ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.9371T>C (p.Met3124Thr)

gnomAD frequency: 0.00005  dbSNP: rs756079906
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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) RCV000726523 SCV000345222 uncertain significance not provided 2016-08-23 criteria provided, single submitter clinical testing
GeneDx RCV000726523 SCV000577398 uncertain significance not provided 2017-03-31 criteria provided, single submitter clinical testing The M3131T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The M3131T variant is observed in 3/6610 (0.05%) alleles from individuals of Finnish background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This substitution occurs at a position where amino acids with similar properties to Methionine are tolerated across species. However, this variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function.
Invitae RCV002522032 SCV003264070 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2022-08-20 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 3131 of the SYNE1 protein (p.Met3131Thr). This variant is present in population databases (rs756079906, gnomAD 0.09%). 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: 290630). 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 C25"). 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 Omics RCV000726523 SCV003825216 uncertain significance not provided 2019-08-21 criteria provided, single submitter clinical testing

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