Submissions for variant NM_000090.4(COL3A1):c.13G>A (p.Val5Met)

gnomAD frequency: 0.00001  dbSNP: rs1461198652

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000507209	SCV000603138	uncertain significance	not specified	2016-10-19	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000702640	SCV000831502	uncertain significance	Ehlers-Danlos syndrome, type 4	2023-03-24	criteria provided, single submitter	clinical testing	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. 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 not expected to disrupt COL3A1 protein function. ClinVar contains an entry for this variant (Variation ID: 439514). This variant has not been reported in the literature in individuals affected with COL3A1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 5 of the COL3A1 protein (p.Val5Met).
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV001170883	SCV001333505	uncertain significance	Familial thoracic aortic aneurysm and aortic dissection	2019-04-03	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV001170883	SCV001342553	uncertain significance	Familial thoracic aortic aneurysm and aortic dissection	2023-09-07	criteria provided, single submitter	clinical testing	This missense variant replaces valine with methionine at codon 5 of the COL3A1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 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 1/31394 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	RCV003322779	SCV004028267	uncertain significance	not provided	2023-02-16	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 does not alter 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	RCV000702640	SCV004822911	uncertain significance	Ehlers-Danlos syndrome, type 4	2023-12-13	criteria provided, single submitter	clinical testing	This missense variant replaces valine with methionine at codon 5 of the COL3A1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has not been reported in individuals affected with cardiovascular disorders in the literature. This variant has been identified in 1/31394 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.