Total submissions: 5
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Ambry Genetics | RCV000164990 | SCV000215684 | likely benign | Hereditary cancer-predisposing syndrome | 2018-12-29 | criteria provided, single submitter | clinical testing | In silico models in agreement (benign);Co-occurence with mutation in same gene (phase unknown) |
Gene |
RCV000429937 | SCV000516135 | likely benign | not specified | 2018-03-08 | criteria provided, single submitter | clinical testing | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. |
Invitae | RCV000461904 | SCV000551950 | uncertain significance | Hereditary nonpolyposis colorectal neoplasms | 2019-11-16 | criteria provided, single submitter | clinical testing | This sequence change replaces proline with serine at codon 437 of the PMS2 protein (p.Pro437Ser). The proline residue is weakly conserved and there is a moderate physicochemical difference between proline and serine. This variant is not present in population databases (rs200726484, ExAC no frequency). This variant has been observed in an individual affected with colon cancer in the Leiden Open-source Variation Database (PMID: 21520333). However, in that individual, a pathogenic allele was also identified in PMS2, which suggests that this c.1309C>T variant was not the primary cause of disease. ClinVar contains an entry for this variant (Variation ID: 185547). An in vitro experimental study has shown that this missense change does not affect the DNA mismatch repair activity of the PMS2 protein (PMID: 27435373). 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. |
Color | RCV000164990 | SCV000691007 | likely benign | Hereditary cancer-predisposing syndrome | 2017-08-18 | criteria provided, single submitter | clinical testing | |
Integrated Genetics/Laboratory Corporation of America | RCV000586893 | SCV000697292 | uncertain significance | not provided | 2016-12-22 | criteria provided, single submitter | clinical testing | Variant summary: The PMS2 c.1309C>T (p.Pro437Ser) variant causes a missense change involving a non-conserved nucleotide, which 4/5 in silico tools predict a benign. A functional study indicates that the variant of interest acted comparable to wild type MMR function. In addition, the variant of interest was reported to co-occur with another pathogenic PMS2 variant, c.1079_1080del, in an individual diagnosed with CrC at 43 y/o. LOVD - InSiGHT cites the variant in a male (adenocarc conlon transversum); AMS criteria negative; TUMOR_IHC: MLH1: positive; MSH2: positive; MSH6: positive; PMS2: negative; MLH1 Methylation: no methylation; Method: MS-MLPA; Indicates that the patient carried another pathogenic PMS2 variant c.1079_1080del (Classified as Class 5 by InSiGHT). Therefore, the patient described in LOVD is likely to be the same patient reported in the published reference. Furthermore, the IHC pattern supports the notion that the co-occuring PMS2 variant was the likely cause of colorectal cancer in this patient. The variant of interest was not observed in controls (ExAC, 1000 Gs, or ESP). A clinical diagnostic laboratory cites the variant as "likely benign." Therefore, due to the reported co-occurrence, and comparable wild type MMR properties, the variant of interest has been classified as a "Variant of Uncertain Significance - Possibly Benign." |