ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.23248C>T (p.Leu7750Phe)

gnomAD frequency: 0.00001  dbSNP: rs778500015
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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 RCV000800291 SCV000939996 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2021-09-01 criteria provided, single submitter clinical testing This sequence change replaces leucine with phenylalanine at codon 7679 of the SYNE1 protein (p.Leu7679Phe). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and phenylalanine. This variant is present in population databases (rs778500015, ExAC 0.001%). This variant has not been reported in the literature in individuals affected with SYNE1-related conditions. 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 C15"). 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.
GeneDx RCV001759521 SCV001997230 uncertain significance not provided 2020-01-14 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect
Revvity Omics, Revvity RCV001759521 SCV003824632 uncertain significance not provided 2021-03-06 criteria provided, single submitter clinical testing
Athena Diagnostics RCV001759521 SCV005620600 uncertain significance not provided 2024-07-29 criteria provided, single submitter clinical testing Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is uninformative in assessment of its pathogenicity. (http://gnomad.broadinstitute.org) Polyphen and MutationTaster yielded discordant predictions regarding whether this amino acid change is damaging to the protein.

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