ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.11395G>A (p.Glu3799Lys)

gnomAD frequency: 0.00003  dbSNP: rs879779013
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000725800 SCV000339491 uncertain significance not provided 2017-02-28 criteria provided, single submitter clinical testing
GeneDx RCV000725800 SCV000621088 uncertain significance not provided 2017-09-28 criteria provided, single submitter clinical testing The E3784K variant in the SYNE1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The E3784K variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). The E3784K variant is a non-conservative amino acid substitution, which occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret E3784K as a variant of uncertain significance.
Invitae RCV001855166 SCV002199814 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2023-06-30 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 3784 of the SYNE1 protein (p.Glu3784Lys). This variant is present in population databases (no rsID available, gnomAD 0.0009%). 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: 286166). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.

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