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Aliases for XPNPEP3 Gene

Aliases for XPNPEP3 Gene

  • X-Prolyl Aminopeptidase 3 2 3 5
  • X-Prolyl Aminopeptidase (Aminopeptidase P) 3, Putative 2 3
  • X-Prolyl Aminopeptidase 3, Mitochondrial 2 3
  • Intermediate Cleaving Peptidase 55 2 3
  • X-Pro Aminopeptidase 3 3 4
  • APP3 3 4
  • Probable Xaa-Pro Aminopeptidase 3 3
  • Aminopeptidase P3 4
  • EC 4
  • NPHPL1 3
  • ICP55 3

External Ids for XPNPEP3 Gene

Previous GeneCards Identifiers for XPNPEP3 Gene

  • GC22P039583
  • GC22P041253
  • GC22P024215

Summaries for XPNPEP3 Gene

Entrez Gene Summary for XPNPEP3 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]

GeneCards Summary for XPNPEP3 Gene

XPNPEP3 (X-Prolyl Aminopeptidase 3) is a Protein Coding gene. Diseases associated with XPNPEP3 include Nephronophthisis-Like Nephropathy 1 and Late-Onset Nephronophthisis. GO annotations related to this gene include metallopeptidase activity and aminopeptidase activity.

Gene Wiki entry for XPNPEP3 Gene

No data available for UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for XPNPEP3 Gene

Genomics for XPNPEP3 Gene

Regulatory Elements for XPNPEP3 Gene

Enhancers for XPNPEP3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22F040764 0.9 Ensembl ENCODE 20.5 -92.2 -92177 1.8 POLR2A CREM SPI1 XPNPEP3 ST13 LOC101927257 LOC100313968 GC22M040968
GH22F040682 1.2 FANTOM5 Ensembl ENCODE 18 -172.9 -172868 3.6 TBL1XR1 RAD21 EGR1 ZNF366 ZNF143 FOS CREM EGR2 ZNF263 ZNF654 XPNPEP3 LOC101927257 ST13 MCHR1 GC22M040968 LOC100313968
GH22F040780 0.5 ENCODE 17.4 -75.3 -75280 2.0 SCRT1 DPF2 RAD21 HIC1 GATA3 POLR2A SCRT2 ZNF600 XPNPEP3 SLC25A17 ST13 LOC101927257 LOC100313968 GC22M040968
GH22F040875 0.5 ENCODE 17.1 +21.2 21188 5.5 ZNF316 MAFF ZNF362 POLR2A EMSY MAFK XPNPEP3 GC22P040894 PIR48000
GH22F040720 0.5 Ensembl ENCODE 16.8 -135.8 -135778 1.4 ELF3 PKNOX1 INSM2 KLF17 FEZF1 ZNF366 SCRT2 ZNF391 EGR2 ZNF263 XPNPEP3 LOC101927257 ST13 GC22M040968 LOC100313968
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around XPNPEP3 on UCSC Golden Path with GeneCards custom track

Genomic Location for XPNPEP3 Gene

40,857,077 bp from pter
40,932,819 bp from pter
75,743 bases
Plus strand

Genomic View for XPNPEP3 Gene

Genes around XPNPEP3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
XPNPEP3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for XPNPEP3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for XPNPEP3 Gene

Proteins for XPNPEP3 Gene

  • Protein details for XPNPEP3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Probable Xaa-Pro aminopeptidase 3
    Protein Accession:
    Secondary Accessions:
    • B2R9G1
    • B7Z790
    • B7Z7B2
    • Q6I9V9
    • Q8NDA6
    • Q9BV27
    • Q9BVH0

    Protein attributes for XPNPEP3 Gene

    507 amino acids
    Molecular mass:
    57034 Da
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for XPNPEP3 Gene


neXtProt entry for XPNPEP3 Gene

Post-translational modifications for XPNPEP3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for XPNPEP3 Gene

No data available for DME Specific Peptides for XPNPEP3 Gene

Domains & Families for XPNPEP3 Gene

Gene Families for XPNPEP3 Gene

Suggested Antigen Peptide Sequences for XPNPEP3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase M24B family.
  • Belongs to the peptidase M24B family.
genes like me logo Genes that share domains with XPNPEP3: view

Function for XPNPEP3 Gene

Molecular function for XPNPEP3 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Release of any N-terminal amino acid, including proline, that is linked to proline, even from a dipeptide or tripeptide.

