ClinVar Genomic variation as it relates to human health

The p.G750D pathogenic mutation (also known as c.2249G>A), located in exon 13 of the PMS2 gene, results from a G to A substitution at nucleotide position 2249. The glycine at codon 750 is replaced by aspartate, an amino acid with similar properties. In one study, this alteration was detected in trans with a full gene PMS2 deletion and the severe phenotype in this family was consistent with biallelic PMS2 mutations. The proband was diagnosed with rectal cancer at age 22 and a brain tumor at age 23, while a brother was diagnosed with colorectal cancer (CRC) at age 21. The proband's tumor as well as adjacent normal tissue demonstrated loss of PMS2 expression on IHC (Senter et al. Gastroenterology. 2008 August; 135(2): 419–428). In another family, the p.G750D alteration was reported in conjunction with the PMS2 frameshift mutation c.2019delT in a proband with café-au-lait macules, a glioblastoma at age 31, and CRC at age 32. Tumor testing showed MSI-H and absence of PMS2 staining on IHC. This patient's family history included hematologic cancers, renal cancer, and CRC (van Galen et al. Hereditary Cancer in Clinical Practice. 2011, 9(Suppl 1):P38). This alteration was also reported in a suspected Lynch syndrome family and the proband had co-occurrence with PMS2 p.E330_E381del. The clinical features of the proband included: CRC diagnosed twice at ages 22 and 32, polyps at age 38, a glioblastoma at age 40, and café-au-lait macules (Lavoine N et al. J. Med. Genet. 2015 Nov;52:770-8). In another study, this alteration was reported in conjunction with PMS2 p.S46I in a male with colon cancer diagnosed at ages 41 and 50 and tumor results demonstrated MSI-H as well as loss of PMS2 expression on IHC (Goodenberger ML et al. Genet. Med. 2016 Jan;18:13-9). Based on an internal structural analysis, this variant is anticipated to result in a significant decrease in protein structural stability (Gueneau E et al. Nat. Struct. Mol. Biol. 2013 Apr; 20(4):461-8). This missense alteration is located in a region that has a low rate of benign missense variation (Lek M et al. Nature. 2016 Aug 18;536(7616):285-91; DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. Firth H.V. et al. 2009. Am.J.Hum.Genet. 84, 524-533 (DOI: dx.doi.org/10/1016/j.ajhg.2009.03.010)). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

PS4_STR, PS3, PM2_SUP

The PMS2 c.2249G>A variant is predicted to result in the amino acid substitution p.Gly750Asp. This variant has been reported to occur with other PMS2 pathogenic variants in individuals with suspected mismatch repair deficiency syndrome and/or colorectal cancer (Senter et al. 2008. PubMed ID: 18602922; Lavoine et al. 2015. PubMed ID: 26318770; Table S1, Goodenberger et al. 2016. PubMed ID: 25856668). In at least one case, the variants were determined to be on opposite alleles (Senter et al. 2008. PubMed ID: 18602922). However, in at least two individuals with colorectal cancer there was a second pathogenic PMS2 variant present; however, phase was not determined (Supplemental Data, Bodo et al. 2015. PubMed ID: 26116798; Table S1, Goodenberger et al. 2016. PubMed ID: 25856668). Studies have shown that this variant, and PMS2 variants overall, were not significantly associated with an increased risk of ovarian or breast cancer (Table S7, Lilyquist et al. 2017. PubMed ID: 28888541; Supplemental Data, Lilyquist et al. 2017. PubMed ID: 28888541). Functional studies have shown that this variant impacts protein function (Drost et al. 2013. PubMed ID: 24027009; Table A2, Shuen et al. 2019. PubMed ID: 30608896). This variant is reported in 0.00089% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-6018253-C-T). This variant has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from uncertain to likely pathogenic to pathogenic. (https://www.ncbi.nlm.nih.gov/clinvar/variation/91334/); however, the majority of submitters favor likely pathogenic/pathogenic. Taken together, we interpret this variant as likely pathogenic.

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 30608896, 24027009]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 18602922, 30608896, 26318770]. This variant is expected to disrupt protein structure [Myriad internal data].

Variant summary: PMS2 c.2249G>A (p.Gly750Asp) results in a non-conservative amino acid change located in the MutL, C-terminal, dimerisation domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 249726 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.2249G>A has been reported in the literature in individuals affected with constitutional mismatch repair deficiency syndrome (e.g., Senter_2008, Lavoine_2015, Shuen_2019) as well as other individuals affected with cancers associated with Lynch syndrome (e.g., Goodenberger_2016, Bono_2021, Lilyquist_2017, Fanale_2022). Experimental studies have shown that the variant compromises mismatch repair efficiency (e.g., Drost_PMS2_2013, Bodo_2015). The following publications have been ascertained in the context of this evaluation (PMID: 26116798, 34371384, 24027009, 35223509, 25856668, 26318770, 28888541, 18602922, 30608896). Nine submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments (pathogenic, n = 2; likely pathogenic, n = 5; VUS, n = 2). Based on the evidence outlined above, the variant was classified as likely pathogenic.

