ClinVar Genomic variation as it relates to human health

Coding sequence variation resulting in a stop codon

The c.3984_3987dupGTCA pathogenic mutation, located in coding exon 9 of the MSH6 gene, results from a duplication of GTCA at nucleotide position 3984, causing a translational frameshift with a predicted alternate stop codon (p.L1330Vfs*12). This mutation is a founder mutation in the Ashkenazi Jewish population (Raskin L et al. Clin. Genet. 2011 Jun;79(6):512-22), and was reported in 19 members of four unrelated Ashkenazi Jewish families affected with colon, endometrial, gastric, ovarian, urinary and breast cancers (Goldberg Y et al. Fam. Cancer. 2010 Jun;9(2):141-50). This mutation (designated as 3987ins4) was also identified in an individual with Ashkenazi Jewish ancestry who was diagnosed with pancreatic cancer (Salo-Mullen EE et al. Cancer. 2015 Dec 15;121(24):4382-8). In addition, this mutation has been reported in multiple patients with constitutional mismatch repair deficiency (CMMR-D) syndrome (Bakry D et al. Eur. J. Cancer. 2014 Mar;50(5):987-96). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation. As such, this alteration is interpreted as a disease-causing mutation.

Variant summary: The MSH6 c.3984_3987dupGTCA (p.Leu1330Valfs) variant results in a premature termination codon, predicted to cause a truncated or absent MSH6 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (e.g. c.3991C>T, p.Arg1331X). One in silico tool predicts a damaging outcome for this variant. This variant was found in 4/123518 control chromosomes at a frequency of 0.0000324, which does not exceed the estimated maximal expected allele frequency of a pathogenic MSH6 variant (0.0001421). The variant has been reported in numerous patients and families in the literature, including several compound heterozygotes with CMMRD. The variant has been described in the literature as an Ashkenazi Jewish founder mutation. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

This c.3984_3987dup variant in the MSH6 gene has been reported in one HNPCC patient (PMID16237223), two endometrial cancer patients (PMID15236168) and three related CRC patients with segregation in two generations (PMID14520694). In addition, a case control study identified this variant in 8/2685 CRC cases, 2/337 endometrial cancer cases and 1/330 control. PMID19851887 suggest this variant to be a founder variant for Ashkenazi Jews. This variant is predicted to cause a frameshift and create a premature stop codon. Based upon above evidence, this c.3984_3987dupGTCA variant in the MSH6 gene is classified pathogenic.

The p.Leu1330ValfsX12 (c.3984_3987dupGTCA) variant in MSH6 has been described as an Ashkenazi Jewish founder variant. It has been in the heterozygous state in over 15 individuals with Lynch syndrome associated cancers and segregated with disease in over 12 affected family members from at least 3 families (Goldberg 2010, Raskin 2011). This variant was shown to be associated with loss of expression of the MSH6 protein in the tumor tissue (Goldberg 2010). Additionally, it has been reported in at least 4 individuals with constitutional mismatch repair deficiency in the compound heterozygous state with another pathogenic MSH6 variant (Bakry 2014, Levi 2015). Additionally, this variant has been identified in 3/9998 of Ashkenazi Jewish chromosomes by gnomAD (http://gnomad.broadinstitute.org). This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 1330 and leads to a premature termination codon 12 amino acids downstream. This termination codon occurs within the last exon and is, therefore, likely to escape nonsense mediated decay (NMD) and result in a truncated protein. Moreover, this variant was classified as Pathogenic on September 5, 2013 by the ClinGen-approved InSiGHT expert panel (SCV000108179.2). In summary, this variant meets criteria to be classified as pathogenic for Lynch syndrome in an autosomal dominant manner. ACMG/AMP Criteria applied: PS4, PVS1_Strong, PP1_strong, PM2.

DNA sequence analysis of the MSH6 gene demonstrated a four base pair duplication in exon 9, c.3984_3987dup. This pathogenic sequence change results in an amino acid frameshift and creates a premature stop codon 11 amino acids downstream of the mutation, p.Leu1330Valfs*12. This pathogenic sequence change is predicted to result in an abnormal transcript, which may be degraded, or may lead to the production of a truncated MSH6 protein with potentially abnormal function. This pathogenic sequence change is considered an Ashkenazi Jewish founder mutation (Goldberg et al. 2010, Raskin et al. 2011) and has previously been found to segregate in several families with colorectal, endometrial, and pancreatic cancer (Peterlongo et al. 2003, Hendriks et al. 2004, Hegde et al. 2005, Salo-Mullen et al. 2015) and in the compound heterozygous state in individuals with constitutional mismatch repair deficiency syndrome (Bakry et al. 2014). This patient has an increased risk of colorectal, endometrial and pancreatic cancers and other MSH6-related cancers. The contribution of this variant to this patient's throat/lung cancer and pancytopenia remains uncertain. Heterozygous pathogenic variants in MSH6 are associated with Lynch syndrome, which is associated with an increased risk of certain cancers, particularly colon and endometrial cancers [OMIM#614350, 608089]. Leukemia and other hematological malignancies can be an unusual presentation of Lynch syndrome (Yu VP, et al., 2009; Bansidhar BJ, 2012). Homozygous or compound heterozygous pathogenic variants in MSH6 lead to a mismatch repair deficiency which is a rare childhood cancer predisposition syndrome with 4 main tumor types: hematologic malignancies, brain/central nervous system tumors, colorectal tumors and multiple intestinal polyps, and other malignancies including embryonic tumors and rhabdomyosarcoma [OMIM#276300].

