Total submissions: 4
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Ambry Genetics | RCV000221642 | SCV000274064 | uncertain significance | Hereditary cancer-predisposing syndrome | 2018-08-17 | criteria provided, single submitter | clinical testing | The p.A854P variant (also known as c.2560G>C), located in coding exon 15 of the PMS2 gene, results from a G to C substitution at nucleotide position 2560. The alanine at codon 854 is replaced by proline, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. |
| Invitae | RCV001853516 | SCV002261257 | uncertain significance | Hereditary nonpolyposis colorectal neoplasms | 2023-06-14 | 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 expected to disrupt PMS2 protein function. ClinVar contains an entry for this variant (Variation ID: 230492). This variant has not been reported in the literature in individuals affected with PMS2-related conditions. The frequency data for this variant in the population databases (gnomAD) is considered unreliable due to the presence of homologous sequence, such as pseudogenes or paralogs, in the genome. This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 854 of the PMS2 protein (p.Ala854Pro). |
| Gene |
RCV003329262 | SCV004036246 | uncertain significance | not provided | 2023-03-21 | criteria provided, single submitter | clinical testing | 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; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: Fukui2011[Chapter]) |
| Baylor Genetics | RCV003462438 | SCV004207869 | uncertain significance | Lynch syndrome 4 | 2023-01-24 | criteria provided, single submitter | clinical testing |