ClinVar Miner

Submissions for variant NM_014140.4(SMARCAL1):c.1736C>T (p.Ser579Leu)

dbSNP: rs1694331040
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001216644 SCV001388449 pathogenic Schimke immuno-osseous dysplasia 2024-01-02 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 579 of the SMARCAL1 protein (p.Ser579Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Schimke immuno-osseous dysplasia (PMID: 11799392, 17089404, 22998683). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 945899). 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 SMARCAL1 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects SMARCAL1 function (PMID: 18805831, 26195148). For these reasons, this variant has been classified as Pathogenic.
Molecular Biology Laboratory, Fundació Puigvert RCV001216644 SCV001425266 likely pathogenic Schimke immuno-osseous dysplasia 2020-02-01 criteria provided, single submitter research

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