Submissions for variant NM_000179.3(MSH6):c.4004A>C (p.Glu1335Ala)

gnomAD frequency: 0.00004  dbSNP: rs564434147

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000129804	SCV000184615	uncertain significance	Hereditary cancer-predisposing syndrome	2023-02-09	criteria provided, single submitter	clinical testing	The p.E1335A variant (also known as c.4004A>C), located in coding exon 10 of the MSH6 gene, results from an A to C substitution at nucleotide position 4004. The glutamic acid at codon 1335 is replaced by alanine, an amino acid with dissimilar properties. This variant was reported in one family that met Amsterdam criteria and segregated with disease. The proband was diagnosed with colon cancer at age 42; however, tumor testing showed wild-type BRAF analysis, microsatellite stability, and normal IHC staining (Pérez-Cabornero L et al. J Mol Diagn. 2013 May;15(3):380-90). This alteration has also been reported as a variant of unknown significance, detected in a low-grade malignant astrocytoma that showed microsatellite stability and loss of staining for MLH1, MSH2, and MSH6 on IHC (Rodríguez-Hernández I et al. PLoS One. 2013 Sep 20;8(9):e76401). This alteration has been identified in individuals diagnosed with breast and/or ovarian cancer (Bonache S et al. J Cancer Res Clin Oncol, 2018 Dec;144:2495-2513; Cock-Rada AM et al. Fam Cancer, 2018 Jan;17:23-30; Nikitin AG et al. Front Oncol. 2020 May;10:666; Lerner-Ellis J et al. J Cancer Res Clin Oncol, 2021 Mar;147:871-879). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence for this variant is conflicting at this time, the clinical significance of this alteration remains unclear.
Invitae	RCV000204360	SCV000261608	uncertain significance	Hereditary nonpolyposis colorectal neoplasms	2023-12-27	criteria provided, single submitter	clinical testing	This sequence change replaces glutamic acid, which is acidic and polar, with alanine, which is neutral and non-polar, at codon 1335 of the MSH6 protein (p.Glu1335Ala). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with colorectal cancer, astrocytoma, or breast and/or ovarian cancers (PMID: 23523604, 24073290, 28528518, 30306255, 32547938). ClinVar contains an entry for this variant (Variation ID: 141327). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Eurofins Ntd Llc (ga)	RCV000656905	SCV000339599	uncertain significance	not provided	2016-02-04	criteria provided, single submitter	clinical testing
Counsyl	RCV000409369	SCV000489131	uncertain significance	Lynch syndrome 5	2016-08-25	criteria provided, single submitter	clinical testing
GeneDx	RCV000656905	SCV000565241	likely benign	not provided	2019-12-18	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 23523604, 28528518, 24073290)
Color Diagnostics, LLC DBA Color Health	RCV000129804	SCV000685482	uncertain significance	Hereditary cancer-predisposing syndrome	2024-01-02	criteria provided, single submitter	clinical testing	This missense variant replaces glutamic acid with alanine at codon 1335 of the MSH6 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been performed for this variant. This variant has been reported in individuals affected with colorectal cancer (PMID: 23523604), astrocytoma (PMID: 24073290), breast and/or ovarian cancer (PMID: 28528518, 32547938) or suspected of having Lynch syndrome (PMID: 31391288). In a large breast cancer case control study, this variant was reported in 2/60466 cases and 4/53461 unaffected controls (PMID: 33471991). This variant has also been identified in 22/271900 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Mendelics	RCV000708898	SCV000837935	uncertain significance	Lynch syndrome	2018-07-02	criteria provided, single submitter	clinical testing
Mendelics	RCV000409369	SCV001135869	uncertain significance	Lynch syndrome 5	2019-05-28	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001375525	SCV001572381	likely benign	not specified	2021-04-01	criteria provided, single submitter	clinical testing	Variant summary: MSH6 c.4004A>C (p.Glu1335Ala) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 8.7e-05 in 242576 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in MSH6 causing Lynch Syndrome (8.7e-05 vs 0.00014), allowing no conclusion about variant significance. c.4004A>C has been reported in the literature in individuals undergoing multigene panel testing for hereditary cancers such as Lynch, low grade astrocytoma and breast (example, Perez-Cabornero_2013, Rodriguez-Hernandez_2013, Cock-Rada_2017, Nikitin_2020). These report(s) do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. At-least two co-occurrences with other pathogenic variant(s) have been reported in the literature and observed at our laboratory (BRCA1 c.5266dupC, p.Gln1756Profs, Nikitin_2020; PALB2 c.1317delG, p.Phe440fs, internal testing), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. A study that computed a tumor characteristic likelihood ratio (TCLR) in combination with in-silico predictors and multifactorial variant prediction (MVP) model including allele frequency, co-occurrence, co-segregation, clinical and family history information classified this variant a "likely benign". Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Some submitters cite overlapping but not all evidences utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as likely benign.
Sema4, Sema4	RCV000129804	SCV002536312	uncertain significance	Hereditary cancer-predisposing syndrome	2021-11-03	criteria provided, single submitter	curation
Myriad Genetics, Inc.	RCV000409369	SCV004018961	likely benign	Lynch syndrome 5	2023-03-29	criteria provided, single submitter	clinical testing	This variant is considered likely benign. 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].
Baylor Genetics	RCV003467121	SCV004195635	uncertain significance	Endometrial carcinoma	2023-07-27	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003917421	SCV004740703	uncertain significance	MSH6-related condition	2024-01-30	criteria provided, single submitter	clinical testing	The MSH6 c.4004A>C variant is predicted to result in the amino acid substitution p.Glu1335Ala. This variant has been reported in individuals with a history of Lynch syndrome, astrocytoma, and breast and/or ovarian cancer (Rodríguez-Hernández et al. 2013. PubMed ID: 24073290; Pérez-Cabornero et al. 2013. PubMed ID: 23523604; Cock-Rada et al. 2018. PubMed ID: 28528518). This variant is reported in 0.031% of alleles in individuals of South Asian descent in gnomAD and has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from likely benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/141327/?new_evidence=true). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000656905	SCV001551880	uncertain significance	not provided		no assertion criteria provided	clinical testing	The MSH6 p.Glu1335Ala variant was identified in 3 of 680 proband chromosomes (frequency: 0.004) from individuals or families with Lynch syndrome, astrocytoma, and breast or ovarian cancer and was not identified in 694 control chromosomes from healthy individuals (Perez-Cabornero 2013, Rodriguez-Hernandez 2013, Cock-Rada 2018). The variant was also identified in dbSNP (ID: rs564434147 as "With Uncertain significance allele"), ClinVar (6x as uncertain significance by Ambry Genetics, Invitae, Counsyl, GeneDx, Color Genomics, and EGL Genetic), and UMD-LSDB (1x as unclassified variant). The variant was not identified in the COGR, Cosmic, MutDB, Zhejiang University Database, Mismatch Repair Genes Variant Database, or Insight Hereditary Tumors databases. The variant was identified in control databases in 18 of 237668 chromosomes at a frequency of 0.00008 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Latino in 7 of 32242 chromosomes (freq: 0.0002), European Non-Finnish in 2 of 108812 chromosomes (freq: 0.00008), and South Asian in 9 of 28764 chromosomes (freq: 0.0003); it was not observed in the African, Other, Ashkenazi Jewish, East Asian, or Finnish populations. The p.Glu1335 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. 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.