ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.188G>A (p.Gly63Glu)

gnomAD frequency: 0.00003  dbSNP: rs763699273
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001221589 SCV001393645 uncertain significance Nephronophthisis 2024-12-16 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 63 of the NPHP3 protein (p.Gly63Glu). This variant is present in population databases (rs763699273, gnomAD 0.07%). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 949984). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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 RCV001732078 SCV001982335 uncertain significance not provided 2021-09-23 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on splicing; 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 RCV002491693 SCV002804032 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2024-01-02 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV001732078 SCV005189790 uncertain significance not provided criteria provided, single submitter not provided

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