Submissions for variant NM_000090.4(COL3A1):c.316G>A (p.Gly106Ser)

gnomAD frequency: 0.00001  dbSNP: rs180938313

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV000460511	SCV000541787	uncertain significance	Ehlers-Danlos syndrome, type 4	2023-10-22	criteria provided, single submitter	clinical testing	This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 106 of the COL3A1 protein (p.Gly106Ser). This variant is present in population databases (rs180938313, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with COL3A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 404286). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt COL3A1 protein function. 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.
Ambry Genetics	RCV001805058	SCV000738512	uncertain significance	Familial thoracic aortic aneurysm and aortic dissection	2016-01-19	criteria provided, single submitter	clinical testing	The p.G106S variant (also known as c.316G>A), located in coding exon 3 of the COL3A1 gene, results from a G to A substitution at nucleotide position 316. The glycine at codon 106 is replaced by serine, an amino acid with similar properties. This variant was previously reported in the SNPDatabase as rs180938313. Based on data from ExAC, the A allele has an overall frequency of approximately 0.002% (3/120802). The highest observed frequency was 0.01% (2/11410) of Latino alleles (Exome Aggregation Consortium (ExAC), Cambridge, MA (URL: http://exac.broadinstitute.org) [Accessed January 19, 2016]). Based on data from the 1000 Genomes Project, the A allele has an overall frequency of approximately 0.05% (1/2098) total alleles studied. The highest observed frequency was 3.57% (1/28) Spanish alleles. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be possibly damaging and tolerated by PolyPhen and SIFT in silico analyses, respectively. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.
Color Diagnostics, LLC DBA Color Health	RCV001805058	SCV002053670	uncertain significance	Familial thoracic aortic aneurysm and aortic dissection	2023-03-09	criteria provided, single submitter	clinical testing	This missense variant replaces glycine with serine at codon 106 of the COL3A1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with COL3A1-related disorders in the literature. This variant has been identified in 5/250722 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
GeneDx	RCV002255381	SCV002526482	uncertain significance	not provided	2022-05-04	criteria provided, single submitter	clinical testing	Has not been previously published as pathogenic or benign to our knowledge; Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not located in the triple helical region, where the majority of pathogenic missense variants occur (HGMD)
All of Us Research Program, National Institutes of Health	RCV000460511	SCV004832895	uncertain significance	Ehlers-Danlos syndrome, type 4	2023-12-01	criteria provided, single submitter	clinical testing	This missense variant replaces glycine with serine at codon 106 of the COL3A1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with cardiovascular disorders in the literature. This variant has been identified in 5/250722 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.