ClinVar Miner

Submissions for variant NM_000090.4(COL3A1):c.3154C>T (p.Pro1052Ser)

dbSNP: rs2153503729
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001961993 SCV002132692 uncertain significance Ehlers-Danlos syndrome, type 4 2023-01-08 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: 1366157). This variant has not been reported in the literature in individuals affected with COL3A1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 1052 of the COL3A1 protein (p.Pro1052Ser).
Ambry Genetics RCV004040341 SCV003965447 uncertain significance Familial thoracic aortic aneurysm and aortic dissection 2023-04-25 criteria provided, single submitter clinical testing The c.3154C>T (p.P1052S) alteration is located in exon 43 (coding exon 43) of the COL3A1 gene. This alteration results from a C to T substitution at nucleotide position 3154, causing the proline (P) at amino acid position 1052 to be replaced by a serine (S). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is not well conserved in available vertebrate species. This alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
All of Us Research Program, National Institutes of Health RCV001961993 SCV004836835 uncertain significance Ehlers-Danlos syndrome, type 4 2023-10-02 criteria provided, single submitter clinical testing This missense variant replaces proline with serine at codon 1052 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 not been identified 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.

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