ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.24139C>T (p.Arg8047Ter)

gnomAD frequency: 0.00001  dbSNP: rs1174316105
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000779496 SCV000916129 uncertain significance SYNE1-Related Disorders 2018-12-03 criteria provided, single submitter clinical testing The SYNE1 c.23926C>T (p.Arg7976Ter) variant is a stop-gained variant that is predicted to result in an absent or truncated protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found through this search. This variant is reported at a frequency of 0.000046 in the European (Finnish) population of the Genome Aggregation Database, but this frequency is based on one allele only in a region of good sequencing coverage. The variant is therefore presumed to be rare. Based on the potential impact of stop-gained variants and the lack of clarifying evidence, the p.Arg7976Ter variant is classified as of uncertain significance but suspicious for pathogenicity for SYNE1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Athena Diagnostics Inc RCV000993164 SCV001145940 pathogenic not provided 2019-02-18 criteria provided, single submitter clinical testing The variant creates a premature nonsense codon, and is therefore predicted to result in the loss of a functional protein. Found in at least one symptomatic patient, and found in general population data that is consistent with pathogenicity.
Invitae RCV001390591 SCV001592375 pathogenic Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2022-06-20 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg7976*) in the SYNE1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SYNE1 are known to be pathogenic (PMID: 19542096, 24319099, 27086870). This variant is present in population databases (no rsID available, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with SYNE1-related conditions. ClinVar contains an entry for this variant (Variation ID: 632476). For these reasons, this variant has been classified as Pathogenic.

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