ClinVar Miner

Submissions for variant NM_000090.3(COL3A1):c.3019G>A (p.Ala1007Thr) (rs201220788)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000621749 SCV000738538 likely benign Cardiovascular phenotype 2018-03-12 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Subpopulation frequency in support of benign classification,Does not segregate with disease in family study (genes with incomplete penetrance)
GeneDx RCV000181103 SCV000233379 uncertain significance not specified 2017-04-18 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the COL3A1 gene. The A1007T variant has not been published as pathogenic or been reported as benign to our knowledge. The A1007T variant is observed in the Exome Aggregation Consortium at a frequency of 12/6614 alleles (0.18%) in Finnish Europeans, and in 2/1006 alleles (0.2%) in European populations in the 1000 Genomes Consortium (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The A1007T 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. However, this substitution occurs at a position that is not conserved across species, and in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Furthermore, although this variant occurs within the triple helical region of the COL3A1 gene it does not affect a Glycine residue in a Gly-X-Y motif, where the majority of pathogenic missense variants occur (Stenson et al., 2014; Symoens et al., 2012).
Invitae RCV000634727 SCV000756067 likely benign Ehlers-Danlos syndrome, type 4 2018-01-23 criteria provided, single submitter clinical testing

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