ClinVar Miner

Submissions for variant NM_014140.4(SMARCAL1):c.1439C>T (p.Pro480Leu)

gnomAD frequency: 0.00001  dbSNP: rs758367100
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001059601 SCV001224228 uncertain significance Schimke immuno-osseous dysplasia 2021-08-31 criteria provided, single submitter clinical testing This sequence change replaces proline with leucine at codon 480 of the SMARCAL1 protein (p.Pro480Leu). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and leucine. This variant is present in population databases (rs758367100, ExAC 0.001%). This missense change has been observed in individual(s) with Schimke immunoosseous dysplasia (PMID: 17089404, 21914180, 22998683). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. 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"). 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.
Revvity Omics, Revvity RCV001059601 SCV002023592 likely pathogenic Schimke immuno-osseous dysplasia 2021-09-21 criteria provided, single submitter clinical testing

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