Mutations in this gene are associated with the autosomal recessive conditions Joubert syndrome, Senior-Loken syndrome, and juvenile nephronopthisis. Homozygous deletions of a larger region including this gene and part of the MALL gene represent a common mechanism amongst affected individuals. See the linked region issue for more details regarding heterozygous carriers of deletions and duplications of this region.
As above, duplications of the genomic region involving this gene and part of the MALL gene are discussed in the linked region issue. At this time, there have been no reports of whole gene duplications of NPHP1 ALONE.