ClinVar Miner

Submissions for variant NM_182961.4(SYNE1):c.16229G>A (p.Arg5410Gln)

gnomAD frequency: 0.00004  dbSNP: rs776100963
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 3
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000756740 SCV000884638 uncertain significance not provided 2017-08-18 criteria provided, single submitter clinical testing The p.Arg5339Gln variant (rs776100963) has not been reported in the medical literature, is not listed in gene-specific variant databases, nor has it been previously identified in our laboratory. It is listed in the Genome Aggregation Database (gnomAD) browser with a frequency in African populations of 0.021% (identified in 5 out of 24,024 chromosomes). The arginine at codon 5339 is weakly conserved considering 12 species (Alamut software v2.9), and several avian species have a glutamine at this position, suggesting this change is evolutionary tolerated. Furthermore, computational analyses suggest this variant does not have a significant effect on SYNE1 protein structure/function (SIFT: tolerated, PolyPhen2: benign, and Mutation Taster: polymorphism). However, based on the available information, the clinical significance of the p.Arg5339Gln variant cannot be determined with certainty.
Labcorp Genetics (formerly Invitae), Labcorp RCV001373980 SCV001570734 uncertain significance Autosomal recessive ataxia, Beauce type; Emery-Dreifuss muscular dystrophy 4, autosomal dominant 2022-08-23 criteria provided, single submitter clinical testing This variant is present in population databases (rs776100963, gnomAD 0.02%). 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 output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 618407). This variant has not been reported in the literature in individuals affected with SYNE1-related conditions. This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 5339 of the SYNE1 protein (p.Arg5339Gln).
Revvity Omics, Revvity RCV000756740 SCV003824658 uncertain significance not provided 2020-06-23 criteria provided, single submitter clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.