Alternative titles; symbolsAMINOPEPTIDASE P3; APP3HGNC Approved Gene Symbol: XPNPEP3Cytogenetic location: 22q13.2 Genomic coordinates (GRCh38): 22:40,857,147...
Alternative titles; symbols
HGNC Approved Gene Symbol: XPNPEP3
Cytogenetic location: 22q13.2 Genomic coordinates (GRCh38): 22:40,857,147-40,932,814 (from NCBI)
XPNPEP3 belongs to a family of X-pro-aminopeptidases (EC 188.8.131.52) that utilize a metal cofactor and remove the N-terminal amino acid from peptides with a proline residue in the penultimate position (summary by Ersahin et al., 2005).
▼ Cloning and Expression
By searching a human genome database, Ersahin et al. (2005) identified XPNPEP3, which they called APP3. The deduced 507-amino acid protein has a calculated molecular mass of 57 kD. APP3 had an N-terminal mitochondrial targeting sequence with 2 sites for proteolytic cleavage, and a C-terminal catalytic domain. Overall, APP3 shares 33% sequence identity with E. coli App, but only 12% and 16% identity, respectively, with human APP1 (XPNPEP1; 602443) or APP2 (XPNPEP2; 300145). Both E. coli App and human APP3 have 2 Mn(2+)-binding sites, 3 residues that contribute to proline binding, 2 histidines required for catalysis, and a dead-end residue for substrate binding that ensures cleavage of an X-pro bond only if X is the N-terminal amino acid. Ersahin et al. (2005) identified a splice variant that includes exon 3 and results in utilization of an translation initiation codon in exon 4 and a deduced protein lacking the N-terminal mitochondrial localization signal. PCR analysis revealed both isoforms in all tissues examined, with highest expression in heart followed by pancreas, kidney, and testis. It was also expressed in T cells, B cells, and monocytes. Transcripts encoding the predicted mitochondrial protein predominated in all samples.
Using Western blot analysis, O'Toole et al. (2010) showed that mature processed XPNPEP3 was expressed at an apparent molecular mass of 51 kD in human, monkey, and dog cell lines. Mature Xpnpep3 was detected in the mitochondrial fraction of homogenized whole mouse kidney, while a doublet at about 57 kD, representing immature Xpnpep3, partitioned in the cytosolic fraction. Immunofluorescence microscopy of rat kidney showed Xpnpep3 was specifically expressed in distal convoluted tubules, cortical collecting duct cells, and intercalated cells, but not in principal cells. Transmission electron microscopy confirmed mitochondrial localization of Xpnpep3 in rat kidney.
▼ Gene Function
By database analysis, O'Toole et al. (2010) identified 426 likely ciliary proteins with an N-terminal penultimate proline (after N-terminal methionine cleavage). Of these proteins, the bacterial ortholog of XPNPEP3 hydrolyzed CEP290 (610142), ALMS1 (606844), and LRRC50 (613190), but not dynein (see 600112).
▼ Gene Structure
Ersahin et al. (2005) determined that the XPNPEP3 gene contains 11 exons. O'Toole et al. (2010) reported that the XPNPEP3 gene spans 70.8 kb.
By genomic sequence analysis, Ersahin et al. (2005) mapped the XPNPEP3 gene to chromosome 22q13.31-q13.33. By genomic sequence analysis, O'Toole et al. (2010) mapped the XPNPEP3 gene to chromosome 22q13.2.
▼ Molecular Genetics
O'Toole et al. (2010) identified homozygosity for a splice site mutation in the XPNPEP3 gene (613553.0001) in affected sibs of a Finnish family with nephronophthisis-like nephropathy-1 (NPHPL1; 613159) and a 4-bp deletion (613553.0002) in the XPNPEP3 gene in affected sibs of a Turkish family with NPHPL1. The affected Finnish sibs were less severely affected, suggesting that a splice site mutation may have resulted in some residual protein product, whereas the affected Turkish sibs were more severely affected and had a truncating mutation predicting complete loss of protein function. O'Toole et al. (2010) postulated a defect in ciliary function as explanation for the phenotype. Mutation analysis of the XPNPEP3 gene in 823 additional families with nephronophthisis-like phenotype did not find any kindred with homozygosity for XPNPEP3 mutation.
