ClinVar Miner

Submissions for variant NM_014625.4(NPHS2):c.353C>T (p.Pro118Leu)

dbSNP: rs869025495
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Blueprint Genetics RCV000208227 SCV000264138 pathogenic Proteinuria 2015-09-28 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000786958 SCV002018364 pathogenic Nephrotic syndrome, type 2 2019-06-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000786958 SCV004049291 pathogenic Nephrotic syndrome, type 2 2023-04-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV000786958 SCV004191557 pathogenic Nephrotic syndrome, type 2 2024-01-27 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003556262 SCV004293850 pathogenic not provided 2023-11-21 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 118 of the NPHS2 protein (p.Pro118Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of nephrotic syndrome (PMID: 15253708, 15264208). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 222762). 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 not expected to disrupt NPHS2 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects NPHS2 function (PMID: 14675423, 24596097). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000786958 SCV005633683 pathogenic Nephrotic syndrome, type 2 2024-02-10 criteria provided, single submitter clinical testing
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare RCV000786958 SCV000925863 pathogenic Nephrotic syndrome, type 2 2018-10-12 no assertion criteria provided clinical testing

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