Submissions for variant NM_000251.3(MSH2):c.4G>A (p.Ala2Thr)

gnomAD frequency: 0.00008  dbSNP: rs63750466

Total submissions: 20

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000076617	SCV000107653	likely benign	Lynch syndrome 1	2018-06-13	reviewed by expert panel	curation	Multifactorial likelihood analysis posterior probability < 0.05 (0.006)
GeneDx	RCV000034558	SCV000149443	likely benign	not provided	2018-11-06	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.
Ambry Genetics	RCV000115534	SCV000184713	likely benign	Hereditary cancer-predisposing syndrome	2018-09-24	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Invitae	RCV001083980	SCV000259383	likely benign	Hereditary nonpolyposis colorectal neoplasms	2024-01-31	criteria provided, single submitter	clinical testing
Counsyl	RCV000076617	SCV000488838	uncertain significance	Lynch syndrome 1	2016-07-05	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000202071	SCV000696273	likely benign	not specified	2019-05-03	criteria provided, single submitter	clinical testing	Variant summary: MSH2 c.4G>A (p.Ala2Thr) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. 5/5 computational tools predict no significant impact on normal splicing. This was confirmed by RT-PCR results (Pagenstecher_2006). The variant allele was found at a frequency of 0.00016 in 217422 control chromosomes (gnomAD and publication data). This frequency is not significantly higher than expected for a pathogenic variant in MSH2 causing Lynch Syndrome (0.00016 vs 0.00057), allowing no conclusion about variant significance. The variant, c.4G>A, has been reported in the literature in individuals affected with Lynch Syndrome, uveal malignant melanoma or autosomal dominant cancer predisposition syndromes (Mangold_2005, Kurzawski_2006, Schrader_2016, Bonadona_2011, Hajkova_2018, Zhang_2015). One publication reported one family where it showed segregation of this variant with Lynch syndrome (Mangold_2005). However, in many reports, not all MMR genes were tested or MLPA applied. Consequently, these reports do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. Furthermore, in some of these families co-occurrences with other pathogenic variants have been reported (MSH2 c.1835C>G, p.Ser612X (Mangold_2005); EPCAM deletion associated with MSH2 promoter methylation (Nagasaka_2010); MSH2 c.1delA (UMD); RAD51C c.97C>T, p.Gln33X (Internal database)), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six clinical diagnostic laboratories and one expert panel (InSiGHT) have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (Likely benign (n=4 to include the expert panel), VUS (n=3)). Based on the evidence outlined above, the variant was classified as likely benign.
University of Washington Department of Laboratory Medicine, University of Washington	RCV000664313	SCV000788246	likely benign	Lynch syndrome	2018-02-01	criteria provided, single submitter	clinical testing	MSH2 p.A2T has been reported to co-occur with a MSH2 nonsense variant and a 3' EPCAM deletion where MSH2 promoter methylation was identified (Mangold 2005, Nagasaka 2010). Functional RNA studies performed on peripheral blood found normal RNA levels in patients that carry p.A2T (Pagenstecher 2006). MSH2 p.A2T was observed at an allele frequency of 0.0724% (14/19320 alleles) in large population cohorts (NHLBI Exome Sequencing Project, The 1000 Genomes Consortium 2015, Lek 2016), and it was observed in 1/208 individuals with atherosclerosis, with no specific information about cancer history (Johnston 2012).
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000034558	SCV000884129	uncertain significance	not provided	2018-02-06	criteria provided, single submitter	clinical testing	The MSH2 c.4G>A; p.Ala2Thr variant (rs63750466) is reported in the literature in multiple individuals with Lynch syndrome (Kurzawski 2006, Mangold 2005a, Mangold 2005b, Nagasaka 2010, Pagenstecher 2006, Parc 2003). However, it has been reported to co-occur with a pathogenic MSH2 nonsense variant (Mangold 2005a) and a 3'EPCAM deletion where MSH2 promoter methylation was seen (Nagasaka 2010). This variant is also reported to co-segregate with disease in a large Lynch syndrome family where loss of the MSH2 protein was seen in four individual's tumors; however, RNA analysis showed normal expression, suggesting this variant may be a marker in this family but the functional consequences are uncertain (Pagenstecher 2006). This variant is considered uncertain by an expert review panel in ClinVar (Variation ID: 41650), and is found in the general population with an overall allele frequency of 0.01% (34/241756 alleles) in the Genome Aggregation Database. This variant occurs in a conserved nucleotide of the Kozak consensus sequence, but computational algorithms do not agree as to the effect this variant may have on the protein (SIFT: Tolerated, PolyPhen2: Probably Damaging). Based on available information, the clinical significance of p.Ala2Thr is uncertain at this time. REFERENCES Kurzawski G et al. Germline MSH2 and MLH1 mutational spectrum including large rearrangements in HNPCC families from Poland (update study). Clin Genet. 2006 Jan;69(1):40-7. Mangold E et al. Spectrum and frequencies of mutations in MSH2 and MLH1 identified in 1,721 German families suspected of hereditary nonpolyposis colorectal cancer. Int J Cancer. 2005a Sep 20;116(5):692-702. Mangold E et al. Tumours from MSH2 mutation carriers show loss of MSH2 expression but many tumours from MLH1 mutation carriers exhibit weak positive MLH1 staining. J Pathol. 2005b Dec;207(4):385-95. Nagasaka T et al. Somatic hypermethylation of MSH2 is a frequent event in Lynch Syndrome colorectal cancers. Cancer Res. 2010 Apr 15;70(8):3098-108. Pagenstecher C et al. Aberrant splicing in MLH1 and MSH2 due to exonic and intronic variants. Hum Genet. 2006 Mar;119(1-2):9-22. Parc Y et al. Cancer risk in 348 French MSH2 or MLH1 gene carriers. J Med Genet. 2003 Mar;40(3):208-13.
