Seroatlas · Human Serome Atlas

XPNPEP3

Xaa-Pro aminopeptidase 3

Also known as: APP3, ICP55, NPHPL1, XPP3_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q9NQH7
Gene: XPNPEP3
Ensembl: ENSG00000196236
Chromosome: 22
Canonical length: 507 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins
Subcellular location: Mitochondria,Cytosol
Quaternary structure: Homodimer

OverviewNCBI Gene

The protein encoded by this gene belongs to the family of X-pro-aminopeptidases that utilize a metal cofactor, and remove the N-terminal amino acid from peptides with a proline residue in the penultimate position. This protein has been shown to localize to the mitochondria of renal cells, and have a role in ciliary function. Mutations in this gene are associated with nephronophthisis-like nephropathy-1. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene, however, expression of some of these isoforms in vivo is not known.[provided by RefSeq, Mar 2011]

Canonical amino-acid sequenceUniProt

507 residues, UniProt reviewed canonical sequence.

>Q9NQH7|XPNPEP3
     1  MPWLLSAPKL VPAVANVRGL SGCMLCSQRR YSLQPVPERR IPNRYLGQPS PFTHPHLLRP
    61  GEVTPGLSQV EYALRRHKLM SLIQKEAQGQ SGTDQTVVVL SNPTYYMSND IPYTFHQDNN
   121  FLYLCGFQEP DSILVLQSLP GKQLPSHKAI LFVPRRDPSR ELWDGPRSGT DGAIALTGVD
   181  EAYTLEEFQH LLPKMKAETN MVWYDWMRPS HAQLHSDYMQ PLTEAKAKSK NKVRGVQQLI
   241  QRLRLIKSPA EIERMQIAGK LTSQAFIETM FTSKAPVEEA FLYAKFEFEC RARGADILAY
   301  PPVVAGGNRS NTLHYVKNNQ LIKDGEMVLL DGGCESSCYV SDITRTWPVN GRFTAPQAEL
   361  YEAVLEIQRD CLALCFPGTS LENIYSMMLT LIGQKLKDLG IMKNIKENNA FKAARKYCPH
   421  HVGHYLGMDV HDTPDMPRSL PLQPGMVITI EPGIYIPEDD KDAPEKFRGL GVRIEDDVVV
   481  TQDSPLILSA DCPKEMNDIE QICSQAS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against XPNPEP3 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): 0.26
Highest tissue expression: 14 nTPM

Expression across tissuesHPA

Tissue

duodenum: 14 nTPM
small intestine: 9.5 nTPM
liver: 7.9 nTPM
thymus: 5.5 nTPM
skin: 5.2 nTPM
heart muscle: 5.1 nTPM

Single-cell type

late spermatids: 458 nCPM
early spermatids: 376 nCPM
respiratory ciliated cells: 136 nCPM
late primary spermatocytes: 136 nCPM
choroid plexus epithelial cells: 116 nCPM
ependymal cells: 114 nCPM

Immune cell

non-classical monocyte: 7 nTPM
plasmacytoid DC: 3.8 nTPM
memory B-cell: 3.7 nTPM
neutrophil: 3.6 nTPM
eosinophil: 2.9 nTPM
total PBMC: 2.8 nTPM

Brain region

white matter: 18 nTPM
cerebellum: 18 nTPM
cerebral cortex: 16 nTPM
hippocampal formation: 16 nTPM
medulla oblongata: 15 nTPM
choroid plexus: 15 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about XPNPEP3.

Disease | AllUniProt

Conditions XPNPEP3 is implicated in, by any mechanism.

Nephronophthisis-like nephropathy 1 (NPHPL1) MIM:613159

Disease | GeneticClinVar

19 pathogenic / likely-pathogenic of 387 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Nephronophthisis-like nephropathy 1
Papillary renal cell carcinoma type 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): 0.88
gnomAD pLI: 0
gnomAD missense Z: -0.1
DepMap mean gene effect: -0.1
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% 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 XPNPEP3 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 XPNPEP3 as an antibody target. Whether an autoantibody or antibody against XPNPEP3 could matter depends on whether native XPNPEP3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

XPNPEP3 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 XPNPEP3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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