Submissions for variant NM_000179.3(MSH6):c.260+2T>G

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV002426247	SCV002744072	likely pathogenic	Hereditary cancer-predisposing syndrome	2021-12-23	criteria provided, single submitter	clinical testing	The c.260+2T>G intronic variant results from a T to G substitution two nucleotides after coding exon 1 in the MSH6 gene. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.
Myriad Genetics, Inc.	RCV003455484	SCV004189267	likely pathogenic	Lynch syndrome 5	2023-08-09	criteria provided, single submitter	clinical testing	This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV004017936	SCV004848379	likely pathogenic	Lynch syndrome	2020-05-13	criteria provided, single submitter	clinical testing	The c.260+2T>G variant in MSH6 has not been previously reported in individuals with Lynch syndrome and was absent from large population studies. This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. Heterozygous loss-of-function of the MSH6 gene is an established disease mechanism in individuals with Lynch syndrome. Another variant affecting the same splice site (c.260+2T>A) has been classified as likely pathogenic by our laboratory. In summary, this variant meets criteria to be classified as likely pathogenic for autosomal dominant Lynch syndrome based upon predicted impact to the protein and absence in controls. ACMG/AMP criteria applied: PVS1, PM2.