Seroatlas · Human Serome Atlas

KDM5A

Lysine-specific demethylase 5A

Also known as: JARID1A, KDM5A_HUMAN, RBBP2

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

Protein identityUniProt · HPA

UniProt accession: P29375
Gene: KDM5A
Ensembl: ENSG00000073614
Chromosome: 12
Canonical length: 1690 aa
Protein class: Cancer-related genes, Disease related genes, Enzymes, Potential drug targets, Predicted intracellular proteins, Transcription factors
Subcellular location: Nuclear bodies,Cytosol

OverviewNCBI Gene

This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein family. The encoded protein plays a role in gene regulation through the histone code by specifically demethylating lysine 4 of histone H3. The encoded protein interacts with many other proteins, including retinoblastoma protein, and is implicated in the transcriptional regulation of Hox genes and cytokines. This gene may play a role in tumor progression. [provided by RefSeq, Aug 2013]

Canonical amino-acid sequenceUniProt

1690 residues, UniProt reviewed canonical sequence.

>P29375|KDM5A
     1  MAGVGPGGYA AEFVPPPECP VFEPSWEEFT DPLSFIGRIR PLAEKTGICK IRPPKDWQPP
    61  FACEVKSFRF TPRVQRLNEL EAMTRVRLDF LDQLAKFWEL QGSTLKIPVV ERKILDLYAL
   121  SKIVASKGGF EMVTKEKKWS KVGSRLGYLP GKGTGSLLKS HYERILYPYE LFQSGVSLMG
   181  VQMPNLDLKE KVEPEVLSTD TQTSPEPGTR MNILPKRTRR VKTQSESGDV SRNTELKKLQ
   241  IFGAGPKVVG LAMGTKDKED EVTRRRKVTN RSDAFNMQMR QRKGTLSVNF VDLYVCMFCG
   301  RGNNEDKLLL CDGCDDSYHT FCLIPPLPDV PKGDWRCPKC VAEECSKPRE AFGFEQAVRE
   361  YTLQSFGEMA DNFKSDYFNM PVHMVPTELV EKEFWRLVSS IEEDVIVEYG ADISSKDFGS
   421  GFPVKDGRRK ILPEEEEYAL SGWNLNNMPV LEQSVLAHIN VDISGMKVPW LYVGMCFSSF
   481  CWHIEDHWSY SINYLHWGEP KTWYGVPSHA AEQLEEVMRE LAPELFESQP DLLHQLVTIM
   541  NPNVLMEHGV PVYRTNQCAG EFVVTFPRAY HSGFNQGYNF AEAVNFCTAD WLPIGRQCVN
   601  HYRRLRRHCV FSHEELIFKM AADPECLDVG LAAMVCKELT LMTEEETRLR ESVVQMGVLM
   661  SEEEVFELVP DDERQCSACR TTCFLSALTC SCNPERLVCL YHPTDLCPCP MQKKCLRYRY
   721  PLEDLPSLLY GVKVRAQSYD TWVSRVTEAL SANFNHKKDL IELRVMLEDA EDRKYPENDL
   781  FRKLRDAVKE AETCASVAQL LLSKKQKHRQ SPDSGRTRTK LTVEELKAFV QQLFSLPCVI
   841  SQARQVKNLL DDVEEFHERA QEAMMDETPD SSKLQMLIDM GSSLYVELPE LPRLKQELQQ
   901  ARWLDEVRLT LSDPQQVTLD VMKKLIDSGV GLAPHHAVEK AMAELQELLT VSERWEEKAK
   961  VCLQARPRHS VASLESIVNE AKNIPAFLPN VLSLKEALQK AREWTAKVEA IQSGSNYAYL
  1021  EQLESLSAKG RPIPVRLEAL PQVESQVAAA RAWRERTGRT FLKKNSSHTL LQVLSPRTDI
  1081  GVYGSGKNRR KKVKELIEKE KEKDLDLEPL SDLEEGLEET RDTAMVVAVF KEREQKEIEA
  1141  MHSLRAANLA KMTMVDRIEE VKFCICRKTA SGFMLQCELC KDWFHNSCVP LPKSSSQKKG
  1201  SSWQAKEVKF LCPLCMRSRR PRLETILSLL VSLQKLPVRL PEGEALQCLT ERAMSWQDRA
  1261  RQALATDELS SALAKLSVLS QRMVEQAARE KTEKIISAEL QKAAANPDLQ GHLPSFQQSA
  1321  FNRVVSSVSS SPRQTMDYDD EETDSDEDIR ETYGYDMKDT ASVKSSSSLE PNLFCDEEIP
  1381  IKSEEVVTHM WTAPSFCAEH AYSSASKSCS QGSSTPRKQP RKSPLVPRSL EPPVLELSPG
  1441  AKAQLEELMM VGDLLEVSLD ETQHIWRILQ ATHPPSEDRF LHIMEDDSME EKPLKVKGKD
  1501  SSEKKRKRKL EKVEQLFGEG KQKSKELKKM DKPRKKKLKL GADKSKELNK LAKKLAKEEE
  1561  RKKKKEKAAA AKVELVKEST EKKREKKVLD IPSKYDWSGA EESDDENAVC AAQNCQRPCK
  1621  DKVDWVQCDG GCDEWFHQVC VGVSPEMAEN EDYICINCAK KQGPVSPGPA PPPSFIMSYK
  1681  LPMEDLKETS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against KDM5A 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): 0.38
Highest tissue expression: 43 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 43 nTPM
thymus: 20 nTPM
testis: 20 nTPM
lymph node: 14 nTPM
tonsil: 14 nTPM
spleen: 13 nTPM

