Submissions for variant NM_000249.4(MLH1):c.299G>A (p.Arg100Gln)

gnomAD frequency: 0.00004  dbSNP: rs63750266

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000590561	SCV000149388	uncertain significance	not provided	2023-05-30	criteria provided, single submitter	clinical testing	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies are inconclusive: protein stability, microsatellite instability, and resistance to MNNG similar to wildtype (Rath et al., 2022) and intermediate loss of mismatch repair function (Ellison et al., 2004); Observed in individuals with colorectal cancer with presence of MLH1 protein on tumor immunohistochemistry analysis (Hampel et al., 2008; Bartley et al., 2012; Shirts et al., 2016; Borras et al., 2017); This variant is associated with the following publications: (PMID: 26333163, 12824425, 26845104, 12202775, 28466842, 25871441, 22086678, 15475387, 18809606, 28765196, 36054288, 16083711, 21120944, 22753075, 29212164, 31697235, 32849802, 17510385, 17210669)
Ambry Genetics	RCV000115479	SCV000185074	uncertain significance	Hereditary cancer-predisposing syndrome	2023-04-17	criteria provided, single submitter	clinical testing	The p.R100Q variant (also known as c.299G>A), located in coding exon 3 of the MLH1 gene, results from a G to A substitution at nucleotide position 299. The arginine at codon 100 is replaced by glutamine, an amino acid with highly similar properties. This variant was previously reported in the germline of two individuals with MSI-H colorectal cancers who had no family history of colon cancer (Hampel H et al. J Clin Oncol. 2008; 26:5783-8; Bartley AN et al. Cancer Prev Res (Phila) 2012; 5:320-7). In a hybrid yeast-human experiment, this variant was previously found to be associated with a decrease in mismatch repair activity and was considered intermediate deficiency (Ellison AR et al. Nucleic Acids Res. 2004; 32:5321-38). This alteration has been classified as an uncertain variant by multifactorial analysis, which integrates the following lines of evidence to produce a quantitative likelihood of pathogenicity: in silico prediction models, segregation with disease, tumor characteristics, mutation co-occurrence, and functional assay results (Thompson B et al. Nat Genet. 2014 Feb;46(2):107-15; available at [www.insight-group.org/variants/classifications/]). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
University of Washington Department of Laboratory Medicine, University of Washington	RCV000075618	SCV000266180	uncertain significance	Lynch syndrome	2015-11-20	criteria provided, single submitter	clinical testing
Invitae	RCV000524288	SCV000284057	uncertain significance	Hereditary nonpolyposis colorectal neoplasms	2024-02-01	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 100 of the MLH1 protein (p.Arg100Gln). This variant is present in population databases (rs63750266, gnomAD 0.003%). This missense change has been observed in individual(s) with Lynch syndrome (PMID: 18809606, 22086678, 26845104). This missense change has been observed to be homozygous or hemizygous in an individual who did not have the expected clinical features for that genetic result (Invitae). ClinVar contains an entry for this variant (Variation ID: 90132). An algorithm developed specifically for the MLH1 gene suggests that this missense change is likely to be deleterious (PMID: 26333163). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on MLH1 function (PMID: 15475387). Studies have shown that this missense change is associated with inconclusive levels of altered splicing (Invitae). This variant disrupts the Arg100 amino acid residue in MLH1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17210669, 17510385, 29212164, 31697235, 32849802). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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.
