ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.1857C>G (p.Ile619Met)

gnomAD frequency: 0.00001  dbSNP: rs780013712
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001055257 SCV001219639 uncertain significance Nephronophthisis 2021-08-31 criteria provided, single submitter clinical testing This sequence change replaces isoleucine with methionine at codon 619 of the NPHP3 protein (p.Ile619Met). The isoleucine residue is highly conserved and there is a small physicochemical difference between isoleucine and methionine. This variant is present in population databases (rs780013712, ExAC 0.004%). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. 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: "Benign"; Align-GVGD: "Class C0"). 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.
Fulgent Genetics, Fulgent Genetics RCV002489642 SCV002791494 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2021-11-18 criteria provided, single submitter clinical testing

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