Seroatlas · Human Serome Atlas

KDM5D

Lysine-specific demethylase 5D

Also known as: HY, HYA, JARID1D, KDM5D_HUMAN, KIAA0234, SMCY

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

Protein identityUniProt · HPA

UniProt accession: Q9BY66
Gene: KDM5D
Ensembl: ENSG00000012817
Chromosome: Y
Canonical length: 1539 aa
Protein class: Enzymes, Plasma proteins, Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoli fibrillar center

OverviewNCBI Gene

This gene encodes a protein containing zinc finger domains. A short peptide derived from this protein is a minor histocompatibility antigen which can lead to graft rejection of male donor cells in a female recipient. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

Canonical amino-acid sequenceUniProt

1539 residues, UniProt reviewed canonical sequence.

>Q9BY66|KDM5D
     1  MEPGCDEFLP PPECPVFEPS WAEFQDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV
    61  DNFRFTPRVQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERKIL DLYSLSKIVI
   121  EEGGYEAICK DRRWARVAQR LHYPPGKNIG SLLRSHYERI IYPYEMFQSG ANHVQCNTHP
   181  FDNEVKDKEY KPHSIPLRQS VQPSKFSSYS RRAKRLQPDP EPTEEDIEKH PELKKLQIYG
   241  PGPKMMGLGL MAKDKDKTVH KKVTCPPTVT VKDEQSGGGN VSSTLLKQHL SLEPCTKTTM
   301  QLRKNHSSAQ FIDSYICQVC SRGDEDDKLL FCDGCDDNYH IFCLLPPLPE IPRGIWRCPK
   361  CILAECKQPP EAFGFEQATQ EYSLQSFGEM ADSFKSDYFN MPVHMVPTEL VEKEFWRLVS
   421  SIEEDVTVEY GADIHSKEFG SGFPVSNSKQ NLSPEEKEYA TSGWNLNVMP VLDQSVLCHI
   481  NADISGMKVP WLYVGMVFSA FCWHIEDHWS YSINYLHWGE PKTWYGVPSL AAEHLEEVMK
   541  MLTPELFDSQ PDLLHQLVTL MNPNTLMSHG VPVVRTNQCA GEFVITFPRA YHSGFNQGYN
   601  FAEAVNFCTA DWLPAGRQCI EHYRRLRRYC VFSHEELICK MAAFPETLDL NLAVAVHKEM
   661  FIMVQEERRL RKALLEKGVT EAEREAFELL PDDERQCIKC KTTCFLSALA CYDCPDGLVC
   721  LSHINDLCKC SSSRQYLRYR YTLDELPTML HKLKIRAESF DTWANKVRVA LEVEDGRKRS
   781  FEELRALESE ARERRFPNSE LLQRLKNCLS EVEACIAQVL GLVSGQVARM DTPQLTLTEL
   841  RVLLEQMGSL PCAMHQIGDV KDVLEQVEAY QAEAREALAT LPSSPGLLRS LLERGQQLGV
   901  EVPEAHQLQQ QVEQAQWLDE VKQALAPSAH RGSLVIMQGL LVMGAKIASS PSVDKARAEL
   961  QELLTIAERW EEKAHFCLEA RQKHPPATLE AIIRETENIP VHLPNIQALK EALTKAQAWI
  1021  ADVDEIQNGD HYPCLDDLEG LVAVGRDLPV GLEELRQLEL QVLTAHSWRE KASKTFLKKN
  1081  SCYTLLEVLC PCADAGSDST KRSRWMEKAL GLYQCDTELL GLSAQDLRDP GSVIVAFKEG
  1141  EQKEKEGILQ LRRTNSAKPS PLAPSLMASS PTSICVCGQV PAGVGVLQCD LCQDWFHGQC
  1201  VSVPHLLTSP KPSLTSSPLL AWWEWDTKFL CPLCMRSRRP RLETILALLV ALQRLPVRLP
  1261  EGEALQCLTE RAIGWQDRAR KALASEDVTA LLRQLAELRQ QLQAKPRPEE ASVYTSATAC
  1321  DPIREGSGNN ISKVQGLLEN GDSVTSPENM APGKGSDLEL LSSLLPQLTG PVLELPEAIR
  1381  APLEELMMEG DLLEVTLDEN HSIWQLLQAG QPPDLDRIRT LLELEKFEHQ GSRTRSRALE
  1441  RRRRRQKVDQ GRNVENLVQQ ELQSKRARSS GIMSQVGREE EHYQEKADRE NMFLTPSTDH
  1501  SPFLKGNQNS LQHKDSGSSA ACPSLMPLLQ LSYSDEQQL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against KDM5D 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): 0.34
Highest tissue expression: 33 nTPM

Expression across tissuesHPA

Tissue

small intestine: 33 nTPM
adrenal gland: 30 nTPM
spleen: 29 nTPM
prostate: 25 nTPM
tongue: 24 nTPM
colon: 22 nTPM

Single-cell type

retinal bipolar cells: 92 nCPM
leydig cells: 85 nCPM
myonuclei: 84 nCPM
oligodendrocytes: 80 nCPM
choroid plexus epithelial cells: 78 nCPM
retinal amacrine cells: 72 nCPM

Immune cell

memory B-cell: 3.2 nTPM
naive B-cell: 2.6 nTPM
plasmacytoid DC: 2.6 nTPM
naive CD4 T-cell: 2.4 nTPM
gdT-cell: 2.3 nTPM
memory CD4 T-cell: 2.2 nTPM

Brain region

choroid plexus: 15 nTPM
white matter: 13 nTPM
medulla oblongata: 12 nTPM
cerebral cortex: 12 nTPM
cerebellum: 11 nTPM
pons: 11 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about KDM5D.

Disease | ImmuneIEDB

Conditions an epitope on KDM5D was assayed in.

rejection of transplanted organs and tissues T cell

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): 0.36
gnomAD pLI: 0.93
gnomAD missense Z: -0.37
DepMap mean gene effect: 0.4
DepMap dependency class: none

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of KDM5D in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads KDM5D as an antibody target. Whether an autoantibody or antibody against KDM5D could matter depends on whether native KDM5D is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

KDM5D 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 KDM5D as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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