ClinVar Miner

Submissions for variant NM_182914.2(SYNE2):c.4423A>G (p.Lys1475Glu) (rs761080544)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV000518314 SCV000615730 uncertain significance not specified 2016-10-25 criteria provided, single submitter clinical testing
GeneDx RCV000767015 SCV000620170 uncertain significance not provided 2017-08-24 criteria provided, single submitter clinical testing The K1475E variant in the SYNE2 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The K1475E variant is observed in 3/66486 (0.0045%) alleles from individuals of non-Finnish European background, in the ExAC dataset (Lek et al., 2016). The K1475E 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. 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. We interpret K1475E as a variant of uncertain significance.
Illumina Clinical Services Laboratory,Illumina RCV001112392 SCV001270049 benign Emery-Dreifuss muscular dystrophy 5, autosomal dominant 2018-03-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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