ClinVar Miner

Submissions for variant NM_006767.4(LZTR1):c.2093C>T (p.Ser698Phe)

dbSNP: rs760064852
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002422446 SCV002730311 uncertain significance Hereditary cancer-predisposing syndrome; Cardiovascular phenotype 2024-02-07 criteria provided, single submitter clinical testing The p.S698F variant (also known as c.2093C>T), located in coding exon 18 of the LZTR1 gene, results from a C to T substitution at nucleotide position 2093. The serine at codon 698 is replaced by phenylalanine, an amino acid with highly 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. Based on the available evidence, the clinical significance of this alteration remains unclear.
Laboratory of Medical Genetics Unit, Bambino Gesù Children's Hospital RCV003315249 SCV004012956 uncertain significance Diffuse midline glioma, H3 K27-altered 2022-05-30 criteria provided, single submitter research
Baylor Genetics RCV003465430 SCV004193629 uncertain significance Schwannomatosis 2 2024-01-15 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003718275 SCV004511668 uncertain significance not provided 2022-11-29 criteria provided, single submitter clinical testing 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. Experimental studies have shown that this missense change affects LZTR1 function (PMID: 31044557). 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 not expected to disrupt LZTR1 protein function. ClinVar contains an entry for this variant (Variation ID: 548121). This variant has not been reported in the literature in individuals affected with LZTR1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 698 of the LZTR1 protein (p.Ser698Phe).
Rare Disease Group, Clinical Genetics, Karolinska Institutet RCV000735828 SCV000778868 uncertain significance Bladder exstrophy no assertion criteria provided research

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