ClinVar Miner

Submissions for variant NM_004646.3(NPHS1):c.1048T>C (p.Ser350Pro) (rs386833863)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000049832 SCV000220812 likely pathogenic Finnish congenital nephrotic syndrome 2014-10-16 criteria provided, single submitter literature only
Fulgent Genetics,Fulgent Genetics RCV000049832 SCV000894188 likely pathogenic Finnish congenital nephrotic syndrome 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV001063172 SCV001228007 pathogenic not provided 2020-10-28 criteria provided, single submitter clinical testing This sequence change replaces serine with proline at codon 350 of the NPHS1 protein (p.Ser350Pro). The serine residue is moderately conserved and there is a moderate physicochemical difference between serine and proline. This variant is present in population databases (rs386833863, ExAC 0.009%). This variant has been observed in individuals affected with congenital nephrotic syndrome (PMID: 9915943, 20172850, 20507940, 27594755). ClinVar contains an entry for this variant (Variation ID: 56419). This variant has been reported to affect NPHS1 protein function (PMID: 11726550, 15213260). This variant disrupts the p.Ser350 amino acid residue in NPHS1. Other variant(s) that disrupt this residue have been observed in individuals with NPHS1-related conditions (PMID: 27325253), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV000049832 SCV001367620 likely pathogenic Finnish congenital nephrotic syndrome 2020-02-18 criteria provided, single submitter clinical testing This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PM2,PS4_MOD,PP3,PP4.
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) RCV000049832 SCV000082241 probable-pathogenic Finnish congenital nephrotic syndrome no assertion criteria provided not provided Converted during submission to Likely pathogenic.
Broad Institute Rare Disease Group, Broad Institute RCV000049832 SCV000924463 likely pathogenic Finnish congenital nephrotic syndrome 2018-06-15 no assertion criteria provided research The heterozygous p.Ser350Pro variant was identified by our study in the compound heterozygous state, along with a VUS, in one individual with nephrotic syndrome. This variant is likely pathogenic based on multiple reports in ClinVar and the literature.

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