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Aliases for XPNPEP3 Gene

Aliases for XPNPEP3 Gene

  • X-Prolyl Aminopeptidase 3 2 3 5
  • X-Prolyl Aminopeptidase 3, Mitochondrial 2 3
  • Intermediate Cleaving Peptidase 55 2 3
  • X-Pro Aminopeptidase 3 3 4
  • APP3 3 4
  • X-Prolyl Aminopeptidase (Aminopeptidase P) 3, Putative 2
  • 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. Gene Ontology (GO) annotations related to this gene include metallopeptidase activity and aminopeptidase activity.

Gene Wiki entry for XPNPEP3 Gene

Additional gene information for XPNPEP3 Gene

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

Genomics for XPNPEP3 Gene

GeneHancer (GH) Regulatory Elements for XPNPEP3 Gene

Promoters and enhancers for XPNPEP3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22I040853 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 560.9 -1.3 -1284 5.5 HDGF ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B E2F8 ZNF207 XPNPEP3 GC22M042079 ST13 EP300 ENSG00000272834 ENSG00000227413 PHF5A ENSG00000232754 TNRC6B XRCC6
GH22I040650 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 16.7 -203.7 -203744 4.9 PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 POLR2B ZNF766 ZNF213 LOC105373038 XPNPEP3 GAPDHP37 MCHR1 L3MBTL2 LOC101927257 SLC25A17 ZC3H7B ST13 PMM1
GH22I040816 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 13.5 -38.3 -38347 3.5 ARID4B SIN3A DMAP1 ZNF2 POLR2B ZNF207 ZNF143 SP3 SP5 NFYC SLC25A17 XPNPEP3 TEF LOC100313968 MIR4766
GH22I040682 Enhancer 1.4 FANTOM5 Ensembl ENCODE 18 -172.8 -172844 3.6 SIN3A ZNF207 ZNF143 FOS ATF7 RUNX3 NCOA1 JUNB REST SMARCA4 XPNPEP3 LOC101927257 ST13 MCHR1 GC22M042190 LOC100313968
GH22I040950 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 10.4 +94.5 94490 3.1 HDGF PKNOX1 SMAD1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 RBX1 EP300 XRCC6 EP300-AS1 ADSL DNAJB7 ST13 XPNPEP3 GC22P040976
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around XPNPEP3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the XPNPEP3 gene promoter:

Genomic Locations for XPNPEP3 Gene

Genomic Locations for XPNPEP3 Gene
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

    Three dimensional structures from OCA and Proteopedia for XPNPEP3 Gene

    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

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

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

Phenotypes From GWAS Catalog 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

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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for XPNPEP3 gene
Compartment Confidence
extracellular 5
mitochondrion 5
nucleus 1
cytosol 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 HDA,IDA 23376485
genes like me logo Genes that share ontologies with XPNPEP3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for XPNPEP3 Gene

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 37
Cobalt Pharma 174
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

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 CGAP 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.

Evidence on tissue expression from TISSUES for XPNPEP3 Gene

  • Lung(4.3)
  • Nervous system(3.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for XPNPEP3 Gene

Germ Layers:
  • mesoderm
  • urinary
  • kidney
genes like me logo Genes that share expression patterns with XPNPEP3: view

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 33 34
  • 99.61 (n)
(Canis familiaris)
Mammalia XPNPEP3 33 34
  • 90.6 (n)
(Bos Taurus)
Mammalia XPNPEP3 33 34
  • 88.03 (n)
(Rattus norvegicus)
Mammalia Xpnpep3 33
  • 87.81 (n)
(Mus musculus)
Mammalia Xpnpep3 34
  • 85 (a)
(Ornithorhynchus anatinus)
Mammalia XPNPEP3 34
  • 84 (a)
(Monodelphis domestica)
Mammalia XPNPEP3 34
  • 81 (a)
(Gallus gallus)
Aves XPNPEP3 33 34
  • 74.48 (n)
(Anolis carolinensis)
Reptilia XPNPEP3 34
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia xpnpep3 33
  • 68.1 (n)
Str.10537 33
(Danio rerio)
Actinopterygii xpnpep3 33 34
  • 61.82 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG9581 33 34
  • 50.71 (n)
CG32454 34
  • 22 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000887 33
  • 50.51 (n)
(Caenorhabditis elegans)
Secernentea R119.2 34
  • 35 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL028W 33
  • 47.77 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ICP55 33 34 36
  • 47.63 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C07645g 33
  • 44.94 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G09300 33
  • 50.07 (n)
(Oryza sativa)
Liliopsida Os12g0563500 33
  • 48.42 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05971 33
  • 47.48 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes icp55 33
  • 47.37 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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 Variation AA Info Type
rs1033070707 uncertain-significance, Nephronophthisis-Like Nephropathy 40,927,070(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1033510166 uncertain-significance, Nephronophthisis-Like Nephropathy 40,928,131(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs115221268 likely-benign, Nephronophthisis-Like Nephropathy 40,929,846(+) T/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs115817476 uncertain-significance, Nephronophthisis-Like Nephropathy 40,932,078(+) C/G 3_prime_UTR_variant, genic_downstream_transcript_variant
rs117568682 likely-benign, benign, Nephronophthisis-Like Nephropathy, Nephronophthisis-like nephropathy 1 40,914,230(+) T/C genic_downstream_transcript_variant, intron_variant

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)

Additional Variant Information 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: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- 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.

Additional Disease Information for XPNPEP3

Genetic Association Database
Human Genome Epidemiology 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 JF … Hildebrandt F (The Journal of clinical investigation 2010) 2 3 4 58
  2. Aminopeptidase P isozyme expression in human tissues and peripheral blood mononuclear cell fractions. (PMID: 15708373) Erşahin C … Simmons WH (Archives of biochemistry and biophysics 2005) 2 3 4 58
  3. Mitochondrial aminopeptidase deletion increases chronological lifespan and oxidative stress resistance while decreasing respiratory metabolism in S. cerevisiae. (PMID: 24116217) Stames EM … O'Toole JF (PloS one 2013) 2 3 58
  4. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for XPNPEP3 Gene

Sources for XPNPEP3 Gene

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