ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.9091A>G (p.Arg3031Gly)

gnomAD frequency: 0.00031  dbSNP: rs144643941
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000726953 SCV000536356 uncertain significance not provided 2017-01-25 criteria provided, single submitter clinical testing The R3038G variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R3038G variant is observed in 10/10354 (0.1%) alleles from individuals of African 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 Arginine 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. Additionally, in silico analysis predicts this variant is probably damaging to the protein structure/function.
Genetic Services Laboratory, University of Chicago RCV000435987 SCV000597342 uncertain significance not specified 2016-10-10 criteria provided, single submitter clinical testing
Invitae RCV000532681 SCV000649225 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2023-10-17 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 3038 of the SYNE1 protein (p.Arg3038Gly). This variant is present in population databases (rs144643941, gnomAD 0.1%). 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: 393008). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The glycine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Eurofins Ntd Llc (ga) RCV000726953 SCV000704417 uncertain significance not provided 2017-01-04 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000726953 SCV002771355 uncertain significance not provided 2021-06-18 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000726953 SCV003818197 uncertain significance not provided 2021-02-09 criteria provided, single submitter clinical testing

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