Enzyme Numbers (IUBMB) for XPNPEP3 Gene

Gene Ontology (GO) - Molecular Function for XPNPEP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004177 aminopeptidase activity IMP 20179356
GO:0008233 peptidase activity IEA --
GO:0008237 metallopeptidase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0030145 manganese ion binding IEA --
genes like me logo Genes that share ontologies with XPNPEP3: view
genes like me logo Genes that share phenotypes with XPNPEP3: view

Human Phenotype Ontology for XPNPEP3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for XPNPEP3

miRNA for XPNPEP3 Gene

miRTarBase miRNAs that target XPNPEP3

Inhibitory RNA Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for XPNPEP3 Gene

Localization for XPNPEP3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for XPNPEP3 Gene


Subcellular locations from

Jensen Localization Image for XPNPEP3 Gene COMPARTMENTS Subcellular localization image for XPNPEP3 gene
Compartment Confidence
extracellular 5
mitochondrion 5
cytosol 1
nucleus 1

Gene Ontology (GO) - Cellular Components for XPNPEP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IDA 20179356
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with XPNPEP3: view

Pathways & Interactions for XPNPEP3 Gene

SuperPathways for XPNPEP3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for XPNPEP3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003094 glomerular filtration IMP 20179356
GO:0006508 proteolysis IEA --
GO:0016485 protein processing IMP 20179356
genes like me logo Genes that share ontologies with XPNPEP3: view

No data available for Pathways by source and SIGNOR curated interactions for XPNPEP3 Gene

Drugs & Compounds for XPNPEP3 Gene

(2) Drugs for XPNPEP3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Manganese Approved Nutra 34
Cobalt Pharma 165
genes like me logo Genes that share compounds with XPNPEP3: view

Transcripts for XPNPEP3 Gene

Unigene Clusters for XPNPEP3 Gene

X-prolyl aminopeptidase (aminopeptidase P) 3, putative:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for XPNPEP3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15
SP1: - - - -
SP2: - - - - -
SP3: - - - -
SP4: - - -
SP5: - -
SP6: -
SP7: - - -

Relevant External Links for XPNPEP3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for XPNPEP3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for XPNPEP3 Gene

Protein differential expression in normal tissues from HIPED for XPNPEP3 Gene

This gene is overexpressed in Adrenal (11.0), Heart (7.9), and Testis (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for XPNPEP3 Gene

Protein tissue co-expression partners for XPNPEP3 Gene

NURSA nuclear receptor signaling pathways regulating expression of XPNPEP3 Gene:


SOURCE GeneReport for Unigene cluster for XPNPEP3 Gene:


mRNA Expression by UniProt/SwissProt for XPNPEP3 Gene:

Tissue specificity: Isoform 1 and isoform 2 are widely expressed, with isoform 1 being more abundant.
genes like me logo Genes that share expression patterns with XPNPEP3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for XPNPEP3 Gene

Orthologs for XPNPEP3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for XPNPEP3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia XPNPEP3 34 35
  • 99.61 (n)
(Canis familiaris)
Mammalia XPNPEP3 34 35
  • 90.6 (n)
(Bos Taurus)
Mammalia XPNPEP3 34 35
  • 88.03 (n)
(Rattus norvegicus)
Mammalia Xpnpep3 34
  • 87.81 (n)
(Mus musculus)
Mammalia Xpnpep3 35
  • 85 (a)
(Ornithorhynchus anatinus)
Mammalia XPNPEP3 35
  • 84 (a)
(Monodelphis domestica)
Mammalia XPNPEP3 35
  • 81 (a)
(Gallus gallus)
Aves XPNPEP3 34 35
  • 74.48 (n)
(Anolis carolinensis)
Reptilia XPNPEP3 35
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia xpnpep3 34
  • 68.1 (n)
Str.10537 34
(Danio rerio)
Actinopterygii xpnpep3 34 35
  • 61.82 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG9581 34 35
  • 50.71 (n)
CG32454 35
  • 22 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000887 34
  • 50.51 (n)
(Caenorhabditis elegans)
Secernentea R119.2 35
  • 35 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL028W 34
  • 47.77 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ICP55 34 35 37
  • 47.63 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C07645g 34
  • 44.94 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G09300 34
  • 50.07 (n)
(Oryza sativa)
Liliopsida Os12g0563500 34
  • 48.42 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05971 34
  • 47.48 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes icp55 34
  • 47.37 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 37 (a)
Species where no ortholog for XPNPEP3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for XPNPEP3 Gene