In a 13-year-old girl, born of consanguineous Iranian parents, with NPHPL1, Alizadeh et al. (2020) identified a homozygous frameshift mutation in the XPNPEP3 gene (613553.0003). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not present in public databases, including gnomAD. Functional studies of the variant were not performed, but it was predicted to elicit nonsense-mediated mRNA, resulting in a loss of function.
▼ Animal Model
O'Toole et al. (2010) showed that suppression of Xpnpep3 expression in zebrafish led to defects in gastrulation that were similar to those showed by ciliary gene morphants, including shortened body axis, small anterior structures, broadening and kinking of the notochord, and elongated somites. These defects were rescued with full-length human XPNPEP3 and with XPNPEP3 lacking the mitochondrial localization signal.
▼ ALLELIC VARIANTS ( 3 Selected Examples):
.0001 NEPHRONOPHTHISIS-LIKE NEPHROPATHY 1
In 3 affected sibs of a consanguineous Finnish family with nephronophthisis-like nephropathy-1 (NPHPL1; 613159), O'Toole et al. (2010) identified a homozygous 1357G-T transversion in the last base of exon 9 of the XPNPEP3 gene, resulting in a gly453-to-cys (G453C) substitution in a highly conserved residue. The mutation occurs in an 80% conserved exonic position of the splice donor consensus sequence, and RT-PCR from lymphoblastoid cells showed that the G453C mutation disrupted correct splicing by activating a cryptic splice site, adding 31 nucleotides from intron 9, and introducing a frameshift that resulted in premature termination in exon 10. There was also a faint band at the size of the wildtype splice product, suggesting some residual correct splicing. The mutation was not found in 118 Western European controls but was found in 1 of 100 Finnish controls. Haplotype analysis suggested a founder effect. All 3 patients developed moderate renal insufficiency (glomerular filtration rate at 30-40% of normal) between 20 and 29 years of age. Renal biopsies showed characteristic features of nephronophthisis, such as thickening, splitting, and attenuation of the tubular basement membrane, atrophic tubules, and mild interstitial fibrosis. Renal ultrasound revealed increased echogenicity in 3 and cysts in 2. All had hypertension. Extrarenal features included essential tremor in 3, high frequency sensorineural hearing loss in 2, and arachnoid cysts on brain imaging in 1. Two also had gout. Skeletal muscle mitochondrial respiratory activity was normal.
.0002 NEPHRONOPHTHISIS-LIKE NEPHROPATHY 1
XPNPEP3, 4-BP DEL, 931AACA
In 2 affected sibs from a consanguineous Turkish family with nephronophthisis-like nephropathy-1 (NPHPL1; 613159), O'Toole et al. (2010) identified a homozygous 4-bp deletion (931delAACA) in exon 6 of the XPNPEP3 gene, resulting in premature termination within the predicted prolidase domain, which is the catalytic domain. The mutation was not found in 150 European controls or in 83 Turkish controls. The mutation was predicted to result in complete loss of protein function. The patients had a severe disorder, with end-stage renal disease by 8 and 9 years of age, respectively. Renal ultrasound and renal histology demonstrated nephronophthisis. In addition, both affected individuals showed a mitochondrial disorder, with isolated complex I deficiency activity in muscle and had seizures, mental retardation, and hypertrophic dilated cardiomyopathy. One had chronic pancreatitis with pancreatic cysts, while the other had hepatic involvement.
.0003 NEPHRONOPHTHISIS-LIKE NEPHROPATHY 1
XPNPEP3, 1-BP INS, 719A
In a 13-year-old girl, born of consanguineous Iranian parents, with nephronophthisis-like nephropathy-1 (NPHPL1; 613159), Alizadeh et al. (2020) identified a homozygous 1-bp insertion (c.719_720insA, NM_022098.2) in exon 4 of the XPNPEP3 gene, resulting in a frameshift and premature termination (Gln241ThrfsTer13). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not present in public databases, including gnomAD. Functional studies of the variant were not performed, but it was predicted to elicit nonsense-mediated mRNA, resulting in a loss of function. She presented with chronic kidney disease at 3 years of age. Follow-up clinical data was not reported.