ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.209T>C (p.Leu70Pro)

gnomAD frequency: 0.00005  dbSNP: rs867826443
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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 RCV001337246 SCV001530839 uncertain significance Nephronophthisis 2024-10-15 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 70 of the NPHP3 protein (p.Leu70Pro). This variant is present in population databases (no rsID available, gnomAD 0.03%). 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: 1034512). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt NPHP3 protein function with a negative predictive value of 80%. 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 RCV002486345 SCV002791320 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2022-03-28 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV003481078 SCV004226924 uncertain significance not provided 2022-08-11 criteria provided, single submitter clinical testing
Ambry Genetics RCV004960805 SCV005464514 uncertain significance Inborn genetic diseases 2024-09-30 criteria provided, single submitter clinical testing The c.209T>C (p.L70P) alteration is located in exon 1 (coding exon 1) of the NPHP3 gene. This alteration results from a T to C substitution at nucleotide position 209, causing the leucine (L) at amino acid position 70 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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