Submissions for variant NM_000249.4(MLH1):c.979C>G (p.Gln327Glu)

gnomAD frequency: 0.00001  dbSNP: rs587782087

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000130590	SCV000185463	uncertain significance	Hereditary cancer-predisposing syndrome	2024-02-14	criteria provided, single submitter	clinical testing	The p.Q327E variant (also known as c.979C>G), located in coding exon 11 of the MLH1 gene, results from a C to G substitution at nucleotide position 979. The glutamine at codon 327 is replaced by glutamic acid, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000199406	SCV000254376	uncertain significance	Hereditary nonpolyposis colorectal neoplasms	2025-01-01	criteria provided, single submitter	clinical testing	This sequence change replaces glutamine, which is neutral and polar, with glutamic acid, which is acidic and polar, at codon 327 of the MLH1 protein (p.Gln327Glu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast cancer (PMID: 32091409). ClinVar contains an entry for this variant (Variation ID: 141891). Invitae Evidence Modeling incorporating data from in vitro experimental studies (internal data) indicates that this missense variant is not expected to disrupt MLH1 function with a negative predictive value of 95%. 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.
Color Diagnostics, LLC DBA Color Health	RCV000130590	SCV000684888	uncertain significance	Hereditary cancer-predisposing syndrome	2022-11-15	criteria provided, single submitter	clinical testing	This missense variant replaces glutamine with glutamic acid at codon 327 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with MLH1-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Counsyl	RCV000663060	SCV000786118	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2018-02-27	criteria provided, single submitter	clinical testing
GeneDx	RCV001564943	SCV001788191	uncertain significance	not provided	2023-03-24	criteria provided, single submitter	clinical testing	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Observed in individuals with acute lymphoblastic leukemia and breast cancer (Zhang et al., 2015; Chen et al., 2020); This variant is associated with the following publications: (PMID: 22753075, 32091409, 26580448)
Myriad Genetics, Inc.	RCV000663060	SCV004018106	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2023-03-13	criteria provided, single submitter	clinical testing	This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.
Baylor Genetics	RCV000663060	SCV004192959	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-25	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV001564943	SCV004220908	uncertain significance	not provided	2024-10-22	criteria provided, single submitter	clinical testing	The MLH1 c.979C>G (p.Gln327Glu) variant has been reported in the published literature in individuals affected with breast cancer (PMID: 32091409 (2020)) and acute lymphoblastic leukemia (PMID: 26580448 (2015)). The frequency of this variant in the general population, 0.000013 (2/152206 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.
All of Us Research Program, National Institutes of Health	RCV003998066	SCV004840935	uncertain significance	Lynch syndrome	2023-10-30	criteria provided, single submitter	clinical testing	This missense variant replaces glutamine with glutamic acid at codon 327 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with MLH1-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV004767084	SCV005381795	uncertain significance	not specified	2024-08-26	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.979C>G (p.Gln327Glu) results in a conservative amino acid change located in the DNA mismatch repair protein, S5 domain 2-like (IPR013507) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251388 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.979C>G has been reported in the literature in one individual affected with B-Lineage ALL E2A-PBX1 Subtype (Zhang_2015). The report does not provide unequivocal conclusions about association of the variant with Lynch Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 26580448). ClinVar contains an entry for this variant (Variation ID: 141891). Based on the evidence outlined above, the variant was classified as uncertain significance.