ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.21259G>T (p.Ala7087Ser)

dbSNP: rs1321824454
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000523876 SCV000621849 uncertain significance not provided 2017-10-27 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the SYNE1 gene. The A7016S variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The A7016S variant is observed in 1/111614 (0.001%) alleles from individuals of European background (Lek et al., 2016). The A7016S 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. However, this substitution 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. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV002525250 SCV003475932 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2021-12-19 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 452997). This variant has not been reported in the literature in individuals affected with SYNE1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 7016 of the SYNE1 protein (p.Ala7016Ser).

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