ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3907C>T (p.Pro1303Ser)

gnomAD frequency: 0.00002  dbSNP: rs373728120
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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 RCV001223251 SCV001395390 uncertain significance Nephronophthisis 2021-08-26 criteria provided, single submitter clinical testing This sequence change replaces proline with serine at codon 1303 of the NPHP3 protein (p.Pro1303Ser). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and serine. This variant is present in population databases (rs373728120, 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 (SIFT, PolyPhen-2, Align-GVGD) all suggest 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.
Fulgent Genetics, Fulgent Genetics RCV002480735 SCV002793544 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2021-11-04 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004740620 SCV005364451 uncertain significance NPHP3-related disorder 2024-05-24 no assertion criteria provided clinical testing The NPHP3 c.3907C>T variant is predicted to result in the amino acid substitution p.Pro1303Ser. This variant has not been reported in the literature in individuals with NPHP3-related disorders. This variant is reported in 0.0039% of alleles in individuals of European (non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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