ClinVar Miner

Submissions for variant NM_000272.5(NPHP1):c.(?_-45)_(*443_?)del

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000227323 SCV000284555 pathogenic Nephronophthisis 2017-01-18 criteria provided, single submitter clinical testing A gross deletion of the genomic region encompassing the full coding sequence of the NPHP1 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. Loss of NPHP1 is known to be pathogenic. Full gene deletions of NPHP1 have been reported in individuals with juvenile nephronophthisis, Bardet-Biedl syndrome, Joubert syndrome, and congenital ocular motor apraxia type Cogan (PMID: 8852662, 10620543, 24746959, 15138899, 10839884). For these reasons, this variant has been classified as Pathogenic.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV001251510 SCV001427156 pathogenic Nephronophthisis 1 2018-10-10 criteria provided, single submitter clinical testing A homozygous deletion encompassing the entire NPHP1 gene has been identified; NM_000272.3(NPHP1):c.(?_-94)_(*462_?)del. The deletion includes at least the entire NPHP1 gene (NP_000263.2), and potentially extends into the adjacent gene, MALL (NP_005425.1). The variant is present in the general population at a frequency of 0.24% (Javorszky, E., et al. (2017)). The variant has been previously described as pathogenic in multiple patients with nephronophthisis. This deletion is the most frequent known cause of nephronophthisis (Chaki, M., et al. (2011), Lindstrand, A., et al. (2014), Hildebrandt, F., et al. (1997), Saunier, S., et al. (2000)). Based on the information available at the time of curation, this variant has been classified as PATHOGENIC.
OMIM RCV001251510 SCV000023849 pathogenic Nephronophthisis 1 2004-07-01 no assertion criteria provided literature only
OMIM RCV002518310 SCV000023850 pathogenic Senior-Loken syndrome 1 2004-07-01 no assertion criteria provided literature only
OMIM RCV002519780 SCV000023851 pathogenic Joubert syndrome with renal defect 2004-07-01 no assertion criteria provided literature only

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