This missense variant replaces glycine with aspartic acid at codon 750 in the nuclease domain of the PMS2 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). Functional studies have shown that this variant protein partially reduces DNA mismatch repair activity compared with wild type protein in in vitro-based assays (PMID: 24027009, 26116798, 30608896). This variant has been reported in heterozygous state with a second pathogenic PMS2 variant (PMID: 18602922, 26116798, 26318770; DOI: 10.1186/1897-4287-9-S1-P38), or in heterozygous state with an unknown second pathogenic variant (PMID: 30608896), in individuals affected with constitutional mismatch repair deficiency (CMMRD). Of note, these individuals had cancer onset age later than typical individuals with CMMRD. This variant has been reported in individuals affected with colorectal cancer exhibiting clinical features of Lynch syndrome (PMID: 25856668, co-occurring with the pathogenic Ser46Ile PMS2 variant), or ovarian cancer (PMID: 34371384). This variant has been identified in 1/249726 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. The partial functional impact and later cancer onset age suggest that this variant may not be associated with the same cancer risk as a typical PMS2 pathogenic variant.

This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 750 of the PMS2 protein (p.Gly750Asp). 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 missense change has been observed in individual(s) with constitutional mismatch repair deficiency syndrome (PMID: 18602922, 26318770, 30608896; https://hccpjournal.biomedcentral.com/articles/10.1186/1897-4287-9-S1-P38). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 91334). 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 with a positive predictive value of 80%. Experimental studies have shown that this missense change affects PMS2 function (PMID: 24027009, 26116798). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

Published functional studies demonstrate a damaging effect: reduced, though not deficient, MMR activity (PMID: 24027009, 30608896); 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; This variant is associated with the following publications: (PMID: 18602922, 18709565, 21376568, 26318770, 26333163, 26116798, 20531397, 25856668, 28152038, 34371384, 31332305, 28888541, 30608896, 23435383, 33471991, 24027009, Fukui2011[Chapter], 37937776)

According to the ClinGen InSiGHT ACMG PMS2 v1.0.0 criteria we chose these criteria: PS3 (supporting pathogenic): Drost et al. 2013, PMID: 24027009, PM3 (medium pathogenic): This variant has been reported to occur with other PMS2 pathogenic variants in individuals with suspected mismatch repair deficiency syndrome and/or colorectal cancer (Senter et al. 2008. PubMed ID: 18602922; Lavoine et al. 2015. PubMed ID: 26318770; Table S1, Goodenberger et al. 2016. PubMed ID: 25856668). In at least one case, the variants were determined to be on opposite alleles (Senter et al. 2008. PubMed ID: 18602922). However, in at least two individuals with colorectal cancer there was a second pathogenic PMS2 variant present; however, phase was not determined (Supplemental Data, Bodo et al. 2015. PubMed ID: 26116798; Table S1, Goodenberger et al. 2016. PubMed ID: 25856668). Strength?, PP3 (medium pathogenic): MAPP/PP2 Prior P score: 0.9603 , PP4 (medium pathogenic): Bodo (2015, PMID: 26116798): ColorectalCa --> MSI & PMS2 lost in Normal and Tumor tissue Senter (2009, PMID: 18602922): IHC results from these probands’ tumor analyses [including c.2249G>A] demonstrated loss of PMS2 expression in their tumors Goodenberger (2016, PMID: 25856668): MSI-H, IHC: PMS2 loss Shuen (2019, PMID: 30608896): PMS2 loss & MMR activity: 8.27

PP3, PP4, PP5, PM2, PM3, PS3_supporting

The PMS2 c.2249G>A, p.(Gly750Asp) variant was identified in the literature in 7 individuals or families with CMMRD, colorectal, ovarian, or breast cancer and was seen in 1 healthy individual (Senter 2008, Bodo 2015, Lavoine 2015, Goodenberger 2016, Shuen 2019, Bono 2021). The variant was also identified in ClinVar (classified as uncertain significance by 2 submitters; as likely pathogenic by Labcorp and 8 other submitters; and as pathogenic by GeneDx and Ambry Genetics). The variant was identified in controls in 27 of 1,603,354 chromosomes (2 homozygous) at a frequency of 0.00002 (Genome Aggregation Database Nov 1 2023 v4.0.0). The variant was observed in trans with pathogenic PMS2 variants in 3 individuals with CMMRD, increasing the likelihood that this c.2249G>A variant has clinical significance (Senter 2008, Lavoine 2015, Bodo 2015). Additionally, the variant was identified in 1 individual with MSI-high colon tumour and confirmed loss of PMS2 expression (Goodenberger 2016). In functional studies, the variant was demonstrated to reduce mismatch repair activity (Drost 2013, Shuen 2019). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.