ClinVar Miner

Submissions for variant NM_003901.4(SGPL1):c.1247A>G (p.Tyr416Cys)

gnomAD frequency: 0.00001  dbSNP: rs779485098
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001056251 SCV001220684 likely pathogenic not provided 2022-07-26 criteria provided, single submitter clinical testing 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. This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 416 of the SGPL1 protein (p.Tyr416Cys). This variant is present in population databases (rs779485098, gnomAD 0.004%). This missense change has been observed in individuals with clinical features of nephrotic syndrome (PMID: 28165339, 32233035; Invitae). ClinVar contains an entry for this variant (Variation ID: 851784). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects SGPL1 function (PMID: 28165339).

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