XPNPEP3 Gene
X-prolyl aminopeptidase 3 (mitochondrial)
Gene Information Card
| Symbol | XPNPEP3 |
|---|---|
| Full Name | X-prolyl aminopeptidase 3 |
| Gene Type | Protein coding |
| Chromosomal Location | 22q13.32 |
| NCBI Gene ID | 63929 ncbi.nlm.nih.gov/gene/63929 |
| Ensembl ID | ENSG00000100227 |
| UniProt ID | Q9NQH7 |
| OMIM ID | 613553 |
| HGNC ID | 28058 |
| Aliases | APP3, NPHPL1, XPNPEP3 |
Description
XPNPEP3 encodes a mitochondrial aminopeptidase that specifically cleaves N-terminal amino acids adjacent to proline residues. The enzyme is involved in mitochondrial protein processing and turnover. Mutations in this gene are associated with nephronophthisis-like nephropathy (NPHPL1), a ciliopathy characterized by renal fibrosis and cyst formation.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Nephronophthisis-like nephropathy 1 (NPHPL1) | Loss-of-function mutations impair mitochondrial aminopeptidase activity, leading to defective ciliary signaling and renal tubular degeneration. | OMIM #613159; ClinVar pathogenic variants |
| Chronic kidney disease (susceptibility) | Hypomorphic variants may contribute to progressive renal fibrosis. | ClinVar; literature association |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Kidney | 12.5 | Medium |
| Liver | 8.3 | Medium |
| Heart | 6.1 | Low |
| Brain | 4.2 | Low |
| Testis | 3.8 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK 293 | 15.2 | High expression |
| HepG2 | 9.7 | Moderate expression |
| K-562 | 5.1 | Low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.433C>T (p.Arg145*) | Nonsense | Rare | Loss of function; truncation |
| c.664G>A (p.Gly222Arg) | Missense | Rare | Impaired catalytic activity |
| c.1042_1043del (p.Leu348Glufs*2) | Frameshift | Rare | Loss of function |
Mutation functional classification
Loss of Function (LOF)
Nonsense and frameshift mutations (e.g., p.Arg145*, p.Leu348Glufs*2) lead to truncated, non-functional protein, causing NPHPL1.
Gain of Function (GOF)
No gain-of-function mutations reported.
Dominant Negative (DN)
No dominant-negative mutations reported.
View complete mutation data：
Gene Ontology (GO)
| • aminopeptidase activity (GO:0004177) | • peptidase activity (GO:0008233) |
| • mitochondrion (GO:0005739) | • proteolysis (GO:0006508) |
| • zinc ion binding (GO:0008270) |
Pathways
• Mitochondrial protein processing (Reactome: R-HSA-8949215)
• Peptide hormone metabolism (Reactome: R-HSA-2980736)
Protein Summary
XPNPEP3 is a 507-amino acid mitochondrial metalloaminopeptidase that removes N-terminal proline residues from peptides. It contains a conserved M24 peptidase domain and requires zinc for catalytic activity. The protein is expressed in kidney, liver, and heart, and localizes to the mitochondrial matrix. Defects in this enzyme disrupt mitochondrial proteostasis and are linked to renal ciliopathy.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| XPNPEP3 Knockout HEK293 Cell Line | EDJ-KQ16163 | Human | 63929 | Details Get a Quote |
| XPNPEP3 Knockout HCT 116 Cell Line | EDJ-KQ46129 | Human | 63929 | Details Get a Quote |
| XPNPEP3 Knockout A-549 Cell Line | EDJ-KQ47357 | Human | 63929 | Details Get a Quote |
| XPNPEP3 Knockout HeLa Cell Line | EDJ-KQ47359 | Human | 63929 | Details Get a Quote |
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