Seroatlas · Human Serome Atlas

APEX2

DNA-(apurinic or apyrimidinic site) endonuclease 2

Also known as: APE2, APEX2_HUMAN, APEXL2, XTH2, ZGRF2

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

Protein identityUniProt · HPA

UniProt accession: Q9UBZ4
Gene: APEX2
Ensembl: ENSG00000169188
Chromosome: X
Canonical length: 518 aa
Protein class: Enzymes, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Nucleoli fibrillar center,Vesicles

OverviewNCBI Gene

Apurinic/apyrimidinic (AP) sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. AP sites are pre-mutagenic lesions that can prevent normal DNA replication so the cell contains systems to identify and repair such sites. Class II AP endonucleases cleave the phosphodiester backbone 5' to the AP site. This gene encodes a protein shown to have a weak class II AP endonuclease activity. Most of the encoded protein is located in the nucleus but some is also present in mitochondria. This protein may play an important role in both nuclear and mitochondrial base excision repair. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2012]

Canonical amino-acid sequenceUniProt

518 residues, UniProt reviewed canonical sequence.

>Q9UBZ4|APEX2
     1  MLRVVSWNIN GIRRPLQGVA NQEPSNCAAV AVGRILDELD ADIVCLQETK VTRDALTEPL
    61  AIVEGYNSYF SFSRNRSGYS GVATFCKDNA TPVAAEEGLS GLFATQNGDV GCYGNMDEFT
   121  QEELRALDSE GRALLTQHKI RTWEGKEKTL TLINVYCPHA DPGRPERLVF KMRFYRLLQI
   181  RAEALLAAGS HVIILGDLNT AHRPIDHWDA VNLECFEEDP GRKWMDSLLS NLGCQSASHV
   241  GPFIDSYRCF QPKQEGAFTC WSAVTGARHL NYGSRLDYVL GDRTLVIDTF QASFLLPEVM
   301  GSDHCPVGAV LSVSSVPAKQ CPPLCTRFLP EFAGTQLKIL RFLVPLEQSP VLEQSTLQHN
   361  NQTRVQTCQN KAQVRSTRPQ PSQVGSSRGQ KNLKSYFQPS PSCPQASPDI ELPSLPLMSA
   421  LMTPKTPEEK AVAKVVKGQA KTSEAKDEKE LRTSFWKSVL AGPLRTPLCG GHREPCVMRT
   481  VKKPGPNLGR RFYMCARPRG PPTDPSSRCN FFLWSRPS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against APEX2 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): 0.37
Highest tissue expression: 15 nTPM

Expression across tissuesHPA

Tissue

esophagus: 15 nTPM
tonsil: 13 nTPM
skin: 12 nTPM
kidney: 11 nTPM
spleen: 11 nTPM
lymph node: 11 nTPM

Single-cell type

migrating cytotrophoblasts: 60 nCPM
cytotrophoblasts: 58 nCPM
syncytiotrophoblasts: 54 nCPM
extravillous trophoblasts: 41 nCPM
esophageal basal cells: 34 nCPM
oocytes: 32 nCPM

Immune cell

NK-cell: 42 nTPM
basophil: 16 nTPM
intermediate monocyte: 14 nTPM
myeloid DC: 14 nTPM
non-classical monocyte: 13 nTPM
eosinophil: 13 nTPM

Brain region

white matter: 7.2 nTPM
thalamus: 7 nTPM
choroid plexus: 6.7 nTPM
hypothalamus: 6.6 nTPM
medulla oblongata: 6.6 nTPM
cerebral cortex: 6.5 nTPM

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): 0.27
gnomAD pLI: 0.97
gnomAD missense Z: 0.56
DepMap mean gene effect: -0.14
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 APEX2 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

PCNA

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads APEX2 as an antibody target. Whether an autoantibody or antibody against APEX2 could matter depends on whether native APEX2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

APEX2 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 APEX2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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