ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.22978C>T (p.Arg7660Trp)

gnomAD frequency: 0.00002  dbSNP: rs202017153
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000391043 SCV000343968 uncertain significance not provided 2016-07-25 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001151675 SCV001312840 uncertain significance Autosomal recessive ataxia, Beauce type 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV001151676 SCV001312841 likely benign Emery-Dreifuss muscular dystrophy 4, 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.
Ambry Genetics RCV001265812 SCV001443984 uncertain significance Inborn genetic diseases 2018-01-06 criteria provided, single submitter clinical testing
Invitae RCV001318993 SCV001509717 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2020-03-18 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with SYNE1-related conditions. ClinVar contains an entry for this variant (Variation ID: 289584). This variant is present in population databases (rs202017153, ExAC 0.05%). This sequence change replaces arginine with tryptophan at codon 7589 of the SYNE1 protein (p.Arg7589Trp). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and tryptophan.
GeneDx RCV000391043 SCV001998027 uncertain significance not provided 2019-10-18 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV000391043 SCV003826492 uncertain significance not provided 2019-10-23 criteria provided, single submitter clinical testing

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