ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.2666T>C (p.Leu889Pro)

gnomAD frequency: 0.00001  dbSNP: rs747876996
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001236180 SCV001408893 uncertain significance Nephronophthisis 2019-09-10 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with NPHP3-related conditions. This variant is present in population databases (rs747876996, ExAC 0.01%). This sequence change replaces leucine with proline at codon 889 of the NPHP3 protein (p.Leu889Pro). The leucine residue is highly conserved and there is a moderate physicochemical difference between leucine and proline.
Fulgent Genetics, Fulgent Genetics RCV002484293 SCV002787470 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2022-01-21 criteria provided, single submitter clinical testing
Ambry Genetics RCV004033305 SCV004990284 uncertain significance Inborn genetic diseases 2023-10-10 criteria provided, single submitter clinical testing The c.2666T>C (p.L889P) alteration is located in exon 19 (coding exon 19) of the NPHP3 gene. This alteration results from a T to C substitution at nucleotide position 2666, causing the leucine (L) at amino acid position 889 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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