ClinVar Miner

Submissions for variant NM_000093.4(COL5A1):c.4906G>A (p.Ala1636Thr) (rs113452150)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000620505 SCV000738583 likely benign Cardiovascular phenotype 2017-02-22 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Other data supporting benign classification,Subpopulation frequency in support of benign classification
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000724954 SCV000332706 uncertain significance not provided 2016-09-02 criteria provided, single submitter clinical testing
GeneDx RCV000200444 SCV000249921 uncertain significance not specified 2016-12-09 criteria provided, single submitter clinical testing The A1636T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The A1636T 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. This substitution occurs at a position where only amino acids with similar properties to Alanine are tolerated across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Missense variants in nearby residues (C1639S, C1639Y) have been reported in the Human Gene Mutation Database in association with EDS (Stenson et al., 2014). Nevertheless, the NHLBI Exome Sequencing Project and the 1000 Genomes Project reports A1636T was observed in 0.1% alleles from individuals of African background, indicating it may be a rare (benign) variant in this population. Finally, the A1636T variant does not affect a Glycine residue in a Gly-X-Y motif in the triple helical region of the COL5A1 gene, where the majority of pathogenic missense variants occur (Stenson et al., 2014; Symoens et al., 2012).Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign
Invitae RCV000538833 SCV000631533 likely benign Ehlers-Danlos syndrome, classic type 2017-12-24 criteria provided, single submitter clinical testing

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