ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.430A>G (p.Lys144Glu)

gnomAD frequency: 0.00001  dbSNP: rs745342273
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000554828 SCV000636165 uncertain significance Nephronophthisis 2021-09-01 criteria provided, single submitter clinical testing This sequence change replaces lysine with glutamic acid at codon 144 of the NPHP3 protein (p.Lys144Glu). The lysine residue is highly conserved and there is a small physicochemical difference between lysine and glutamic acid. This variant is present in population databases (rs745342273, ExAC 0.01%). 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: "Possibly Damaging"; 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.
GeneDx RCV002266984 SCV002549177 likely pathogenic not provided 2023-06-01 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Fulgent Genetics, Fulgent Genetics RCV005027633 SCV005656485 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2024-04-23 criteria provided, single submitter clinical testing

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