ClinVar Miner

Submissions for variant NM_004646.3(NPHS1):c.2404C>T (p.Arg802Trp) (rs386833911)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000793793 SCV000933166 likely pathogenic not provided 2018-09-17 criteria provided, single submitter clinical testing This sequence change replaces arginine with tryptophan at codon 802 of the NPHS1 protein (p.Arg802Trp). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is present in population databases (rs386833911, ExAC 0.01%). This variant has been observed in several individuals affected with nephrotic syndrome (PMID: 9915943, 23595123, 25720465, 11854170). ClinVar contains an entry for this variant (Variation ID: 56471). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant disrupts the p.Arg802 amino acid residue in NPHS1. Other variant that disrupts this residue have been observed in affected individuals (PMID: 9915943), which suggests that this may be a clinically significant amino acid residue. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049884 SCV000082293 probable-pathogenic Finnish congenital nephrotic syndrome no assertion criteria provided not provided Converted during submission to Likely pathogenic.

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