Characterization of the NPHP1 locus: Mutational mechanism involved in deletions in familial juvenile nephronophthisis

Famial juvenile nephronophthisis is an autosomal recessive, genetically het erogeneous kidney disorder representing the most frequent inherited cause o f chronic renal failure in children. A gene, NPHP1, responsible for similar to 85% of the purely renal form of nephronophthisis, has been mapped to 2q 13 and characterized. The major NPHP1 gene defect is a large homozygous del etion found in similar to 80% of the patients. In this study, by large-scal e genomic sequencing and pulsed-held gel electrophoresis analysis, we chara cterized the complex organization of the MPI;IPI locus and determined the m utational mechanism that results in the large deletion observed in most pat ients. We showed that the deletion is 290 kb in size and that NPHP1 is flan ked by two large inverted repeats of similar to 330 kb. In addition, a seco nd sequence of 45 kb located adjacent to the proximal 330-kb repeat was sho wn to be directly repeated 250 kb away within the distal 330-kb repeat dele ting the sequence tag site (STS) 804H10R present in the proximal copy. The patients' deletion breakpoints appear to be located within the 45-kb repent , suggesting an unequal recombination between the two homologous copies of this smaller repeat. Moreover, we demonstrated a non-pathologic rearrangeme nt involving the two 330-kb inverted repeats found in 11 patients and, in t he homozygous state, in 2 (1.3%) control individuals. This could be explain ed by interchromosomal mispairing of the 330-kb inverted repeat, followed b y double recombination or by a prior intrachromosomal mispairing of these r epeats, leading to an inversion of the NPHP1 region, followed by an interch romosomal unequal crossover event. This complex rearrangement, as well as t he common deletion found in most patients, illustrates the high level of re arrangements occurring in the centromeric region of chromosome 2.