Gene Tree for XPNPEP3 (if available)
Gene Tree for XPNPEP3 (if available)

Paralogs for XPNPEP3 Gene

No data available for Paralogs for XPNPEP3 Gene

Variants for XPNPEP3 Gene

Sequence variations from dbSNP and Humsavar for XPNPEP3 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs267607179 Nephronophthisis-like nephropathy 1 (NPHPL1) [MIM:613159], Pathogenic 40,924,482(+) AGCCC(G/T)GTAAG reference, missense
rs761504767 Likely benign 40,922,399(+) GCCCT(C/T)TGCTT reference, synonymous-codon
rs143719656 Uncertain significance 40,886,305(+) TTCTC(A/G)TTCTA intron-variant
rs746834434 Uncertain significance 40,909,157(+) GACAT(G/T)TTAGC reference, missense
rs79385822 Uncertain significance 40,924,369(+) TGCTC(A/G)AAAAT reference, missense

Structural Variations from Database of Genomic Variants (DGV) for XPNPEP3 Gene

Variant ID Type Subtype PubMed ID
esv2667574 CNV deletion 23128226
esv3647784 CNV loss 21293372
nsv1058653 CNV gain 25217958
nsv1109471 CNV deletion 24896259
nsv1109472 CNV deletion 24896259
nsv1114323 CNV deletion 24896259
nsv1124863 CNV duplication 24896259
nsv3635 CNV insertion 18451855
nsv428389 CNV loss 18775914

Variation tolerance for XPNPEP3 Gene

Residual Variation Intolerance Score: 9.05% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.87; 18.15% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for XPNPEP3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for XPNPEP3 Gene

Disorders for XPNPEP3 Gene

MalaCards: The human disease database

(6) MalaCards diseases for XPNPEP3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
nephronophthisis-like nephropathy 1
  • nphpl1
late-onset nephronophthisis
  • medullary cystic disease
senior-loken syndrome-1
  • senior-loken syndrome
hypertension, essential
  • hypertension, essential 3
- elite association - COSMIC cancer census association via MalaCards


  • Nephronophthisis-like nephropathy 1 (NPHPL1) [MIM:613159]: A disorder with features of nephronophthisis, a cystic kidney disease leading to end-stage renal failure. Nephronophthisis is histologically characterized by modifications of the tubules with thickening of the basement membrane, interstitial fibrosis and, in the advanced stages, medullary cysts. Typical clinical manifestation are chronic renal failure, anemia, polyuria, polydipsia, isosthenuria, and growth retardation. Associations with extrarenal symptoms are frequent. In NPHPL1 patients, extrarenal symptoms include hypertension, essential tremor, sensorineural hearing loss and gout. Severely affected individuals can manifest a mitochondrial disorder with isolated complex I deficiency activity in muscle, seizures, mental retardation and hypertrophic dilated cardiomyopathy. {ECO:0000269 PubMed:20179356}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for XPNPEP3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with XPNPEP3: view

No data available for Genatlas for XPNPEP3 Gene

Publications for XPNPEP3 Gene

  1. Individuals with mutations in XPNPEP3, which encodes a mitochondrial protein, develop a nephronophthisis-like nephropathy. (PMID: 20179356) O'Toole J.F. … Hildebrandt F. (J. Clin. Invest. 2010) 2 3 4 64
  2. Aminopeptidase P isozyme expression in human tissues and peripheral blood mononuclear cell fractions. (PMID: 15708373) Ersahin C. … Simmons W.H. (Arch. Biochem. Biophys. 2005) 2 3 4 64
  3. Mitochondrial aminopeptidase deletion increases chronological lifespan and oxidative stress resistance while decreasing respiratory metabolism in S. cerevisiae. (PMID: 24116217) Stames E.M. … O'Toole J.F. (PLoS ONE 2013) 2 3 64
  4. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins J.E. … Dunham I. (Genome Biol. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for XPNPEP3 Gene

Sources for XPNPEP3 Gene

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