Submissions for variant NM_000179.3(MSH6):c.2314C>T (p.Arg772Trp)

dbSNP: rs63750138

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000074732	SCV000107941	pathogenic	Lynch syndrome	2018-10-18	reviewed by expert panel	curation	Multifactorial likelihood analysis posterior probability >0.99
Ambry Genetics	RCV000162422	SCV000212763	pathogenic	Hereditary cancer-predisposing syndrome	2023-04-12	criteria provided, single submitter	clinical testing	The p.R772W variant (also known as c.2314C>T), located in coding exon 4 of the MSH6 gene, results from a C to T substitution at nucleotide position 2314. The arginine at codon 772 is replaced by tryptophan, an amino acid with dissimilar properties. Residue 772 is located in a highly conserved loop of the Lever Domain in the MSH6 protein and is likely to be involved in signal transduction between ATPase and DNA binding domains (Warren JJ et al. Mol. Cell. 2007 May;26(4):579-92). This alteration was identified in a patient diagnosed with colon cancer at age 75 who had no family history of HNPCC-related cancers. Tumor studies showed MSI-High and absent MSH6 on IHC (Plaschke J et al. Hum Mutat. 2004 Mar;23(3):285). In another study, this alteration segregated with disease in a proband and her mother. The proband was diagnosed with colon cancer at age 45 and bladder cancer at age 47 that was MSI-Low with reduced expression of MSH6 on IHC. The proband's mother was diagnosed with endometrial cancer at age 38 and colon cancer at age 59 that showed reduced expression of MSH2 and MSH6 on IHC (Jasperson KW et al. Fam Cancer. 2008;7(4):281-5). In another study, this alteration was identified in an individual diagnosed with endometrial cancer at age 58 that showed loss of MSH6 on IHC (Buchanan DD et al. J Clin Oncol. 2014 Jan 10;32(2):90-100). The p.R772W alteration has also been reported as homozygous in multiple individuals with known familial consanguinity and clinical histories consistent with CMMR-D (Levi Z et al. Clin Genet. 2015 Nov;88(5):474-8; Elhasid R et al. J. Pediatr. Hematol. Oncol. 2015 Nov;37(8):e490-3). 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.
GeneDx	RCV000218399	SCV000279102	pathogenic	not provided	2020-11-03	criteria provided, single submitter	clinical testing	Published functional studies demonstrate a damaging effect: deficient mismatch repair activity (Thompson 2020); Not observed at a significant frequency in large population cohorts (Lek 2016); 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: 24323032, 29345684, 30212499, 30322717, 12732731, 18176851, 14974087, 26333163, 26274037, 25307252, 28449805, 28514183, 30128536, 27498913, 23621914, 30166433, 32849802, 32338768)
Invitae	RCV000524139	SCV000551232	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2024-01-18	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 772 of the MSH6 protein (p.Arg772Trp). This variant is present in population databases (rs63750138, gnomAD 0.003%). This missense change has been observed in individuals with clinical features of Lynch syndrome and constitutional mismatch repair deficiency (PMID: 14974087, 18176851, 24323032, 25307252, 28449805, 28514183; Invitae). ClinVar contains an entry for this variant (Variation ID: 89267). 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 MSH6 protein function with a positive predictive value of 95%. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000074732	SCV000695806	pathogenic	Lynch syndrome	2019-02-15	criteria provided, single submitter	clinical testing	Variant summary: MSH6 c.2314C>T (p.Arg772Trp) results in a non-conservative amino acid change located in the DNA mismatch repair protein MutS, core domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function (ACMG PP3). The variant allele was found at a frequency of 8.1e-06 in 246050 control chromosomes (gnomAD and publication, ACMG PM2). c.2314C>T has been reported in the literature in individuals affected with Lynch Syndrome, colon cancer, endometrial cancer and breast cancer (Plaschke 2004, Buchanan 2014, Sunga 2017, Lu_2018). The reported patients ranged from those fulfilling the Amsterdam-II criteria (Jasperson 2008), revised Bethesda guidelines (Buchanan 2014) as well as not fulfilling the Bethesda guidelines (Plaschke 2004). In addition, in one comprehensively genotyped patient affected by colon and urinary bladder cancer who had reduced expression of the MSH6 protein within the tumor (and normal expression of MLH1 and MSH2) the variant was also found in her affected mother (Jasperson 2008). Loss of MSH6 expression in tumors was also noted in other studies for individuals carrying the variant (Plaschke 2004, Buchanan 2014). Furthermore, this variant has been reported in homozygous state associated with the phenotype for constitutional mismatch repair deficiency (CMMR-D) syndrome; immunohistochemical analysis of skin biopsies revealed MSH6 protein deficiency (Elhasid 2015, Levi 2015). The variant was also found in one female endometrial cancer patient (47 y.o.) as a somatic variant, who carried a frameshift 19bps insertion in MSH6 as a germ-line variant (Goodfellow 2003). Lastly, somatic point mutations affecting a different nucleotide but the same amino acid residue (c.2315G>A [p.R772Q]), have been identified in a colon and a gastric cancer, both with the MSI-H phenotype (Ohmiya et al., 2001). This points to p.Arg772Trp fulfilling the LOH (Loss of Heterozygosity) criteria for tumor suppressor genes and highlighting functional importance of this residue within the MSH6 protein. These data indicate that the variant is likely to be associated with disease (ACMG PS4). A co-occurrence with another pathogenic variant has been reported in our internal database (CHEK2 c.1434delA, p.Glu479fsX3). Three ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely pathogenic. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) has recently classified this variant as a class-5 pathogenic variant using the same evidence outlined above. Based on the evidence outlined above, the variant meets sufficient clinical criteria to be classified as pathogenic.
