ClinVar Genomic variation as it relates to human health

The p.Cys694MetfsX4 variant in MSH6 has been reported in 2 individuals with colorectal cancer (DeRycke 2017 PMID: 28944238, Hansen 2017 PMID: 28195393, Xavier 2019 PMID: 31297992) and in 1 individual with a family history of Lynch-associated tumors (Shirts 2016 PMID: 26845104). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 187516) and is absent from large population studies. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 694 and leads to a premature termination codon 4 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the MSH6 gene is an established disease mechanism in autosomal dominant Lynch syndrome. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PVS1, PM2_Supporting, PS4_Supporting.

The c.2079dupA pathogenic mutation, located in coding exon 4 of the MSH6 gene, results from a duplication of A at nucleotide position 2079, causing a translational frameshift with a predicted alternate stop codon (p.C694Mfs*4). This mutation has been detected in multiple colorectal cancer patients (DeRycke MS et al. Mol Genet Genomic Med. 2017 Jul 23;5:553-569; Hansen MF et al. Clin Genet. 2017 Oct;92:405-414). Of note, this alteration is designated as c.2073_2074insA in published literature. In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

This variant inserts 1 nucleotide in exon 4 of the MSH6 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. 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 (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

This duplication of one nucleotide in MSH6 is denoted c.2079dupA at the cDNA level and p.Cys694MetfsX4 (C694MfsX4) at the protein level. The normal sequence, with the base that is duplicated in brackets, is CAAAAA[dupA]TGCC. The duplication causes a frameshift which changes a Cysteine to a Methionine at codon 694, and creates a premature stop codon at position 4 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. MSH6 c.2079dupA has been reported in individuals with personal and/or a family history of colorectal cancer (Shirts 2016, Hansen2017). Based on currently available evidence, we consider this variant to be pathogenic.

This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation.

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 187516). This premature translational stop signal has been observed in individual(s) with colorectal cancer (PMID: 21520333, 28195393). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Cys694Metfs*4) in the MSH6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH6 are known to be pathogenic (PMID: 18269114, 24362816).

The MSH6 p.Cys694Metfs*4 variant was identified in 2 of 3472 proband chromosomes (frequency: 0.0006) from individuals or families with colorectal, cervical, or prostate cancer (Hansen 2017, Shirts 2015). The variant was also identified in dbSNP (ID: rs267608083) as “With Pathogenic allele”, ClinVar (classified as pathogenic by Ambry Genetics, Invitae, GeneDx and one other clinical laboratory), UMD-LSDB (1x causal), and Insight Hereditary Tumors Database (2x). The variant was not identified in the COGR, Cosmic, Zhejiang University Database, or Mismatch Repair Genes Variant database. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). The c.2079dup variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 694 and leads to a premature stop codon at position 697. This alteration is then predicted to result in a truncated or absent protein and loss of function. Loss of function variants of the MSH6 gene are an established mechanism of disease in Lynch syndrome and is the type of variant expected to cause the disorder. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.