ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.6428A>G (p.Asp2143Gly)

gnomAD frequency: 0.00022  dbSNP: rs189734757
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000352415 SCV000344866 uncertain significance not provided 2016-09-14 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000352415 SCV001145985 uncertain significance not provided 2024-05-22 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 higher than would generally be expected for pathogenic variants in this gene. (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 yielded discordant predictions regarding whether this amino acid change is damaging to the protein.
Labcorp Genetics (formerly Invitae), Labcorp RCV001342185 SCV001536098 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2022-08-06 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 2150 of the SYNE1 protein (p.Asp2150Gly). This variant is present in population databases (rs189734757, gnomAD 0.08%). 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: 290330). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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 RCV000352415 SCV002818085 uncertain significance not provided 2022-07-01 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
Revvity Omics, Revvity RCV000352415 SCV003824721 uncertain significance not provided 2022-10-28 criteria provided, single submitter clinical testing

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