Color Diagnostics, LLC DBA Color Health	RCV000162422	SCV000908396	pathogenic	Hereditary cancer-predisposing syndrome	2023-01-23	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with tryptophan at codon 772 of the MSH6 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). A functional study has shown that this variant causes a significant loss of mismatch repair activity compared to wild type protein in a cell-free in vitro assay (PMID: 32849802). This variant has also been shown to have an incomplete impact on mRNA splicing, expressing both truncated and reference transcripts (PMID: 32849802). This variant has been reported in individuals affected with colorectal, endometrial, and bladder cancer (PMID: 14974087, 18176851, 24323032, 36293153), breast cancer (PMID: 30128536), and reported three times among a suspected Lynch syndrome cohort (PMID: 28514183). This variant has also been reported in homozygous carriers from families affected with constitutive mismatch repair deficiency syndrome (PMID: 25307252, 26274037, 30166433). This variant has been identified in 2/251130 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen	RCV000218399	SCV001250448	pathogenic	not provided	2023-09-01	criteria provided, single submitter	clinical testing	MSH6: PS4, PM1, PM2, PP3, PS3:Supporting
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000218399	SCV001470348	pathogenic	not provided	2021-10-08	criteria provided, single submitter	clinical testing	The frequency of this variant in the general population, 0.000008 (2/251130 chromosomes, http://gnomad.broadinstitute.org), is consistent with pathogenicity. In the published literature, the variant has been reported in individuals with colorectal, breast, ovarian, endometrial, and prostate cancer (PMIDs: 32338768 (2020), 30128536 (2018), 30322717 (2018), 28449805 (2017), 24323032 (2014), 14974087 (2004)). It has also been reported in the homozygous state in three children with CMMRD (PMIDs: 26274037 (2015), 25307252 (2015)). Additionally, a functional study indicated this variant has significantly reduced DNA mismatch repair activity in vitro, and the variant was characterized as being pathogenic based on multifactorial analysis (PMID: 32849802 (2020)). Based on the available information, this variant is classified as pathogenic.
Revvity Omics, Revvity	RCV000218399	SCV002023525	pathogenic	not provided	2023-06-14	criteria provided, single submitter	clinical testing
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV002467437	SCV002762823	pathogenic	Lynch syndrome 5	2022-12-09	criteria provided, single submitter	research	PS4_STR, PS3, PM2_SUP, PM5, PP1
Myriad Genetics, Inc.	RCV002467437	SCV004185585	pathogenic	Lynch syndrome 5	2023-08-16	criteria provided, single submitter	clinical testing	This variant is considered pathogenic. Functional studies indicate this variant impacts protein function [PMID: 31965077]. This variant is expected to disrupt protein structure [Myriad internal data]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 18176851, 30166433, 25307252].
Baylor Genetics	RCV003466943	SCV004198135	pathogenic	Endometrial carcinoma	2022-08-16	criteria provided, single submitter	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001353694	SCV000592604	likely pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	The p.Arg772Trp variant was identified in the literature in 2 of 54 proband chromosomes (frequency 0.037) from individuals with colon cancer and was not identified in 190 chromosomes from healthy control individuals (Jasperson 2008, Plaschke 2004). This variant was also reported in dbSNP (rs63750138) “with untested allele”, in the HGMD, “InSiGHT Colon Cancer Database”, the “MMR Genes Variant Database” and in the Exome Variant Server ESP Project with a frequency of 0.0007 in African American alleles, suggesting that this variant may be present at low frequency in certain populations of origin. Plaschke (2004) describes a patient with the variant who had loss of MSH6 protein expression in a late onset tumour of the colon, and suggests that that the late onset of disease in this patient may be interpreted as reduced penetrance of the variant. In another study, the p.Arg772Trp variant was identified as a somatic mutation in an individual with early onset endometrial cancer who also had a germline MSH6 mutation (Goodfellow 2003), and Jasperson (2008) suggests that the somatic variant in this patient’s tumour may have inactivated the wild-type allele, leading to the early onset of this cancer. A different variant at this amino acid position, p.Arg772Gln, was identified by Ohmiya (2001) in two cases as a somatic variant in one colon and one stomach tumor, increasing the likelihood that this position is important to MSH6 protein function. The p.Arg772 residue is conserved across mammals and lower organisms and computational analyses (PolyPhen2, SIFT, AlignGVGD, BLOSUM) suggest that the p.Arg772Trp variant may impact the protein. In addition, this residue is noted to be situated within the DNA binding domain (Goodfellow 2003) and one in-silico study suggests that this variant likely has an affect on MSH6 function (Terui 2013). However, this information is not predictive enough to assume pathogenicity. This individual is reported as homozygous for this variant and had a skin biopsy that was reported as MSH6 deficient and also had weak MSH2 deficiency by immunohistochemistry and also had other features of biallelic mismatch repair (MMR) syndrome (café au-lait spots) increasing the likelihood this variant is pathogenic. Notably, this variant also segregated in homozygous form in an affected family member who also had features of biallelic MMR deficiency and an associated cancer (AML). In summary, based on the above information the clinical significance of this variant cannot be determined at this time although we would lean towards a more pathogenic role for this variant. Therefore this variant is classified as predicted pathogenic.
Mayo Clinic Laboratories, Mayo Clinic	RCV000218399	SCV000691930	pathogenic	not provided		no assertion criteria provided	clinical testing