Submissions for variant NM_000179.3(MSH6):c.4001G>A (p.Arg1334Gln)

dbSNP: rs267608122

Total submissions: 16

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000074974	SCV000108190	pathogenic	Lynch syndrome	2013-09-05	reviewed by expert panel	research	Multifactorial likelihood analysis posterior probability >0.99
GeneDx	RCV000160701	SCV000211330	pathogenic	not provided	2022-02-28	criteria provided, single submitter	clinical testing	Not observed in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 21081928, 23621914, 24362816, 18566915, 12547705, 15236168, 12373605, 20028993, 18415027, 27601186, 24705251, 26681312, 28502729, 24728189, 27768684, 17453009, 30283497, 29887214, 10508506, 8063241, 21836479, 31297337, 31447099, 32719484, 21120944, 17531815, 12019211, 34178123, 30787465)
Ambry Genetics	RCV000491705	SCV000580100	pathogenic	Hereditary cancer-predisposing syndrome	2022-03-24	criteria provided, single submitter	clinical testing	The c.4001G>A pathogenic mutation (also known as p.R1334Q), located in coding exon 9 of the MSH6 gene, results from a G to A substitution at nucleotide position 4001. The amino acid change results in arginine to glutamine at codon 1334, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 9, which makes it likely to have some effect on normal mRNA splicing. In silico splice site analysis predicts that this alteration will weaken the native splice donor site and RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This mutation has been reported in multiple Lynch syndrome patients as well as families and this variant segregated with disease in these families (Wijnen J et al. Nat Genet. 1999;23(2):142-144; Gille et al. Br J Cancer. 2002;87(8):892-897; Overbeek LI et al. Br J Cancer. 2007;96(10):1605-1612; Lagerstedt-Robinson K et al. Oncol. Rep. 2016 Nov;36(5):2823-2835). Functional studies have also demonstrated the pathogenicity of this variant (Houlleberghs H et al. PLoS Genet. 2017 May;13(5):e1006765). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Invitae	RCV000542786	SCV000624960	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2023-12-31	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1334 of the MSH6 protein (p.Arg1334Gln). RNA analysis indicates that this missense change induces altered splicing and likely disrupts the C-terminus of the protein. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Lynch syndrome (LS) and LS-associated cancers (PMID: 10508506, 15236168, 17453009, 21081928, 21836479, 26681312). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 89506). An algorithm developed specifically for the MSH6 gene suggests that this missense change is likely to be tolerated (PMID: 23621914). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in skipping of exon 9 and introduces a new termination codon (Invitae). However the mRNA is not expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
Counsyl	RCV000576708	SCV000677749	likely pathogenic	Lynch syndrome 5	2017-03-31	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000491705	SCV000690430	pathogenic	Hereditary cancer-predisposing syndrome	2023-04-18	criteria provided, single submitter	clinical testing	This variant causes a G>A nucleotide substitution at the last nucleotide of exon 9 of the MSH6 gene. Splice site prediction tools suggest that this variant may impact RNA splicing. A RT-PCR analysis of RNA derived from two carriers has reported out-of-frame skipping of exon 9 (UMD database, http://139.124.156.133/4D_molecules/UMD230309.html). This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with Lynch syndrome (PMID: 12547705, 17453009, 18566915, 27601186; UMD database) and in individuals affected with endometrial cancer (PMID: 33467402) and colorectal cancer (PMID: 26681312). Multifactorial likelihood model using health history, in silico, and experimental data has suggested this variant has a high probability of being pathogenic (InSiGHT database, http://insight-database.org/). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH6 function is a known mechanism of disease. Based on the available evidence, this variant is classified as Pathogenic.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000074974	SCV000711435	pathogenic	Lynch syndrome	2018-06-15	criteria provided, single submitter	clinical testing	The p.Arg1334Gln variant in MSH6 has been reported in 4 individuals with MSH6-as sociated cancers and segregated with disease in 7 affected relatives from 2 fami lies (Hendriks 2004, Overbeek 2007, van Puijenbroek 2008, Klarskov 2011). It was absent from large population studies. This variant affects the last base of the exon, which is part of the 5? splice region and computational tools predict alt ered splicing, which is expected to lead to an altered or absent protein. Consis tent with this, tumors from patients harboring this variant showed absence of MS H6 protein (Hendriks 2004, Klarskov 2011). This variant was classified as Pathog enic on Sept 5, 2013 by the ClinGen-approved InSiGHT Expert Panel (ClinVar SCV00 0108190.2). In summary, this variant meets criteria to be classified as pathogen ic for Lynch syndrome. ACMG/AMP criteria applied: PP1_Str, PS4_Mod, PM2, PS3_Mod , PP3 (Richards 2015).
