ClinVar Miner

Submissions for variant NM_000179.2(MSH6):c.2410A>G (p.Lys804Glu) (rs1064793552)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000481034 SCV000566412 uncertain significance not provided 2015-04-30 criteria provided, single submitter clinical testing This variant is denoted MSH6 c.2410A>G at the cDNA level, p.Lys804Glu (K804E) at the protein level, and results in the change of a Lysine to a Glutamic Acid (AAA>GAA). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. MSH6 Lys804Glu was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Since Lysine and Glutamic Acid differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. MSH6 Lys804Glu occurs at a position that is conserved in mammals and is located in domain III of the MutS domain (Terui 2013) In silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. Based on currently available information, it is unclear whether MSH6 Lys804Glu is pathogenic or benign. We consider it to be a variant of uncertain significance.
Invitae RCV000528139 SCV000624758 uncertain significance Hereditary nonpolyposis colon cancer 2018-07-20 criteria provided, single submitter clinical testing This sequence change replaces lysine with glutamic acid at codon 804 of the MSH6 protein (p.Lys804Glu). The lysine residue is moderately conserved and there is a small physicochemical difference between lysine and glutamic acid. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with MSH6-related disease. ClinVar contains an entry for this variant (Variation ID: 418961). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV000572051 SCV000664667 uncertain significance Hereditary cancer-predisposing syndrome 2016-07-14 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Insufficient evidence
Integrated Genetics/Laboratory Corporation of America RCV000781592 SCV000919759 uncertain significance not specified 2018-09-14 criteria provided, single submitter clinical testing Variant summary: MSH6 c.2410A>G (p.Lys804Glu) results in a conservative amino acid change located in the DNA mismatch repair protein MutS, core domain of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 245332 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.2410A>G in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

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