Frameshift variant predicted to result in protein truncation as the last 31 amino acids are lost and replaced with 11 incorrect amino acids; Observed in the heterozygous state in individuals with a personal or family history of cancer consistent with pathogenic variants in this gene and considered an Ashkenazi Jewish founder variant (Peterlongo 2003, Goldberg 2010, Raskin 2011, Salo-Mullen 2015, Cox 2018, Lee 2018); Case control studies suggest this variant is associated with colon and endometrial cancer (Raskin 2011); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Also known as 3987insGTCA and 3987ins4; This variant is associated with the following publications: (PMID: 28514183, 29144512, 30152102, 22219001, 12454801, 21155762, 19851887, 14520694, 26822575, 25642631, 26544533, 26440929, 25307252, 26681312, 29485237, 30498870, 30077346, 24440087, 30702970, 30322717, 31730237, 29625052, 26689913, 31447099)

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

This frameshift variant alters the translational reading frame of the MSH6 mRNA and causes the premature termination of MSH6 protein synthesis. In the published literature, the variant has been reported as an Ashkenazi Jewish founder mutation and is found in families with hereditary non-polyposis colorectal cancer (HNPCC) (PMID: 14520694 (2003), 15236168 (2004), 19851887 (2010), 21155762 (2011)), pancreatic cancer (PMID: 26440929 (2015)), endometrial cancer (PMID: 26681312 (2015)), glioblastoma (PMID: 29625052 (2018)), ovarian cancer (PMID: 30322717 (2018)), and breast cancer (PMID: 30498870 (2019)). This variant has also been found in a compound heterozygous state in individuals with constitutional mismatch repair deficiency syndrome (CMMRD) (PMID: 24440087 (2014), 25307252 (2015)). Based on the available information, this variant is classified as pathogenic.

This variant inserts 4 nucleotides in exon 9 of the MSH6 gene, creating a frameshift and premature translation stop signal in the last coding exon. This mutant transcript is predicted to escape nonsense-mediated decay and be expressed as a truncated protein. This variant has been reported as a recurring mutation in Ashkenazi Jews (PMID: 19851887, 21155762) and has been observed in many individuals affected with Lynch syndrome-associated cancers (PMID: 14520694, 15236168, 16237223, 19851887, 21155762, 26440929, 26681312, 30498870, 34086170). This variant has also been reported in the compound heterozygous state with a second MSH6 mutation in individuals affected with constitutional mismatch repair deficiency syndrome (PMID: 24440087). This variant has been identified in 3/246806 chromosomes 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 sequence change creates a premature translational stop signal (p.Leu1330Valfs*12) in the MSH6 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 31 amino acid(s) of the MSH6 protein. This variant is present in population databases (rs751033488, gnomAD 0.04%). This premature translational stop signal has been observed in individual(s) with clinical features of Lynch syndrome or constitutional mismatch repair deficiency syndrome (PMID: 14520694, 15236168, 16237223, 19851887, 21155762, 24440087, 26440929). It is commonly reported in individuals of Ashkenazi Jewish ancestry (PMID: 19851887, 21155762). This variant is also known as 3987ins4. ClinVar contains an entry for this variant (Variation ID: 89496). For these reasons, this variant has been classified as Pathogenic.

The MSH6 c.3984_3987dup; p.Leu1330ValfsTer12 variant (rs267608121) is reported in the literature in numerous heterozygous individuals affected with Lynch syndrome and in homozygous or compound heterozygous individuals with constitutional mismatch repair syndrome (Raskin 2011, Diaz-Velasquez 2023, Levi 2015). This variant is recognized as a founder variant in the Ashkenazi Jewish population (Raskin 2011). This variant is reported in ClinVar (Variation ID: 89496) and is found in the Ashkenazi Jewish population with an allele frequency of 0.03% (3/34406 alleles) in the Genome Aggregation Database. This variant causes a frameshift by inserting four nucleotides, resulting in a truncated protein. Based on available information, this variant is considered to be pathogenic. References: Raskin L et al. Characterization of two Ashkenazi Jewish founder mutations in MSH6 gene causing Lynch syndrome. Clin Genet. 2011 Jun;79(6):512-22. PMID: 21155762. Diaz-Velasquez CE et al. Evaluation of genetic alterations in hereditary cancer susceptibility genes in the Ashkenazi Jewish women community of Mexico. Front Genet. 2023 Feb 10;14:1094260. PMID: 36845387. Levi Z et al. The gastrointestinal manifestation of constitutional mismatch repair deficiency syndrome: from a single adenoma to polyposis-like phenotype and early onset cancer. Clin Genet. 2015 Nov;88(5):474-8. PMID: 25307252.

The MSH6 p.Leu1330Valfs*12 variant was identified in 16 of 7108 proband chromosomes (frequency: 0.002) from individuals or families with Lynch syndrome, or endometrial or pancreatic cancer and was present in 1 of 6988 control chromosomes (frequency: 0.0002) from healthy individuals (Peterlongo 2003, Raskin 2011, Salo-Mullen 2015, Barak 2010). The variant was also identified in dbSNP (ID: rs751033488) as "With Pathogenic allele", ClinVar (classified as pathogenic by Invitae, Ambry Genetics, GeneDx and seven other submitters) and the Insight Colon Cancer Gene Variant Database (as class 5: pathogenic). The variant was not identified in UMD-LSDB nor was it identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). This variant has been described in the literature as a founder mutation in the Ashkenazi Jewish population (Goldberg 2010, Raskin 2011) and has also been identified as co-occurring with a pathogenic MSH6 variant (c.3959delCAAG, p.Ala1320Glufs*6) in multiple individuals with constitutional mismatch repair deficiency (Bakry 2014). The c.3984_3987dup variant is predicted to cause a frameshift which alters the protein's amino acid sequence beginning at codon 1330 and leads to a premature stop codon 12 codons downstream. 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.