ClinVar Miner

Submissions for variant NM_003901.4(SGPL1):c.665G>A (p.Arg222Gln)

dbSNP: rs769259446
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centogene AG - the Rare Disease Company RCV000495961 SCV001426653 pathogenic Nephrotic syndrome 14 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001851363 SCV002152961 pathogenic not provided 2021-07-01 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 430861). This variant has been observed in individual(s) with clinical features of SGPL1-related conditions (PMID: 28165343, 30517686, 31130284). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs769259446, ExAC 0.006%). This sequence change replaces arginine with glutamine at codon 222 of the SGPL1 protein (p.Arg222Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine. 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: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg222 amino acid residue in SGPL1. Other variant(s) that disrupt this residue have been observed in individuals with SGPL1-related conditions (PMID: 28165339), which suggests that this may be a clinically significant amino acid residue. Experimental studies have shown that this variant affects SGPL1 protein function (PMID: 28165343).
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre RCV000495961 SCV004231785 pathogenic Nephrotic syndrome 14 2023-05-12 criteria provided, single submitter clinical testing
OMIM RCV000495961 SCV000583996 pathogenic Nephrotic syndrome 14 2023-08-24 no assertion criteria provided literature only
GeneReviews RCV000495961 SCV001469005 not provided Nephrotic syndrome 14 no assertion provided literature only
Yale Center for Mendelian Genomics, Yale University RCV001849385 SCV002107050 likely pathogenic Nephrotic syndrome 2017-11-10 no assertion criteria provided literature only

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