Submission Details

The relationship between NPHP1 (nephrocystin) and Nephronophthisis was evaluated using the ClinGen Clinical Validity Framework on 27 January 2021. Nephronophthisis is an autosomal recessively inherited disease characterised by renal failure, with onset under the age of 30. Affected children develop polyuria and polydipsia, and growth retardation with an inactive urinary sediment. Their kidneys are small or normal-sized and hyperechoic with corticomedullary cysts and tubular basement membrane abnormalities. Nephronophthisis 1 (MIM:256100) is the commonest inherited cause of kidney failure in children and affects one in 50,000 (Waldherr 1982, PMID:7072145). About 20% affected individuals have extrarenal features such as retinitis pigmentosa (Senior Loken syndrome, MIM:266900), or cerebellar vermis hypoplasia and other multiorgan abnormalities (Joubert syndrome, MIM:609583). (Simms 2009, PMID:21660307). Other extra-renal features include liver fibrosis, gaze palsies, situs inversus and skeletal defects. In addition, at least 20 different genes are affected in nephronophthisis, and variants in NPHP1 account for 20% of all cases. Each of the affected proteins has a slightly different function but is involved in ciliary function.

LUMPING and SPLITTING: Using the criteria of the ClinGen Lumping and Splitting Working Group, there are assertions for different disease entities (nephronophthisis, Senior-Loken syndrome, Joubert syndrome) for NPHP1 mutations, but there was a consistent inheritance pattern of AR, and the disease mechanism for all these conditions was a loss of function. Therefore, all of the disease entities have been lumped into one disease entity.

The gene for nephronophthisis 1 was mapped to chromosome 2p13 in a cohort of 18 multiplex families with nephronophthisis resulting in a LOD score of 4.78 at theta = 0.05 in 1993 (Antignac 1993, PMID:7981755). Subsequently, individuals were demonstrated with a homozygous large deletion about 250 kb with a 100 kb inverted duplication involving both the NPHP1 and BENE (MALL) genes (Saunier 1997, PMID:9361039). A 4.8 kb band was absent on Southern blotting consistent with a homozygous deletion of NPHP1 (Konrad 1996, PMID:8852662), and 60-80% of affected individuals have at least a single copy of this deletion (Saunier 1997, PMID:9361039). Deletions are not due to a founder effect but rather occur because of the flanking low copy number repetitive sequences that potentially enable a stem-loop structure on the DNA strand and homologous recombination (Saunier 2000, PMID:10712196). The disease mechanism is loss of function. There are more than 200 reports of homozygous deletions (Hildebrandt 2001, PMID:11168925; Otto 2006, PMID:18076122; Halbritter 2013, PMID:23559409). There are also numerous compound heterozygous variants due to a null variant plus a second variant including missense variants (Caridi 2006, PMID:16762963; Otto 2006, PMID:18076122; Halbritter 2013, PMID:23559409) as well as case reports. A case control study of 5605 adults with end-stage kidney failure from 12 countries were compared with a control population matched for ethnicity. Twenty-six (0.5%) of those with kidney failure had homozygous deletions but none of 3311 normal kidney donors (OR= 31.45 (1.91 to 516.36, p=0.01)) (Snoek 2018, PMID:29654215). Genetic evidence reached the maximum score (12 points). This gene-disease relationship is also supported by the function of the gene product nephrocystin 1. There is no correlation between variant type and extrarenal features. Thus, there is no variant type or location that predominates in any of Senior-Loken or Joubert syndrome.

NPHP1 appears to be located in the ciliary axoneme, in the transition zone and in the microtubular organising centre within the cell. Its precise function is not known but it is probably a scaffolding protein involved in cell-cell adhesion, that is able to recruit signalling molecules into specialized protein complexes (Mollet 2005, PMID:15661758). It interacts with the products of many other NPHP genes, located in the primary cilium, including NPHP4 and RPGRIP1L at the transition zone, that link it with inversin (NPHP2) (Mollet 2005, PMID:15661758); and p130cas, Tensin, Filamin and Focal adhesion kinase 2 all involved in cell-cell adhesion and cell signalling as demonstrated with coimmunoprecipitation and by yeast two hybrid screens (Donaldson 2002, PMID:12006559; 2000 PMID:10739664). NPHP1 colocalises with PALS1, PATJ and Par6 which are involved in tight function formation (Delous 2009, PMID:19755384). It is important in the Wnt and Shh signalling pathways.

Nephrocystin is mainly expressed in the ureteric epithelial cells and tubular precursors in the kidney (Lindstrom 2018, PMID:29449453), and localizes to the transition zone at the ciliary base (Fliegauf 2006, PMID:16885411). Expression is abnormal in tracheal cells from patients with nephronophthisis, and patient-derived cells have some subtle abnormalities of ciliary motility (Fliegauf 2006, PMID:16885411). A mouse knockout has no kidney phenotype but has retinal and sperm abnormalities (Mouse Genome Informatics, PMID:30407599; Jiang 2008, PMID:18684731; Devi 2015, PMID:26198798). Zebrafish, in a combination of nphp1 and nphp4 morpholinos, have increased kidney cysts (Slanchev 2011, PMID:21596840). Likewise in C elegans disruption of both nphp1 and nphp4 compromise ciliary structure (Yee 2015, PMID: 26540106). In a non-patient derived cell culture model, shRNA-knockdown of NPHP1 results in abnormal cilia formation and can be rescued with re-expression of human NPHP1 (Delous 2009, PMID:19755384). Likewise CRISPR-Cas 9 induced NPHP1 deletion in NIH 3T3 cells results in fewer ciliated cells that are rescued by re-expression of plasmid Nphp1 (Wiegering 2018, PMID:29650680). Thus the score for experimental evidence for a gene-disease association was also the maximum (6 points). Both the clinical evidence and experimental evidence have been upheld and replicated over time. The only reservations about the experimental data were the facts that the function of NPHP1 was not precisely known and it had no functional assay for its measurement. In addition all the models were complicated and often required a mutation in a second gene (such as nphp4) in addition to nphp1, to develop the typical cystic phenotype.

In summary, the clinical validity classification of DEFINITIVE for the relationship between NPHP1 and Nephronophthisis 1 was approved by the Cystic Kidney disease GCEP on 27 January 2021 using the Gene Clinical Validity Standard Operating Procedure (SOP) version 8.