ClinVar Miner

Submissions for variant NM_022042.4(SLC26A1):c.1073C>T (p.Ser358Leu)

gnomAD frequency: 0.00032  dbSNP: rs148832260
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV000234844 SCV001368734 likely pathogenic Nephrolithiasis, calcium oxalate 2016-01-01 criteria provided, single submitter clinical testing This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM2,PP3.
CeGaT Center for Human Genetics Tuebingen RCV000681877 SCV001371194 likely pathogenic not provided 2020-04-01 criteria provided, single submitter clinical testing
Invitae RCV000681877 SCV001381783 uncertain significance not provided 2023-12-21 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 358 of the SLC26A1 protein (p.Ser358Leu). This variant is present in population databases (rs148832260, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with nephrolithiasis (PMID: 27210743, 30586318). ClinVar contains an entry for this variant (Variation ID: 242375). 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 expected to disrupt SLC26A1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects SLC26A1 function (PMID: 27210743, 36719378). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
OMIM RCV000234844 SCV000292031 pathogenic Nephrolithiasis, calcium oxalate 2023-05-15 no assertion criteria provided literature only
Gharavi Laboratory, Columbia University RCV000681877 SCV000809356 pathogenic not provided 2018-09-16 no assertion criteria provided research

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