ClinVar Miner

Submissions for variant NM_182914.3(SYNE2):c.15413C>T (p.Thr5138Met)

gnomAD frequency: 0.00011  dbSNP: rs145018323
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001111089 SCV001268596 likely benign Emery-Dreifuss muscular dystrophy 5, autosomal dominant 2018-01-12 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Invitae RCV001111089 SCV002250284 uncertain significance Emery-Dreifuss muscular dystrophy 5, autosomal dominant 2023-09-10 criteria provided, single submitter clinical testing 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 disruptive. 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. ClinVar contains an entry for this variant (Variation ID: 881822). This variant has not been reported in the literature in individuals affected with SYNE2-related conditions. This variant is present in population databases (rs145018323, gnomAD 0.01%). This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 5138 of the SYNE2 protein (p.Thr5138Met).
Revvity Omics, Revvity RCV001111089 SCV003818851 uncertain significance Emery-Dreifuss muscular dystrophy 5, autosomal dominant 2019-10-30 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003405320 SCV004116120 uncertain significance SYNE2-related condition 2023-02-22 criteria provided, single submitter clinical testing The SYNE2 c.15413C>T variant is predicted to result in the amino acid substitution p.Thr5138Met. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.016% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/14-64610596-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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