Color Diagnostics, LLC DBA Color Health	RCV000115534	SCV000902739	likely benign	Hereditary cancer-predisposing syndrome	2022-01-01	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000034558	SCV001134367	likely benign	not provided	2021-08-09	criteria provided, single submitter	clinical testing
Institute of Human Genetics, University of Leipzig Medical Center	RCV001262884	SCV001440919	uncertain significance	Breast carcinoma	2019-01-01	criteria provided, single submitter	clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	RCV000034558	SCV002009326	uncertain significance	not provided	2021-11-03	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000115534	SCV002534527	likely benign	Hereditary cancer-predisposing syndrome	2021-04-09	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000202071	SCV002552181	likely benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV003149608	SCV003838426	uncertain significance	Breast and/or ovarian cancer	2021-10-08	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV000076617	SCV004018428	benign	Lynch syndrome 1	2023-03-24	criteria provided, single submitter	clinical testing	This variant is considered benign. This variant has been observed in trans with a known pathogenic variant in one or more individuals lacking clinical features consistent with gene-specific recessive disease. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752].
PreventionGenetics, part of Exact Sciences	RCV004534721	SCV004744178	likely benign	MSH2-related disorder	2021-01-28	criteria provided, single submitter	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Biesecker Lab/Clinical Genomics Section, National Institutes of Health	RCV000034558	SCV000043334	variant of unknown significance	not provided	2012-07-13	no assertion criteria provided	research	Converted during submission to Uncertain significance.
Mayo Clinic Laboratories, Mayo Clinic	RCV000202071	SCV000257190	uncertain significance	not specified		no assertion criteria provided	research
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001356983	SCV001552292	uncertain significance	Malignant tumor of breast		no assertion criteria provided	clinical testing	The MSH2 p.Ala2Thr variant was identified in 15 of 38724 proband chromosomes (frequency: 0.0004) from individuals or families with lynch syndrome or colorectal cancer (Bonadona 2011, Dymerska 2010, Johnston 2012, Kurzawski 2006, Mangold 2005, Nagasaka 2010, Parc 2003). The variant was identified in dbSNP (ID: rs63750466) as “With Uncertain significance allele”, ClinVar (as uncertain significance, reviewed by an expert panel including 6x as uncertain significance and 2x as likely benign), Clinvitae (5x), UMD-LSDB (30x as neutral), Mismatch Repair Genes Variant Database, and in the Insight Hereditary Tumors database (19x). In UMD the variant was identified with a co-occurring pathogenic MSH2 variant (c.1delA, p.Met1?), increasing the likelihood that the p.Ala2Thr variant does not have clinical significance. The variant was not identified in the COGR, Cosmic, MutDB, or Zhejiang University databases. The variant was identified in control databases in 34 of 241756 chromosomes at a frequency of 0.0001 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: “Other” in 1 of 5740 chromosomes (freq: 0.0002), European in 25 of 109176 chromosomes (freq: 0.0002), and Finnish in 8 of 21430 chromosomes (freq: 0.0004); it was not observed in the African, Latino, Ashkenazi Jewish, East Asian, or South Asian populations. The p.Ala2 residue is conserved across mammals and other organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In one study, Immunohistochemical analysis of this variant in tumors from relatives (mother and son - both of whom were carriers of the variant) revealed a loss of MSH2 protein expression; this finding supported a pathogenic role for the MSH2, c.4G>A, p.Ala2Thr variant (Mangold 2005). In another publication this variant is reported to segregate with the disease in several family members (at least 10 meioses) and showed loss of MSH2 expression in tumors of four affected family members. This variant is clearly linked to the disease in this specific family (Pagenstecher 2006). However, there is conflicting evidence in the literature; this variant was identified in an individual as co-occurring with pathogenic variant in MSH2 (c.1835C>G, p.S612X) (Lucci-Cordisco 2006, Mangold 2005). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.