NM_000179.3:c.3261delC
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_000179.3(MSH6):c.3261delC(p.Phe1088SerfsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,610,026 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000179.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.00000665 AC: 1AN: 150382Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1459644Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 726290
GnomAD4 genome 0.00000665 AC: 1AN: 150382Hom.: 0 Cov.: 32 AF XY: 0.0000136 AC XY: 1AN XY: 73330
ClinVar
Submissions by phenotype
not provided Pathogenic:10
MSH6: PVS1, PS4:Moderate -
The MSH6 c.3261del; p.Phe1088SerfsTer2 variant (rs267608078) is a recurrent alteration in individuals with Lynch syndrome or associated cancers (Baglietto 2010, Meric-Bernstam 2016, Tavakkol 2012, van der Post 2010, Wijnen 1999). This variant has also been observed in the homozygous or compound heterozygous state in individuals with constitutional mismatch repair deficiency (Ando 2021, Lavoine 2015). This variant is found in the general population with an overall allele frequency of 0.001% (4/280,876 alleles) in the Genome Aggregation Database (v2.1.1). This variant causes a frameshift by deleting a single nucleotide, so it is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. References: Ando T et al. Intensive surveillance endoscopy for multiple gastrointestinal tumors in a patient with constitutional mismatch repair deficiency: case report. BMC Gastroenterol. 2021 Aug 23;21(1):326. PMID: 34425783. Baglietto L et al. Risks of Lynch syndrome cancers for MSH6 mutation carriers. J Natl Cancer Inst. 2010 Feb 3;102(3):193-201. PMID: 20028993 . Lavoine N et al. Constitutional mismatch repair deficiency syndrome: clinical description in a French cohort. J Med Genet. 2015 Nov;52(11):770-8. PMID: 26318770. Meric-Bernstam F et al. Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol. Ann Oncol. 2016 May;27(5):795-800. PMID: 26787237. Tavakkol Z et al. Germline mutation in MSH6 associated with multiple malignant neoplasms in a patient With Muir-Torre syndrome. J Clin Oncol. 2012 Aug 1;30(22):e195-8. PMID: 22734033. van der Post R et al. Risk of urothelial bladder cancer in Lynch syndrome is increased, in particular among MSH2 mutation carriers. J Med Genet. 2010 Jul;47(7):464-70. PMID: 20591884. Wijnen J et al. Familial endometrial cancer in female carriers of MSH6 germline mutations. Nat Genet. 1999 Oct;23(2):142-4. PMID: 10508506. -
This variant alters the translational reading frame of the MSH6 mRNA and causes the premature termination of MSH6 protein synthesis. In the published literature, this variant has been reported in individuals affected with a Lynch syndrome associated cancer (PMIDs: 20028993 (2010), 20591884 (2010), 22734033 (2012), 26787237 (2016), 29371908 (2018)) and CMMRD (PMID: 32042422 (2020)). The frequency of this variant in the general population, 0.000014 (4/280876 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. -
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek 2016); Observed in the heterozygous state in patients with Lynch-related cancers consistent with pathogenic variants in this gene (Plaschke 2004, Hampel 2005, Baglietto 2010, Sjursen 2010, Talseth-Palmer 2010, Meric-Bernstam 2016); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 26552419, 26787237, 15872200, 29371908, 20591884, 20028993, 15483016, 20487569, 20587412, 26866578, 27601186, 27486176, 25980754, 10508506, 22734033, 26681312, 28528517, 26318770, 30730459, 30322717, 30093976, 31447099, 31845022, 31921681, 32832836, 32042422, 17557300, 32719484, 30787465, 33087929) -
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Lynch syndrome Pathogenic:6
PVS1; PP4_Strong -
Variant summary: The MSH6 c.3261delC (p.Phe1088Serfs) 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. p.Arg1172fs). One in silico tool predicts a damaging outcome for this variant. This variant was found in 21/120336 control chromosomes at a frequency of 0.0001745, which is approximately equal to the estimated maximal expected allele frequency of a pathogenic MSH6 variant (0.0001421). However, the variant has been reported in many HNPCC patients in the literature in heterozygous state. The variant has also been cited in homozygous and compound heterozygous states in patients with early onset cancer phenotypes (Ilencikova_PedBlodCanc_2011 and Auclair_HumMut_2007, respectively). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. -
Coding sequence variation resulting in a stop codon -
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The p.Phe1088SerfsX2 variant in MSH6 has been reported in the heterozygous state in >5 individuals with MSH6-associated cancers (Baglietto 2010 PMID: 20028993, Meric-Bernstam 2016 PMID: 26787237), and in the compound heterozygous state in 1 individual with constitutional mismatch repair deficiency syndrome (CMMRD) who also carried another MSH6 variant (Lavoine 2015 PMID: 26318770). This variant has been identified in 0.01% (1/10370) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org). It is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 1088 and leads to a premature termination codon 2 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Heterozygous loss of function of function of the MSH6 gene is an established disease mechanism in Lynch Syndrome. Furthermore, this variant was classified as Pathogenic on Sept. 5, 2013 by the ClinGen-approved InSiGHT Expert Panel (ClinVar Variation ID: 89363). In summary, this variant meets criteria to be classified as pathogenic for Lynch Syndrome in an autosomal dominant manner. ACMG/AMP Criteria applied: PS4_Supporting, PM2_Supporting, PVS1. -
