2-47800297-C-T
Variant summary
Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PM1PM2PP3_StrongPP5_Very_Strong
The NM_000179.3(MSH6):c.2314C>T(p.Arg772Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R772Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_000179.3 missense
Scores
Clinical Significance
Conservation
Publications
- intellectual developmental disorder with dysmorphic facies and behavioral abnormalitiesInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
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ACMG classification
Our verdict: Pathogenic. The variant received 16 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MSH6 | NM_000179.3 | c.2314C>T | p.Arg772Trp | missense_variant | Exon 4 of 10 | ENST00000234420.11 | NP_000170.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MSH6 | ENST00000234420.11 | c.2314C>T | p.Arg772Trp | missense_variant | Exon 4 of 10 | 1 | NM_000179.3 | ENSP00000234420.5 |
Frequencies
GnomAD3 genomes 0.00000658 AC: 1AN: 152060Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000796 AC: 2AN: 251130 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461876Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 727238 show subpopulations
GnomAD4 genome 0.00000658 AC: 1AN: 152060Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74250 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Pathogenic:5
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Published functional studies demonstrate a damaging effect: deficient mismatch repair activity (PMID: 32849802); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at a significant frequency in large population cohorts (gnomAD); 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, 17531815, 21120944, 32338768, 28888541, 36293153, 35451682, 29922827, 31391288, 34445333, 33804961, 31965077, 32849802) -
MSH6: PS4, PM1, PM2, PP1, PS3:Supporting -
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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. -
Lynch syndrome 5 Pathogenic:3
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]. -
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PS4_STR, PS3, PM2_SUP, PM5, PP1 -
Lynch syndrome Pathogenic:3
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. -
Multifactorial likelihood analysis posterior probability >0.99 -
The p.Arg772Trp variant in MSH6 has not been previously reported in 6 individuals with Lynch syndrome (LS) or LS-associated cancers and segregated with disease in 1 affected relative from 1 family (Plaschke 2004 PMID: 14974087, Jasperson 2008 PMID: 18176851, Buchanan 2014 PMID: 24323032, Sunga 2017 PMID: 28449805, Carter 2018 PMID: 30322717, Nguyen-Dumont 2020 PMID: 32338768). Immunohistochemistry performed on tumors sampled from 4 individuals showed either reduction or loss of MSH6 expression (Plaschke 2004 PMID: 14974087, Jasperson 2008 PMID: 18176851, Buchanan 2014 PMID: 24323032). Additionally, this variant has been reported in 3 other individuals with a personal and/or family history of cancer who had been referred for germline cancer genetic testing (Espenschied 2017 PMID: 28514183). Furthermore, this variant has been reported as in the homozygous state in an individual with constitutional mismatch repair deficiency (CMMRD) and their sibling who had clinical features of the disease. Immunohistochemistry performed on skin biopsies from these children were found to be deficient in MSH6 expression (Elhasid 2015 PMID: 26274037). This variant has also been identified in 0.001% (1/68020) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, gnomAD v3.1.2). In vitro functional studies provide some evidence that this variant impairs mismatch repair activity (Thompson 2020 PMID: 32849802) and computational prediction tools and conservation analyses are consistent with pathogenicity. Moreover, this variant was classified as pathogenic on Oct 18, 2018 by the ClinGen-approved International Society for Gastrointestinal Hereditary Tumours (InSiGHT) expert panel (Variation ID 89267). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PS4_Moderate, PS3_Moderate, PM2_Supporting, PP3. -
Hereditary cancer-predisposing syndrome Pathogenic:2
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. -
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. -
Carcinoma of colon Pathogenic:1
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. -
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
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; internal data). Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this MSH6 variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 1,370,736 individuals referred to our laboratory for MSH6 testing. ClinVar contains an entry for this variant (Variation ID: 89267). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) 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 (internal data). For these reasons, this variant has been classified as Pathogenic. -
Endometrial carcinoma Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at