ClinVar Miner

Submissions for variant NM_000251.3(MSH2):c.1861C>T (p.Arg621Ter)

dbSNP: rs63750508
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Total submissions: 18
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000076305 SCV000107327 pathogenic Lynch syndrome 2013-09-05 reviewed by expert panel research Coding sequence variation introducing premature termination codon
Labcorp Genetics (formerly Invitae), Labcorp RCV000524364 SCV000260744 pathogenic Hereditary nonpolyposis colorectal neoplasms 2023-11-24 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg621*) in the MSH2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH2 are known to be pathogenic (PMID: 15849733, 24362816). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Lynch syndrome and colorectal cancer (PMID: 8566964, 12624141, 17569143, 18772310, 20007843, 21598002, 21642682, 24415873). ClinVar contains an entry for this variant (Variation ID: 90804). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000414448 SCV000490618 pathogenic not provided 2020-12-01 criteria provided, single submitter clinical testing Nonsense 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 in large population cohorts (Lek et al., 2016) Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database Observed in patients with Lynch-related cancers and tumor studies consistent with pathogenic variants in this gene (Maliaka 1996, Parc 2003, Zavodna 2006, Overbeek 2007, Papp 2007, van Puijenbroek 2008, Bonadona 2011, Brieger 2011, Everett 2014, Kury 2014, Vierkoetter 2014, Goodfellow 2015, Sunga 2017, Jiang 2019, Rashid 2019) This variant is associated with the following publications: (PMID: 31615790, 32658311, 31660093, 30521064, 29489754, 28944238, 17453009, 28874130, 27863258, 25093288, 26552419, 16830052, 25504677, 23741719, 18415027, 24415873, 21642682, 21598002, 20007843, 18772310, 12624141, 28449805, 25525159, 25006859, 17569143, 8566964)
Ambry Genetics RCV000491286 SCV000580383 pathogenic Hereditary cancer-predisposing syndrome 2021-10-21 criteria provided, single submitter clinical testing The p.R621* pathogenic mutation (also known as c.1861C>T), located in coding exon 12 of the MSH2 gene, results from a C to T substitution at nucleotide position 1861. This changes the amino acid from an arginine to a stop codon within coding exon 12. This mutation has been reported in multiple HNPCC/Lynch syndrome families; several who meet Amsterdam criteria and/or have tumors that demonstrated loss of MSH2 and MSH6 by IHC (Maliaka YK et al. Hum. Genet. 1996 Feb;97(2):251-5; Weber TK et al. Cancer Res. 1997 Sep;57(17):3798-803; Niessen RC et al. Gut 2006 Dec;55(12):1781-8; Overbeek LIH et al. Br. J. Cancer. 2007 May;96(10):1605-1612; Papp J et al. World J. Gastroenterol. 2007 May;13(19):2727-32; Vierkoetter KR et al. Gynecol Oncol, 2014 Oct;135:81-4; Kang SY et al. Int J Cancer, 2015 Apr;136:1568-78; Dominguez-Valentin M et al. Front Oncol, 2016 Aug;6:189; Jiang W et al. Int J Cancer, 2019 05;144:2161-2168; Rashid MU et al. Hered Cancer Clin Pract, 2019 Oct;17:29; Wischhusen JW et al. Cancer Epidemiol Biomarkers Prev, 2020 01;29:193-199; Shao D et al. Cancer Sci, 2020 Feb;111:647-657; Yanus GA et al. Eur J Med Genet, 2020 Mar;63:103753; Akcay IM et al. Int J Cancer, 2021 01;148:285-295). 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000414448 SCV000601443 pathogenic not provided 2017-05-22 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000491286 SCV000684988 pathogenic Hereditary cancer-predisposing syndrome 2022-05-06 criteria provided, single submitter clinical testing This variant changes 1 nucleotide in exon 12 of the MSH2 gene, creating a 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 or suspected of having Lynch syndrome (PMID: 8566964, 12624141, 17569143, 18772310, 20007843, 21598002, 21642682, 27629256), or colorectal cancer (PMID: 24415873, 26552419, 29967336). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001328039 SCV000696226 pathogenic Hereditary nonpolyposis colon cancer 2021-03-04 criteria provided, single submitter clinical testing Variant summary: MSH2 c.1861C>T (p.Arg621X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the 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. The variant was absent in 251474 control chromosomes. c.1861C>T has been reported in the literature in multiple individuals affected with MSH2-associated cancers (Maliaka_1996, Papp_2007, Bonadona_2011, Vierkoetter_2014, Kang_2015, Dominguez-Valentin_2016). These data indicate that the variant is very likely to be associated with disease. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000602838 SCV000744278 pathogenic Lynch syndrome 1 2015-09-21 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000763492 SCV000894278 pathogenic Lynch syndrome 1; Mismatch repair cancer syndrome 1; Muir-Torré syndrome 2018-10-31 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000414448 SCV002017561 pathogenic not provided 2019-10-29 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000491286 SCV002534419 pathogenic Hereditary cancer-predisposing syndrome 2021-02-06 criteria provided, single submitter curation
Myriad Genetics, Inc. RCV000602838 SCV004187924 pathogenic Lynch syndrome 1 2023-08-04 criteria provided, single submitter clinical testing This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
Baylor Genetics RCV000602838 SCV004196206 pathogenic Lynch syndrome 1 2024-03-25 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000602838 SCV000734202 pathogenic Lynch syndrome 1 no assertion criteria provided clinical testing
Constitutional Genetics Lab, Leon Berard Cancer Center RCV001249915 SCV001423932 pathogenic Lynch-like syndrome 2019-07-01 no assertion criteria provided clinical testing
Medical Genetics Laboratory, Umraniye Training and Research Hospital, University of Health Sciences RCV001650893 SCV001870403 pathogenic Breast carcinoma 2021-09-12 no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000414448 SCV001956297 pathogenic not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000414448 SCV002035462 pathogenic not provided no assertion criteria provided clinical testing

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