ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.4075A>G (p.Thr1359Ala)

gnomAD frequency: 0.00004  dbSNP: rs377718960
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000598041 SCV000702159 uncertain significance not provided 2016-10-06 criteria provided, single submitter clinical testing
Invitae RCV001363881 SCV001560011 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2021-12-02 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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 497566). This variant has not been reported in the literature in individuals affected with SYNE1-related conditions. This variant is present in population databases (rs377718960, gnomAD 0.01%). This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 1366 of the SYNE1 protein (p.Thr1366Ala).
Athena Diagnostics Inc RCV000598041 SCV001880871 uncertain significance not provided 2023-02-20 criteria provided, single submitter clinical testing Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is uninformative in assessment of its pathogenicity (http://gnomad.broadinstitute.org). Computational tools predict that this variant is not damaging.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002271534 SCV002555980 uncertain significance not specified 2022-06-17 criteria provided, single submitter clinical testing Variant summary: SYNE1 c.4096A>G (p.Thr1366Ala) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 5.2e-05 in 249422 control chromosomes. To our knowledge, no occurrence of c.4096A>G in individuals affected with Emery-Dreifuss Muscular Dystrophy 4, Autosomal Dominant and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.
Revvity Omics, Revvity Omics RCV000598041 SCV003826413 uncertain significance not provided 2020-07-23 criteria provided, single submitter clinical testing

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