Submissions for variant NM_000179.3(MSH6):c.2689A>T (p.Asn897Tyr)

dbSNP: rs1064794771

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000484487	SCV000569914	uncertain significance	not provided	2016-04-11	criteria provided, single submitter	clinical testing	This variant is denoted MSH6 c.2689A>T at the cDNA level, p.Asn897Tyr (N897Y) at the protein level, and results in the change of an Asparagine to a Tyrosine (AAT>TAT). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. MSH6 Asn897Tyr was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Since Asparagine and Tyrosine differ in some properties, this is considered a semi-conservative amino acid substitution. MSH6 Asn897Tyr occurs at a position that is not conserved and is located in domain III of the MutS domain (Terui 2013). In silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. Based on currently available evidence, it is unclear whether MSH6 Asn897Tyr is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.
Invitae	RCV000705957	SCV000834983	uncertain significance	Hereditary nonpolyposis colorectal neoplasms	2023-10-04	criteria provided, single submitter	clinical testing	This sequence change replaces asparagine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 897 of the MSH6 protein (p.Asn897Tyr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MSH6-related conditions. ClinVar contains an entry for this variant (Variation ID: 420892). 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 not expected to disrupt MSH6 protein function. 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.
Color Diagnostics, LLC DBA Color Health	RCV000775790	SCV000910239	uncertain significance	Hereditary cancer-predisposing syndrome	2023-12-04	criteria provided, single submitter	clinical testing	This missense variant replaces asparagine with tyrosine at codon 897 of the MSH6 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with MSH6-related disorders in the literature. This variant has not been identified 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.
Ambry Genetics	RCV000775790	SCV001177241	uncertain significance	Hereditary cancer-predisposing syndrome	2023-06-27	criteria provided, single submitter	clinical testing	The p.N897Y variant (also known as c.2689A>T), located in coding exon 4 of the MSH6 gene, results from an A to T substitution at nucleotide position 2689. The asparagine at codon 897 is replaced by tyrosine, an amino acid with dissimilar properties. This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV002465685	SCV002760663	uncertain significance	not specified	2023-08-15	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV004003338	SCV004838493	uncertain significance	Lynch syndrome	2023-08-08	criteria provided, single submitter	clinical testing