Revvity Omics, Revvity	RCV000160701	SCV002017592	pathogenic	not provided	2022-04-26	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV000576708	SCV004018973	pathogenic	Lynch syndrome 5	2023-03-29	criteria provided, single submitter	clinical testing	This variant is considered pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad internal data]. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 25085752].
Baylor Genetics	RCV001355904	SCV004198133	pathogenic	Endometrial carcinoma	2022-08-23	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000160701	SCV004222027	pathogenic	not provided	2023-06-15	criteria provided, single submitter	clinical testing	The MSH6 c.4001G>A (p.Arg1334Gln) variant has been reported in the published literature in affected individuals with colorectal cancer (PMIDs: 12373605 (2002), 15236168 (2004), 17453009 (2007), 21836479 (2011), 26681312 (2015), 30264118 (2018), 31447099 (2019), and 34178123 (2021)), breast cancer (PMIDs: 26681312 (2015) and 33471991)), endometrial cancer (PMIDs: 10508506 (1999) and 15236168 (2004), 33467402 (2021)), lung cancer (PMID: 31297337 (2019)), as well as in individuals diagnosed with Lynch Syndrome (PMIDs: 18566915 (2009), 20028993 (2010), and 27601186 (2016)). It was also found in a tumor as a somatic variant (PMID: 29887214 (2018)). Functional studies have demonstrated that this variant is damaging to protein function (PMIDs: 185669115 (2009), 28531214 (2017), and 30264118 (2018)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, this variant is classified as pathogenic.
All of Us Research Program, National Institutes of Health	RCV000074974	SCV004835194	pathogenic	Lynch syndrome	2023-11-28	criteria provided, single submitter	clinical testing	This variant causes a G>A nucleotide substitution at the last nucleotide of exon 9 of the MSH6 gene. Splice site prediction tools suggest that this variant may impact RNA splicing. A RT-PCR analysis of RNA derived from two carriers has reported out-of-frame skipping of exon 9 (UMD database, http://139.124.156.133/4D_molecules/UMD230309.html). This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with Lynch syndrome (PMID: 12547705, 17453009, 18566915, 27601186; UMD database) and in individuals affected with endometrial cancer (PMID: 33467402) and colorectal cancer (PMID: 26681312). Multifactorial likelihood model using health history, in silico, and experimental data has suggested this variant has a high probability of being pathogenic (InSiGHT database, http://insight-database.org/). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH6 function is a known mechanism of disease. Based on the available evidence, this variant is classified as Pathogenic.
Mayo Clinic Laboratories, Mayo Clinic	RCV000202090	SCV000257296	uncertain significance	not specified		no assertion criteria provided	research
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001355904	SCV001550922	likely pathogenic	Endometrial carcinoma		no assertion criteria provided	clinical testing	The MSH6 p.Arg1334Gln variant was identified in 5 of 3358 proband chromosomes (frequency: 0.001) from Dutch, Danish and Norwegian individuals or families with HNPCC (Wijnen_1999_10508506, Nilbert_2009_18566915, Gille_2002_12373605 , Hendriks_2004_15236168, Overbeek_2007_17453009). A bioinformatics tool, CoDP (Combination of the Different Properties), that integrates the prediction results of three methods, namely MAPP, PolyPhen-2 and SIFT and two other structural properties, found the variant had no impact on the MSH6 protein (Terui_2013_23621914). The variant was also identified in dbSNP (ID: rs267608122) “With Likely pathogenic,Pathogenic allele”, ClinVar (classified as pathogenic, reviewed by an expert panel(2013); submitters: pathogenic by InSIGHT and Ambry Genetics, likely pathogenic by GeneDx and uncertain significance by Mayo Clinic Genetic Testing Laboratories), Clinvitae (4x), Cosmic (1x in a glioma), UMD-LSDB (4x as causal), Mismatch Repair Genes Variant Database, and Insight Hereditary Tumors Database (9x). The variant was not identified in GeneInsight-COGR, MutDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Arg1334 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact of the variant Gln to the protein; this information is not very predictive of pathogenicity. The p.Arg1334Gln variant occurs in the last nucleotide of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In addition, 4 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. 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.
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000160701	SCV001932998	pathogenic	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000160701	SCV001953985	pathogenic	not provided		no assertion criteria provided	clinical testing