Alternative titles; symbolsKIAA0673NEPHRORETININHGNC Approved Gene Symbol: NPHP4Cytogenetic location: 1p36.31 Genomic coordinates (GRCh38): 1:5,862,809-5,992...
Alternative titles; symbols
HGNC Approved Gene Symbol: NPHP4
Cytogenetic location: 1p36.31 Genomic coordinates (GRCh38): 1:5,862,809-5,992,424 (from NCBI)
▼ Cloning and Expression
Using markers covering the nephronophthisis-4 (NPHP4; 606966) locus on 1p36, Mollet et al. (2002) carried out haplotype analysis of families affected with nephronophthisis that were not linked to previously identified nephronophthisis loci. They narrowed the NPHP4 critical interval to a 1-cM region containing 6 genes, the sequences of which were available in public databases. They detected 5 mutations in the coding region of the KIAA0673 gene, which had been shown by Ishikawa et al. (1998) to be expressed in the kidney and was predicted to encode a protein containing an SH3-interacting motif. Northern blot analysis using a partial NPHP4 cDNA detected weak expression of 2 major transcripts of approximately 4.5 and 7.5 kb in kidney, skeletal muscle, heart, and liver, and to a lesser extent in brain and lung. Mollet et al. (2002) obtained a full-length NPHP4 cDNA by 5-prime and 3-prime RACE-PCR and RT-PCR. They stated that NPHP4 gene encodes a 1,250-amino acid protein that shares 86% identity with the mouse ortholog. In an erratum, they indicated that an error in sequence analysis had led to the masking of a methionine codon located 176 amino acids upstream of the previously reported initiation codon. Correction of this error indicated that NPHP4 contains 1,426 amino acids.
By use of high-resolution haplotype analysis and by demonstration of 9 likely loss-of-function mutations in 6 affected families with NPHP4, Otto et al. (2002) also identified the NPHP4 gene. They found that the deduced 1,426-amino acid protein, which they called nephroretinin, is highly conserved in evolution, with a homolog in C. elegans. Northern blot analysis revealed broad expression of a 5-kb transcript, with strong expression in skeletal muscle; dot blot analysis detected strong expression in skeletal muscle and testis.
By immunostaining mouse retina, Roepman et al. (2005) determined that Nphp1 was expressed in branching processes emanating from inner nuclear neurons, in the postsynaptic layer of the outer plexiform layer, and in cell bodies of photoreceptors. It also localized diffusely in the inner segment compartment of photoreceptors.
▼ Gene Structure
Mollet et al. (2002) and Otto et al. (2002) determined that the NPHP4 gene contains 30 exons.
Mollet et al. (2002) and Otto et al. (2002) independently cloned the NPHP4 gene from the nephronophthisis-4 critical interval on 1p36.
▼ Gene Function
Mollet et al. (2002) demonstrated the interaction of NPHP4 with NPHP1 (607100), suggesting that these 2 proteins participate in a common signaling pathway.
Mollet et al. (2005) demonstrated that NPHP4 localized to the primary cilia in polarized epithelial tubular cells, particularly at the basal bodies, and associated with alpha-tubulin (see 602529), suggesting a common role for the nephrocystin proteins in ciliary function. However, NPHP4 was also detected at the centrosomes of dividing cells and close to the cortical actin cytoskeleton in polarized cells. The proteins p130Cas (BCAR1; 602941) and PTK2B (601212) were also detected in the NPHP4-containing complex, confirming the role of the nephrocystin proteins in cell-cell and cell-matrix adhesion signaling events. Mollet et al. (2005) suggested that NPHP1 and NPHP4 belong to a multifunctional complex localized in actin- and microtubule-based structures involved in cell-cell and cell-matrix adhesion signaling, as well as in cell division.
By yeast 2-hybrid analysis, Roepman et al. (2005) determined that NPHP4 interacted with C2 domain-containing RPGRIP1 (605446) isoforms. Analysis of the interaction in the presence of Ca(2+) chelators indicated that the binding was Ca(2+) independent. NPHP1 colocalized with C2-containing RPGRIP1 isoforms in bovine and mouse retina. Mutations in NPHP4 associated with Senior-Loken syndrome-4 (606996) and mutations in RPGRP1 associated with Leber congenital amaurosis-6 (605446) disrupted the interaction between the 2 proteins.
Delous et al. (2009) showed that nephrocystin mRNA expression was dramatically increased during cell polarization, and shRNA-mediated knockdown of either NPHP1 or NPHP4 in MDCK cells resulted in delayed tight junction (TJ) formation, abnormal cilia formation, and disorganized multilumen structures when grown in a 3-dimensional collagen matrix. Some of these phenotypes were similar to those reported for cells depleted of the TJ proteins PALS1 (MPP5; 606958) or PAR3 (PARD3; 606745). A physical interaction between these nephrocystins and PALS1 as well as their partners PATJ (INADL; 603199) and PAR6 (PARD6A; 607484) was demonstrated, and the proteins partially colocalized in human renal tubules. The authors concluded that the nephrocystins play an essential role in epithelial cell organization, suggesting a mechanism by which the histopathologic features of nephronophthisis might develop.
