ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3898G>A (p.Gly1300Arg)

gnomAD frequency: 0.00002  dbSNP: rs774681590
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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 RCV002045778 SCV002306638 uncertain significance Nephronophthisis 2020-11-27 criteria provided, single submitter clinical testing This sequence change replaces glycine with arginine at codon 1300 of the NPHP3 protein (p.Gly1300Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine. This variant is present in population databases (rs774681590, ExAC 0.004%). This variant has not been reported in the literature in individuals 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"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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 RCV002486704 SCV002776380 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2021-10-14 criteria provided, single submitter clinical testing

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