ClinVar Miner

Submissions for variant NM_001005373.4(LRSAM1):c.1619G>T (p.Ser540Ile)

gnomAD frequency: 0.00001  dbSNP: rs1400819662
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000528608 SCV000652022 uncertain significance Charcot-Marie-Tooth disease axonal type 2P 2024-08-29 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 540 of the LRSAM1 protein (p.Ser540Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Charcot-Marie-Tooth disease (PMID: 32376792). ClinVar contains an entry for this variant (Variation ID: 472793). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt LRSAM1 protein function with a positive predictive value of 80%. 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.
Molecular Genetics Laboratory, London Health Sciences Centre RCV001173638 SCV001336740 uncertain significance Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing
GeneDx RCV001755885 SCV002007726 uncertain significance not provided 2021-01-22 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 32376792)
Ambry Genetics RCV002395451 SCV002703219 uncertain significance Inborn genetic diseases 2020-01-13 criteria provided, single submitter clinical testing The p.S540I variant (also known as c.1619G>T), located in coding exon 20 of the LRSAM1 gene, results from a G to T substitution at nucleotide position 1619. The serine at codon 540 is replaced by isoleucine, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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