ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.5228A>G (p.Asp1743Gly)

gnomAD frequency: 0.00005  dbSNP: rs555731770
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000993185 SCV001145976 uncertain significance not provided 2024-09-18 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) Computational tools yielded predictions that this variant may result in the gain of a cryptic splice site without affecting the natural splice sites. Polyphen and MutationTaster predict this amino acid change may be benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV001317541 SCV001508209 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2022-07-03 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 1750 of the SYNE1 protein (p.Asp1750Gly). This variant is present in population databases (rs555731770, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with SYNE1-related conditions. ClinVar contains an entry for this variant (Variation ID: 805575). 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: "Benign"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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 RCV000993185 SCV005389809 uncertain significance not provided 2024-04-01 criteria provided, single submitter clinical testing 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

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