Total submissions: 3
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Invitae | RCV001052653 | SCV001216874 | pathogenic | Nephronophthisis | 2023-07-14 | criteria provided, single submitter | clinical testing | This sequence change affects an acceptor splice site in intron 5 of the NPHP3 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in NPHP3 are known to be pathogenic (PMID: 18371931, 23559409). This variant is present in population databases (rs780148543, gnomAD 0.008%). Disruption of this splice site has been observed in individual(s) with clinical features of nephronophthisis (PMID: 24776604). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 848816). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. |
Gene |
RCV001797150 | SCV002039043 | pathogenic | not provided | 2023-07-18 | criteria provided, single submitter | clinical testing | Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 24776604, 31964843, 36090483) |
Fulgent Genetics, |
RCV002505602 | SCV002810883 | pathogenic | Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome | 2022-04-07 | criteria provided, single submitter | clinical testing |