ClinVar Miner

Submissions for variant NM_001848.2(COL6A1):c.2809A>G (p.Lys937Glu) (rs117583120)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000431648 SCV000229789 uncertain significance not provided 2018-07-19 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000279845 SCV000436577 benign Collagen VI-related myopathy 2018-01-13 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000431648 SCV000510585 uncertain significance not provided 2016-11-08 criteria provided, single submitter clinical testing Converted during submission to Uncertain significance.
GeneDx RCV000177845 SCV000567531 uncertain significance not specified 2017-06-28 criteria provided, single submitter clinical testing A variant of unknown significance has been identified in the COL6A1 gene. The K937E variant has not been published as a pathogenic variant, nor has it been reported as a benign polymorphism to our knowledge. The K937E variant was not observed with any significant frequency in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, but the 1000 Genomes Project reports K937E was observed in 2/1006 (0.2%) alleles from individuals of European background. The K937E variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In silico analysis predicts this variant is probably damaging to the protein structure/function. However, this substitution occurs at a position where amino acids with similar properties to Lysine are tolerated across species. Additionally, missense variants in nearby residues have not been reported in the Human Gene Mutation Database in association with COL6A1-related disorders (Stenson et al., 2014). Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV001087752 SCV000657051 likely benign Bethlem myopathy 1 2019-12-31 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000431648 SCV001143270 likely benign not provided 2018-11-26 criteria provided, single submitter clinical testing

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