Submissions for variant NM_000251.2(MSH2):c.1275A>G (p.Glu425=) (rs63751650)

Total submissions: 13

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000487506	SCV000149409	likely benign	not provided	2020-08-21	criteria provided, single submitter	clinical testing	In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 27601186, 15849733, 21404120, 24728189, 24556621, 24549055, 16341550, 27696107, 32849802, 31332305)
Invitae	RCV001082316	SCV000166260	benign	Hereditary nonpolyposis colorectal neoplasms	2020-12-07	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000115500	SCV000187466	likely benign	Hereditary cancer-predisposing syndrome	2019-10-07	criteria provided, single submitter	clinical testing	Co-occurence with mutation in same gene (phase unknown);Other data supporting benign classification
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics	RCV000487506	SCV000339840	uncertain significance	not provided	2016-02-29	criteria provided, single submitter	clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen	RCV000487506	SCV000575205	uncertain significance	not provided	2016-09-01	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000487506	SCV000601427	likely benign	not provided	2019-11-12	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000487506	SCV000696204	benign	not provided	2017-07-14	criteria provided, single submitter	clinical testing	Variant summary: The MSH2 c.1275A>G (p.Glu425Glu) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change in the second to last nucleotide in exon 7.. This variant was found in 12/120260 control chromosomes at a frequency of 0.0000998, predominantly in individuals of European descent (0.00017; 11/65934 chrs). The variant is also observed in gnomAD dataset at slightly higher frequencies (0.00026; 33/126394 European chrs tested). Although these frequencies do not exceed the estimated maximal expected allele frequency of a pathogenic MSH2 variant (0.0005683), the variant may be a functional ethnic polymorphism. The variant has been reported in affected individuals in the literaure, including being present in an unaffected family members or a proband as well as absent in three affected family members from two unrelated pedigrees (Pagenstecher_2006, Leongamornlert_2014), showing a lack of segregation with disease. Additionally, the variant was present in affected individuals who carried second pathogenic mutations in other genes related to hereditary cancers (two pathogenic mutations in the MUTYH gene from Pagenstecher_2006; a pathogenic ATM variant from Leongamornlert_BJC_2014; a frameshift variant in AXIN2 gene from Rohlen_2016; and a pathogenic CHEK2 (c.1100delC) variant from internal LCA sample. RT-PCR studies showed the variant to result in a deletion of 48 bp due to activation of a cryptic splice site in exon 7. However, because it was only a partial effect, a considerable amount of full-length transcript can still be synthesized from the mutant allele which may be sufficient for maintaining MMR activity in a cell even in case of a somatic mutation in the normal allele (Pagenstecher_2006); tumors from carriers of this variant showed normal MSI-S and IHC further supportive of a non-pathogenic outcome for this variant. Multiple clinical diagnostic laboratories/reputable databases classified this variant as VUS while others have classified it as VUS/likely benign. Taken together, based on a high preponderance for an alternate molecular basis of disease among reported patients in the literature and our internal co-occurrence data, this variant is classified as benign.
