Submissions for variant NM_000179.3(MSH6):c.4001G>C (p.Arg1334Pro)

dbSNP: rs267608122

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000219938	SCV000277547	pathogenic	Hereditary cancer-predisposing syndrome	2024-10-31	criteria provided, single submitter	clinical testing	The c.4001G>C pathogenic mutation (also known as p.R1334P), located in coding exon 9 of the MSH6 gene, results from a G to C substitution at nucleotide position 4001. The amino acid change results in arginine to proline at codon 1334, an amino acid with dissimilar 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. This variant has been identified in a proband who met Amsterdam II criteria for Lynch syndrome and tumor demonstrated high microsatellite instability with loss of MSH6 expression by immunohistochemistry (Yang C et al. Mol Genet Genomic Med, 2023 Feb;11:e2104). This nucleotide position is well conserved in available vertebrate species. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Another alteration impacting the same donor site (c.4001G>A) has been shown to have a similar impact on splicing identified in several probands, one of whom has a Lynch syndrome-associated tumor that demonstrated loss of MSH6 expression by immunohistochemistry (Ambry internal data). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000459481	SCV000551274	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2024-09-23	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 1334 of the MSH6 protein (p.Arg1334Pro). 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 individuals with clinical features of Lynch syndrome (PMID: 36691871; internal data). ClinVar contains an entry for this variant (Variation ID: 233214). 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. 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 (PMID: 36691871). However the mRNA is not expected to undergo nonsense-mediated decay. This variant disrupts the c.4001G nucleotide in the MSH6 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 10508506, 21836479; internal data). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Diagnostic Molecular Genetics Laboratory, Memorial Sloan Kettering Cancer Center	RCV001810439	SCV002060005	likely pathogenic	Lynch syndrome	2022-01-12	criteria provided, single submitter	clinical testing	The heterozygous germline variant, MSH6 c.4001G>C changes an Arginine to Proline at amino acid position 1334 (p.Arg1334Pro) and affects the last nucleotide of exon 9. This variant is absent from large population databases (1000 Genomes, ESP, and Broad ExAc). Computational prediction tools (SpliceSiteFinder, MaxEntScan, NNSPLICE and GeneSplicer) predict a complete loss of the intron 9 canonical splice donor site. Our functional study by RNA analysis (DMG internal data) demonstrated that this variant completely abolished normal splicing and caused exon 9 skipping, which is expected to lead to a prematurely truncated or abnormal protein. Our results indicate that this variant likely contributes to cancer predisposition through disruption of normal splicing, and is classified as likely pathogenic.
Genetics and Molecular Pathology, SA Pathology	RCV001810439	SCV002761772	pathogenic	Lynch syndrome	2022-05-13	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV003316228	SCV004018087	likely pathogenic	Lynch syndrome 5	2023-03-10	criteria provided, single submitter	clinical testing	This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 36691871]. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 36691871].
Clinical Genetics Laboratory, Skane University Hospital Lund	RCV001810439	SCV004024268	likely pathogenic	Lynch syndrome	2023-08-11	criteria provided, single submitter	clinical testing