ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.9419C>T (p.Ala3140Val)

gnomAD frequency: 0.00016  dbSNP: rs146402274
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000726114 SCV000342073 uncertain significance not provided 2018-09-14 criteria provided, single submitter clinical testing
GeneDx RCV000726114 SCV000577081 uncertain significance not provided 2017-04-11 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the SYNE1 gene. The A3147V variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The A3147V variant is observed in 4/10,386 (0.04%) alleles from individuals of African background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The A3147V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Alanine are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV001217208 SCV001389041 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2023-10-03 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 3147 of the SYNE1 protein (p.Ala3147Val). This variant is present in population databases (rs146402274, gnomAD 0.05%). 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: 288074). 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.
Revvity Omics, Revvity RCV000726114 SCV003827014 uncertain significance not provided 2020-07-13 criteria provided, single submitter clinical testing

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