Counsyl	RCV000412390	SCV000488458	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2016-04-01	criteria provided, single submitter	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000212517	SCV000592345	uncertain significance	not specified	2014-06-02	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000115479	SCV000684813	uncertain significance	Hereditary cancer-predisposing syndrome	2023-03-09	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with glutamine at codon 100 of the MLH1 protein. Computational prediction tools and conservation analyses suggest that this variant may have deleterious impact on protein structure and function. A functional study that examined this variant in the context of a human-yeast hybrid protein reported partial loss-of-function (PMID: 15475387). In another functional study done in human embryonic stem cells, the variant demonstrated a similar lack of response to DNA damage to a functionally abnormal variant, but resulted in limited microsatellite instability (PMID: 36054288). This variant has been reported in four individuals affected with colorectal cancer (PMID: 18809606, 22086678, 26845104 and the InSiGHT database) with tumor samples from at least three individuals that exhibited microsatellite instability (PMID: 18809606, 22086678 and the InSiGHT database). This variant also has been reported in breast cancer case-control meta-analysis in 1 affected and 3 unaffected individuals (PMID: 33471991; LOVD DB-ID: MLH1_000129). This variant failed to exhibit a significant association with pancreatic cancer (PMID: 32980694). This variant has been identified in 4/251360 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same position, p.Arg100Pro, is considered to be disease-causing (ClinVar variation ID: 90133), suggesting that arginine or similar amino acid at this position is important for the protein function. Although there is a suspicion that this variant may be associated with disease, additional studies are necessary 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	RCV000590561	SCV000696158	uncertain significance	not provided	2017-06-30	criteria provided, single submitter	clinical testing	Variant summary: The MLH1 c.299G>A (p.Arg100Gln) variant causes a missense change involving the alteration of a conserved nucleotide and it is located in the Histidine kinase-like ATPase, C-terminal domain (IPR003594). 3/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). One functional study shows 34-66% loss of MMR function but was performed in hybrid human-yeast genes (Ellison_NAR_2004). The variant of interest has been found in a large, broad control population, ExAC in 2/121214 control chromosomes at a frequency of 0.0000165, which does not exceed the estimated maximal expected allele frequency of a pathogenic MLH1 variant (0.0007105). This variant was reported in CRC patients without strong evidence for causality and including discordant MSI and IHC results (Bartley_PMS2_CanPrevRes_2011, Hampel_MSH6_JClin Onc_2008). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as uncertain significance. Taken together, this variant is classified as VUS until more definitive functional and clinical study results become available.
Fulgent Genetics, Fulgent Genetics	RCV000764480	SCV000895551	uncertain significance	Mismatch repair cancer syndrome 1; Muir-Torré syndrome; Colorectal cancer, hereditary nonpolyposis, type 2	2021-07-06	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000590561	SCV001500301	uncertain significance	not provided	2020-08-01	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV000412390	SCV004018184	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2023-03-15	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	RCV000412390	SCV004195045	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2023-10-19	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000075618	SCV004835264	uncertain significance	Lynch syndrome	2023-06-26	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with glutamine at codon 100 of the MLH1 protein. Computational prediction tools and conservation analyses suggest that this variant may have deleterious impact on protein structure and function. A functional study that examined this variant in the context of a human-yeast hybrid protein reported partial loss-of-function (PMID: 15475387). In another functional study done in human embryonic stem cells, the variant demonstrated a similar lack of response to DNA damage to a functionally abnormal variant, but resulted in limited microsatellite instability (PMID: 36054288). This variant has been reported in four individuals affected with colorectal cancer (PMID: 18809606, 22086678, 26845104 and the InSiGHT database) with tumor samples from at least three individuals that exhibited microsatellite instability (PMID: 18809606, 22086678 and the InSiGHT database). This variant also has been reported in breast cancer case-control meta-analysis in 1 affected and 3 unaffected individuals (PMID: 33471991; LOVD DB-ID: MLH1_000129). This variant failed to exhibit a significant association with pancreatic cancer (PMID: 32980694). This variant has been identified in 4/251360 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different variant affecting the same position, p.Arg100Pro, is considered to be disease-causing (ClinVar variation ID: 90133), suggesting that arginine or similar amino acid at this position is important for the protein function. Although there is a suspicion that this variant may be associated with disease, additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
GenomeConnect - Invitae Patient Insights Network	RCV001535467	SCV001749389	not provided	Mismatch repair cancer syndrome 1; Colorectal cancer, hereditary nonpolyposis, type 2		no assertion provided	phenotyping only	Variant interpreted as Uncertain significance and reported on 11-01-2019 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.