Williams et al. (2011) showed that the conserved proteins Mks1 (609883), Mksr1 (B9D1), Mksr2 (B9D2; 611951), Tmem67 (609884), Rpgrip1l (610937), Cc2d2a (612013), Nphp1, and Nphp4 functioned at an early stage of ciliogenesis in C. elegans. These 8 proteins localized to the ciliary transition zone and established attachments between the basal body and transition zone membrane. They also provided a docking site that restricted vesicle fusion to vesicles containing ciliary proteins.
▼ Molecular Genetics
In patients with juvenile nephronophthisis mapping to 1p36 (NPHP4; 606966), Mollet et al. (2002) found 5 mutations in the NPHP4 gene: 3 nonsense, 1 frameshift, and 1 missense (607215.0001-607215.0005). The nonsense and frameshift mutations resulted in putative truncated proteins, and the missense mutation affected a residue within a highly conserved motif. Because of an error in the original sequencing of the NPHP4 gene, Mollet et al. (2002) published a table with the revised designations of the mutations.
Otto et al. (2002) demonstrated mutations in the NPHP4 gene in patients with juvenile nephronophthisis.
Senior-Loken Syndrome 4
Otto et al. (2002) identified 2 loss-of-function mutations in the NPHP4 gene (607215.0006-607215.0007) in patients with Senior-Loken syndrome-4 (SLSN4; 606996), demonstrating that NPHP4 and SLSN4 are allelic.
▼ ALLELIC VARIANTS ( 7 Selected Examples):
.0001 NEPHRONOPHTHISIS 4
In a consanguineous family, Mollet et al. (2002) demonstrated that juvenile nephronophthisis (NPHP4; 606966) was caused by homozygosity for a 2368G-T transversion in exon 18 of the NPHP4 gene, resulting in a glu790-to-ter (E790X) substitution. This mutation was originally published as GLU614TER (E614X); the corrected numbering appeared in an erratum.
.0002 NEPHRONOPHTHISIS 4
In a consanguineous family, Mollet et al. (2002) demonstrated that juvenile nephronophthisis (NPHP4; 606966) was related to homozygosity for a 2377C-T transition in exon 18 of the NPHP4 gene, resulting in a gln793-to-ter (Q793X) substitution. This mutation was originally published as GLN617TER (Q617X); the corrected numbering appeared in an erratum.
.0003 NEPHRONOPHTHISIS 4
In a nonconsanguineous family, Mollet et al. (2002) demonstrated that juvenile nephronophthisis (NPHP4; 606966) was related to heterozygosity for a 2044C-T transition in exon 16 of the NPHP4 gene, resulting in an arg682-to-ter (R682X) substitution. This mutation was originally published as ARG506TER (R506X); the corrected numbering appeared in an erratum.
.0004 NEPHRONOPHTHISIS 4
In a consanguineous family, Mollet et al. (2002) demonstrated that juvenile nephronophthisis (NPHP4; 606966) was related to homozygosity for a 2972T-C transition in exon 21 of the NPHP4 gene, resulting in a phe991-to-ser (F991S) substitution. This mutation was originally published as PHE815SER (F815S); the corrected numbering appeared in an erratum.
.0005 NEPHRONOPHTHISIS 4
NPHP4, 1-BP DEL, 3272T
In a nonconsanguineous family, Mollet et al. (2002) demonstrated that juvenile nephronophthisis (NPHP4; 606966) was related to a 3272delT mutation in exon 23 of the NPHP4 gene, resulting in a frameshift and premature termination (Val1091fsTer1121). The mutation was present in heterozygous state; only the maternal mutation was detected. This mutation was originally published as 2744delT; the corrected numbering appeared in an erratum.
.0006 SENIOR-LOKEN SYNDROME 4
In 3 sibs of Turkish origin with Senior-Loken syndrome-4 (SLSN4; 606996), Otto et al. (2002) demonstrated homozygosity for a gln779-to-ter (Q779X) mutation in the NPHP4 gene. Polak et al. (1983) and Schuermann et al. (2002) provided clinical data concerning these patients. They developed end-stage renal disease (ESRD) at ages 28, 30, and 35 years. All 3 had retinal changes suggestive of Leber amaurosis congenita (see 204000).
.0007 SENIOR-LOKEN SYNDROME 4
In a French family, Otto et al. (2002) found that 4 individuals with Senior-Loken syndrome-4 (SLSN4; 606996) were homozygous for an arg658-to-ter (R658X) mutation in the NPHP4 gene. The patients developed end-stage renal disease at ages 6, 10, 17, and 22 years. Ophthalmologic data were reported by Fillastre et al. (1976). One individual had amblyopia and rotary nystagmus with grossly impaired vision starting at age 8 months; funduscopy showed retinochoroidal atrophy surrounded by pigment. Two individuals showed abnormal ERG findings with diminished amplitude.