFWRLVN SIEEDVTVEY GADIHSKEFG SGFPVSDSKR HLTPEEEEYA TSGWNLNVMP
   481  VLEQSVLCHI NADISGMKVP WLYVGMVFSA FCWHIEDHWS YSINYLHWGE PKTWYGVPSL
   541  AAEHLEEVMK KLTPELFDSQ PDLLHQLVTL MNPNTLMSHG VPVVRTNQCA GEFVITFPRA
   601  YHSGFNQGYN FAEAVNFCTA DWLPAGRQCI EHYRRLRRYC VFSHEELICK MAACPEKLDL
   661  NLAAAVHKEM FIMVQEERRL RKALLEKGIT EAEREAFELL PDDERQCIKC KTTCFLSALA
   721  CYDCPDGLVC LSHINDLCKC SSSRQYLRYR YTLDELPAML HKLKVRAESF DTWANKVRVA
   781  LEVEDGRKRS LEELRALESE ARERRFPNSE LLQQLKNCLS EAEACVSRAL GLVSGQEAGP
   841  HRVAGLQMTL TELRAFLDQM NNLPCAMHQI GDVKGVLEQV EAYQAEAREA LASLPSSPGL
   901  LQSLLERGRQ LGVEVPEAQQ LQRQVEQARW LDEVKRTLAP SARRGTLAVM RGLLVAGASV
   961  APSPAVDKAQ AELQELLTIA ERWEEKAHLC LEARQKHPPA TLEAIIREAE NIPVHLPNIQ
  1021  ALKEALAKAR AWIADVDEIQ NGDHYPCLDD LEGLVAVGRD LPVGLEELRQ LELQVLTAHS
  1081  WREKASKTFL KKNSCYTLLE VLCPCADAGS DSTKRSRWME KELGLYKSDT ELLGLSAQDL
  1141  RDPGSVIVAF KEGEQKEKEG ILQLRRTNSA KPSPLASSST ASSTTSICVC GQVLAGAGAL
  1201  QCDLCQDWFH GRCVSVPRLL SSPRPNPTSS PLLAWWEWDT KFLCPLCMRS RRPRLETILA
  1261  LLVALQRLPV RLPEGEALQC LTERAISWQG RARQALASED VTALLGRLAE LRQRLQAEPR
  1321  PEEPPNYPAA PASDPLREGS GKDMPKVQGL LENGDSVTSP EKVAPEEGSG KRDLELLSSL
  1381  LPQLTGPVLE LPEATRAPLE ELMMEGDLLE VTLDENHSIW QLLQAGQPPD LERIRTLLEL
  1441  EKAERHGSRA RGRALERRRR RKVDRGGEGD DPAREELEPK RVRSSGPEAE EVQEEEELEE
  1501  ETGGEGPPAP IPTTGSPSTQ ENQNGLEPAE GTTSGPSAPF STLTPRLHLP CPQQPPQQQL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against KDM5C can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.35
Highest tissue expression: 45 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 45 nTPM
thymus: 41 nTPM
esophagus: 33 nTPM
ovary: 32 nTPM
cerebellum: 32 nTPM
parathyroid gland: 32 nTPM

Single-cell type

esophageal apical cells: 86 nCPM
neutrophils: 85 nCPM
thyrotrophs: 78 nCPM
somatotrophs: 64 nCPM
endometrial glandular cells: 62 nCPM
thymocytes: 61 nCPM

Immune cell

gdT-cell: 1.5 nTPM
memory CD8 T-cell: 1.4 nTPM
neutrophil: 1.3 nTPM
MAIT T-cell: 1.2 nTPM
non-classical monocyte: 1.2 nTPM
classical monocyte: 1.1 nTPM

Brain region

cerebellum: 46 nTPM
cerebral cortex: 45 nTPM
choroid plexus: 44 nTPM
thalamus: 43 nTPM
hypothalamus: 42 nTPM
medulla oblongata: 42 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about KDM5C.

Disease | AllUniProt

Conditions KDM5C is implicated in, by any mechanism.

Intellectual developmental disorder, X-linked, syndromic, Claes-Jensen type (MRXSCJ) MIM:300534

Disease | GeneticClinVar

192 pathogenic / likely-pathogenic of 1,207 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Syndromic X-linked intellectual disability Claes-Jensen type
Spastic paraplegia
Inborn genetic diseases
Intellectual disability
Thyroid cancer, nonmedullary, 1

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.17
gnomAD pLI: 1
gnomAD missense Z: 5.15
DepMap mean gene effect: -0.21
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of KDM5C in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

ZMYND8

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads KDM5C as an antibody target. Whether an autoantibody or antibody against KDM5C could matter depends on whether native KDM5C is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

KDM5C is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label KDM5C as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Loading the interactive Seroatlas protein explorer...