ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.17533G>A (p.Val5845Met)

gnomAD frequency: 0.00001  dbSNP: rs535699185
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000713610 SCV000344710 uncertain significance not provided 2016-08-10 criteria provided, single submitter clinical testing
GeneDx RCV000713610 SCV000576790 uncertain significance not provided 2017-04-19 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the SYNE1 gene. The V5774M variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The V5774M variant is observed in 51/15508 (0.3%) alleles from individuals of South Asian background, (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The V5774M variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. However, this substitution occurs at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Athena Diagnostics Inc RCV000713610 SCV000844235 uncertain significance not provided 2018-05-08 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003417919 SCV004115757 uncertain significance SYNE1-related condition 2023-02-15 criteria provided, single submitter clinical testing The SYNE1 c.17320G>A variant is predicted to result in the amino acid substitution p.Val5774Met. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.28% of alleles in individuals of South Asian descent in gnomAD, which may be too common to be a primary cause of disease (http://gnomad.broadinstitute.org/variant/6-152623012-C-T). Although we suspect that this variant may be benign, 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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