CSER _CC_NCGL, University of Washington	RCV000735971	SCV000864160	uncertain significance	Colon polyps	2017-12-01	criteria provided, single submitter	research	Found in patient having exome sequencing due to suspicion for hereditary colon cancer and/or polyps. Patient is a 61 year old female with a history of 5-10 colon polyps and family history of colorectal cancer and/or polyps. This interpretation considers GERP score and allele frequency data, in addition to published reports of the variant in the literature, available at the time of review.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories	RCV000487506	SCV000884133	uncertain significance	not provided	2018-01-30	criteria provided, single submitter	clinical testing	The MSH2 c.1275A>G; p.Glu425Glu variant (rs63751650) is reported in the medical literature in individuals with Lynch syndrome (Mangold 2005, Pagenstecher 2006, Rohlin 2017), however, it was reported to not co-segregate with disease (Pagenstecher 2006). Additionally, this variant was found in an individual with prostate cancer who also carried a pathogenic ATM variant (Leongamornlert 2014). Functional analysis of p.Glu425Glu suggests this variant causes partial exon skipping (Pagenstecher 2006), but the clinical significance of this is uncertain. The p.Glu425Glu variant is reported in ClinVar (Variation ID: 90589), and is found in the general population with an overall allele frequency of 0.01% (35/276878 alleles) in the Genome Aggregation Database. This variant occurs in the second to last nucleotide in exon 7 and computational algorithms predict this variant to slightly weaken the nearby canonical donor splice site (Alamut v.2.10). Based on available information, the clinical significance of the p.Glu425Glu variant is uncertain at this time. REFERENCES Leongamornlert D et al. Frequent germline deleterious mutations in DNA repair genes in familial prostate cancer cases are associated with advanced disease. Br J Cancer. 2014 Mar 18;110(6):1663-72. 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. 2005 Sep 20;116(5):692-702. 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. Rohlin A et al. Expanding the genotype-phenotype spectrum in hereditary colorectal cancer by gene panel testing. Fam Cancer. 2017 Apr;16(2):195-203.
Color Health, Inc	RCV000115500	SCV000902695	likely benign	Hereditary cancer-predisposing syndrome	2016-03-08	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000487506	SCV001713983	uncertain significance	not provided	2019-09-05	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000202073	SCV000257130	uncertain significance	not specified		no assertion criteria provided	clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System	RCV001357605	SCV001553121	uncertain significance	Carcinoma of colon		no assertion criteria provided	clinical testing	The MSH2 p.Glu425= variant was identified in 3 of 4626 proband chromosomes (frequency: 0.0006) from Swedish, British and American individuals or families with CRC/CRC phenotypes or ovarian cancer and was not identified in 3056 control chromosomes from healthy individuals (Song 2014, Rohlin 2017). The variant was analysed for RNA expression levels in affected patients and it was found to cause an in-frame deletion of 48 base pairs in exon 7 resulting in partial skipping of exon 7 due to the creation of a cryptic splice site (Pagenstecher 2006). In this study, family testing for APC was negative and the allele was inherited from the healthy mother; in addition, segregation was excluded as the proband and her 2 affected siblings were compound heterozygotes for 2 pathogenic mutations in MUTYH (c.494A>G; p.Y165C and c.1395_1397delGGA; p.Glu466del; Aretz et al., unpublished data). The variant also co-occurred with a pathogenic AXIN2 variant (c.254del/p.Leu85TyrfsX24) in 1 proband with a CRC phenotype (Rohlin 2017). The variant was identified by our laboratory in 1 individual with colon cancer, co-occurring with a pathogenic EPCAM variant c.859-?_945+415+?del. The variant was also identified in dbSNP (ID: rs63751650) as “With Uncertain significance allele”, in ClinVar (classified as uncertain significance, reviewed by an expert panel 2013; likely benign by Invitae and Ambry Genetics, and uncertain significance by InSIGHT, GeneDx, EGL Genetic Diagnostics, Praxis fuer Hamngenetik Tuebingen, Quest Diagnostics Nichols Institute San Juan Capistrano and Mayo Clinic), Clinvitae (5x), UMD-LSDB (5x as neutral), Insight Colon Cancer Gene Variant Database (2x class 3), Mismatch Repair Genes Variant Database, Insight Hereditary Tumors Database (2x class 3); it was not identified in the COGR, Cosmic, MutDB, and Zhejiang Colon Cancer Database. The variant was identified in control databases in 35 of 276878 chromosomes at a frequency of 0.0001 increasing the likelihood this could be a low frequency variant (Genome Aggregation Database Feb 27, 2017). Observations by population include African in 2 of 24034 chromosomes (freq: 0.00008), European Non-Finnish in 33 of 126394 chromosomes (freq: 0.0003); it was not observed in the Other, Latino, Ashkenazi Jewish, East Asian, European Finnish, and South Asian populations. The p.Glu425= variant is not expected to have clinical significance because it does not result in a change of amino acid. The c.1275A>G variant occurs in the second last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing; however, 2 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 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.