Single-cell type

neutrophils: 483 nCPM
neutrophil progenitors: 325 nCPM
nk-cells: 188 nCPM
adrenal cortex cells: 186 nCPM
cone photoreceptor cells: 182 nCPM
early primary spermatocytes: 182 nCPM

Immune cell

basophil: 65 nTPM
neutrophil: 63 nTPM
eosinophil: 45 nTPM
NK-cell: 36 nTPM
MAIT T-cell: 32 nTPM
naive B-cell: 32 nTPM

Brain region

white matter: 51 nTPM
cerebellum: 45 nTPM
choroid plexus: 42 nTPM
cerebral cortex: 38 nTPM
basal ganglia: 38 nTPM
medulla oblongata: 36 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about KDM5A.

Disease | AllUniProt

Conditions KDM5A is implicated in, by any mechanism.

El Hayek-Chahrour neurodevelopmental syndrome (NEDEHC) MIM:620820

Disease | GeneticClinVar

12 pathogenic / likely-pathogenic of 309 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

El Hayek-Chahrour neurodevelopmental disorder
Intellectual disability
Seizure
Clear cell carcinoma of kidney

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): 0.16
gnomAD pLI: 1
gnomAD missense Z: 2.25
DepMap mean gene effect: -0.18
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 9% 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

ARID DNA-binding domain
Zinc finger, PHD-type
JmjC domain
JmjN domain
Zinc finger, C5HC2-type
Zinc finger, FYVE/PHD-type
Zinc finger, RING/FYVE/PHD-type
Lysine-specific demethylase-like domain
Zinc finger, PHD-type, conserved site
Zinc finger, PHD-finger
ARID DNA-binding domain superfamily
Lysine-specific demethylase 5, C-terminal helical domain
PHD-finger
ARID/BRIGHT DNA binding domain
JmjC domain, hydroxylase
jmjN domain
C5HC2 zinc finger
PLU-1-like protein
Lysine-specific demethylase 5, C-terminal helical domain
Lysine-specific demethylase 5A, second PHD finger
Lysine-specific demethylase 5A, third PHD-finger
Lysine-specific demethylase 5A, first PHD-finger
Lysine-specific demethylase 5A, ARID domain

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of KDM5A 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 KDM5A as an antibody target. Whether an autoantibody or antibody against KDM5A could matter depends on whether native KDM5A is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

KDM5A 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 KDM5A as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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