This variant deletes 1 nucleotide in exon 5 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. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with Lynch syndrome, Muir-Torre syndrome and constitutional mismatch repair deficiency syndrome (PMID: 15236168, 15483016, 17117178, 17557300, 20007843, 20487569, 20587412, 22480969, 22734033, 27064304). This variant has been identified in 1/30714 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. -
Lynch syndrome 5 Pathogenic:4Other:1
Variant interpreted as Pathogenic and reported on 03-09-2020 by Lab or GTR ID 1197. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. -
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Criteria applied: PVS1,PS4,PM2_SUP -
Endometrial carcinoma Pathogenic:4
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_x000D_ Criteria applied: PVS1, PS4_MOD -
Hereditary cancer-predisposing syndrome Pathogenic:2
This variant deletes 1 nucleotide in exon 5 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 been reported in individuals and families affected with Lynch syndrome, Muir-Torre syndrome, or constitutional mismatch repair deficiency syndrome (PMID: 15236168, 15483016, 17117178, 17557300, 20007843, 20487569, 20587412, 22480969, 22734033, 27064304). This variant has been identified in 1/30714 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. -
The c.3261delC pathogenic mutation, located in coding exon 5 of the MSH6 gene, results from a deletion of one nucleotide at nucleotide position 3261, causing a translational frameshift with a predicted alternate stop codon (p.F1088Sfs*2). This mutation has been reported in multiple hereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome families; several whose LS-associated tumors demonstrating high microsatellite instability and/or loss of MSH6 staining by immunohistochemistry (IHC) (Wijnen J et al. Nat. Genet. 1999 Oct;23:142-4; Kets CM et al. Br J Cancer, 2006 Dec;95:1678-82; Devlin LA et al. Ulster Med J, 2008 Jan;77:25-30; Talseth-Palmer BA et al. Hered. Cancer Clin. Pract. 2010 May;8:5; van der Post RS et al. J. Med. Genet. 2010 Jul;47:464-70; Bonnet D et al. Dig Liver Dis, 2012 Jun;44:515-22; Sjursen W et al. Mol Genet Genomic Med, 2016 Mar;4:223-31; Lagerstedt-Robinson K et al. Oncol Rep. 2016 Nov;36(5):2823-2835; Chan GHJ et al. Oncotarget, 2018 Jul;9:30649-30660; Carter NJ et al. Gynecol Oncol, 2018 12;151:481-488; Matejcic M et al. JCO Precis Oncol, 2020 Jan;4:32-43; Ylmaz A et al. Int J Colorectal Dis, 2020 Feb;35:351-353). This mutation has also been reported in the homozygous state as well as compound heterozygous with a second mutation in MSH6 in several patients with Constitutional Mismatch Repair Deficiency (CMMRD) syndrome (Auclair J et al. Hum Mutat. 2007 Nov;28(11):1084-90; Xu M et al. Biomed Rep, 2020 Mar;12:134-138; Ando T et al. BMC Gastroenterol, 2021 Aug;21:326). 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. -
Endometrial carcinoma;C1833477:Lynch syndrome 5;C5436807:Mismatch repair cancer syndrome 3 Pathogenic:1
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Carcinoma of colon Pathogenic:1
The p.Phe1088SerfsX2 variant was identified in 15 of 6554 proband chromosomes (frequency: 0.002) from individuals or families with Lynch syndrome (Bonadona 2011, Devlin 2008, Hampel 2005, Hendriks 2004, Overbeek 2007, Plaschke 2004, Sjursen 2010). The variant was also identified in dbSNP (ID: rs267608078) “With pathogenic allele”, Clinvitae database (2x as pathogenic), InSiGHT Colon Cancer Gene Variant Database (24x as pathogenic), the ClinVar database (classified as a pathogenic variant by an expert panel), GeneInsight COGR database 1x and UMD (27x as a causal variant). The p.Phe1088SerfsX2 deletion variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 1088 and leads to a premature stop codon at position 1089. 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 this 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. -
Mismatch repair cancer syndrome 3 Pathogenic:1
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Lynch-like syndrome Pathogenic:1
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Gastric cancer Pathogenic:1
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Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
This sequence change creates a premature translational stop signal (p.Phe1088Serfs*2) 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 frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This premature translational stop signal has been observed in individual(s) with Lynch syndrome (PMID: 10508506, 15483016, 18301448, 20007843, 20028993, 20587412, 20591884, 22734033). Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this MSH6 variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 1,370,736 individuals referred to our laboratory for MSH6 testing. ClinVar contains an entry for this variant (Variation ID: 89363). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at