ClinVar Miner

Submissions for variant NM_004646.4(NPHS1):c.616C>A (p.Pro206Thr)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV003471552 SCV004191393 likely pathogenic Finnish congenital nephrotic syndrome 2024-03-09 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003575105 SCV004368992 pathogenic not provided 2024-01-24 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 206 of the NPHS1 protein (p.Pro206Thr). This variant is present in population databases (rs201822740, gnomAD 0.05%). This missense change has been observed in individuals with nephrotic syndrome (PMID: 31328266, 34859019). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt NPHS1 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV003575105 SCV005079320 uncertain significance not provided 2023-08-15 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31216994, 34859019, 31328266)

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