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 disorder 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 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.
Labcorp Genetics (formerly Invitae), Labcorp 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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