Submissions for variant NM_000249.4(MLH1):c.191A>G (p.Asn64Ser)

gnomAD frequency: 0.00003  dbSNP: rs63750952

Total submissions: 19

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000513562	SCV000211108	likely benign	not provided	2020-10-21	criteria provided, single submitter	clinical testing	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies are inconclusive: reduced MMR activity, no impact on nuclear localization, and conflicting results regarding mutator effect, PMS2 binding, MLH1 protein expression (Ellison 2004, Plotz 2006, Takahashi 2007, Wanat 2007, Hardt 2011, Bolz 2012, Drost 2018); Observed in individuals with MLH1-related cancers including segregation with disease in one family, as well as in individuals with melanoma (Wijnen 1997, Spaepen 2006, Hardt 2011, Shindo 2017, Yehia 2018); This variant is associated with the following publications: (PMID: 17135187, 21404117, 23741719, 29684080, 17510385, 17210669, 25525159, 9311737, 22843852, 15475387, 26552419, 16736289, 24362816, 28767289, 30504929, 31697235, 31332305, 32719484, 30755392)
Labcorp Genetics (formerly Invitae), Labcorp	RCV000075426	SCV000218899	benign	Hereditary nonpolyposis colorectal neoplasms	2024-12-19	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000217492	SCV000276267	uncertain significance	Hereditary cancer-predisposing syndrome	2024-05-27	criteria provided, single submitter	clinical testing	The p.N64S variant (also known as c.191A>G), located in coding exon 2 of the MLH1 gene, results from an A to G substitution at nucleotide position 191. The asparagine at codon 64 is replaced by serine, an amino acid with highly similar properties. This alteration has been identified in several colorectal cancer cohorts that are suspicious for Lynch syndrome and, in at least one case, the tumor retained expression of MLH1 and MSH2 on immunohistochemical staining (Wijnen J et al. Am. J. Hum. Genet. 1997 Aug;61:329-35; Spaepen M et al. Fam. Cancer 2006;5:179-89; Hardt K et al. Fam. Cancer 2011 Jun;10:273-84; Stojcev Z et al. Acta Biochim Pol, 2013 Jun;60:195-8). One report shows that this alteration segregates with 5 of 6 siblings affected with colorectal cancer (Spaepen M et al. Fam. Cancer 2006;5:179-89). In another report, this alteration was found to co-occur with MLH1 c.986A>C, a functionally validated splicing mutation, in a patient with three gastrointestinal primary tumors diagnosed at 47. The MLH1 p.N64S alteration was inherited from the proband's mother who was unaffected at age 71, and while the paternal family history met Amsterdam criteria, suggesting the father likely carried the MLH1 c.986A>C pathogenic mutation, the inheritance of this alteration was not confirmed (Hardt K et al. Fam. Cancer 2011 Jun;10:273-84). Numerous functional studies show reduced but not abolished function including yeast mutator assays, expression assays, in vitro mismatch repair assays and heterodimerization assays (Ellison AR et al. Nucleic Acids Res. 2004 Oct;32:5321-38; Plotz G et al. Nucleic Acids Res. 2006 Nov;34:6574-86; Takahashi M et al. Cancer Res. 2007 May;67:4595-604; Wanat JJ et al. Hum. Mol. Genet. 2007 Feb;16:445-52; Hardt K et al. Fam. Cancer 2011 Jun;10:273-84). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
CeGaT Center for Human Genetics Tuebingen	RCV000513562	SCV000609098	likely pathogenic	not provided	2021-01-01	criteria provided, single submitter	clinical testing
Counsyl	RCV000490571	SCV000611601	uncertain significance	Lynch syndrome 1	2017-06-29	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000217492	SCV000684783	uncertain significance	Hereditary cancer-predisposing syndrome	2024-01-17	criteria provided, single submitter	clinical testing	This missense variant replaces asparagine with serine at codon 64 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). Functional studies have inconclusive results, with several showing this variant results in partial loss of mismatch repair function and moderately reduced protein stability and binding ability to PMS2 protein (PMID: 17135187, 17510385, 21404117, 30504929, 36054288). Another cell-based functional assay also demonstrated the variant resulted in partial protein stability, however, the variant also displayed positive damage response signaling and DNA repair function (PMID: 36054288). This variant has been reported in individuals from Lynch syndrome families (PMID: 9311737, 16736289, 21404117). In one of these families, two affected siblings were carriers of this variant but their affected sister with microsatellite instability-high tumor did not carry this variant (PMID: 16736289). Three unaffected siblings from this family did not carry this variant. In another family, this variant co-occurred in trans with a different pathogenic variant in the MLH1 gene (PMID: 21404117, 31332305). This variant has also been reported in individuals affected with endometrial cancer (PMID: 26552419) or pancreatic cancer (PMID: 28767289). In a large breast cancer case-control study, this variant was observed in 6/60466 cases and 5/53461 unaffected controls (PMID: 33471991) This variant has been identified in 10/282844 chromosomes 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.
Center for Personalized Medicine, Children's Hospital Los Angeles	RCV000584818	SCV000692543	uncertain significance	Global developmental delay; Choreoathetosis; Aqueductal stenosis	2016-03-15	criteria provided, single submitter	clinical testing
Mendelics	RCV000708912	SCV000837994	uncertain significance	Lynch syndrome	2018-07-02	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000513562	SCV000889392	uncertain significance	not provided	2024-07-11	criteria provided, single submitter	clinical testing	The MLH1 c.191A>G (p.Asn64Ser) variant has been reported in the published literature in individuals and families with colorectal cancer (PMID: 21404117 (2011), 16736289 (2006), 9311737 (1997)), endometrial cancer (PMID: 26552419 (2015)), and pancreatic cancer (PMID: 28767289 (2017)). In a large scale breast cancer association study, this variant was found in individuals with breast cancer as well as reportedly healthy individuals (PMID: 33471991 (2021); LOVD3 Shared (https://databases.lovd.nl/shared/MLH1)). Functional studies have observed the variant having intermediate levels of MLH1 expression, mismatch repair activity, and PMS2 interaction (PMID: 30504929 (2018), 26552419 (2015), 22843852 (2012), 21404117 (2011), 17510385 (2007), 17210669 (2007), 17135187 (2006), 15475387 (2004)). Another functional study observed the variant as having no effect on microsatellite instability (MSI) or DNA damage response (PMID: 36054288 (2022)). Therefore, more evidence is needed to determine the effect of this variant on protein function. The frequency of this variant in the general population, 0.00007 (9/129152 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.
Institute of Human Genetics, University of Leipzig Medical Center	RCV001262297	SCV001440111	uncertain significance	Muir-Torré syndrome	2019-01-01	criteria provided, single submitter	clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	RCV000513562	SCV002009370	uncertain significance	not provided	2021-11-03	criteria provided, single submitter	clinical testing
MGZ Medical Genetics Center	RCV002288569	SCV002581763	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2022-08-08	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV002288569	SCV004018166	likely benign	Colorectal cancer, hereditary nonpolyposis, type 2	2024-11-18	criteria provided, single submitter	clinical testing	This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 27363726].
Baylor Genetics	RCV002288569	SCV004195090	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2024-03-28	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000708912	SCV004835246	uncertain significance	Lynch syndrome	2023-11-30	criteria provided, single submitter	clinical testing	This missense variant replaces asparagine with serine at codon 64 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). Functional studies have shown that this variant results in a partial loss of mismatch repair function and moderately reduced protein stability and binding ability to PMS2 protein (PMID: 17135187, 17510385, 21404117, 30504929, 36054288). This variant has been reported in individuals from Lynch syndrome families (PMID: 9311737, 16736289, 21404117). In one of these families, two affected siblings were carriers of this variant but their affected sister with microsatellite instability-high tumor did not carry this variant (PMID: 16736289). Three unaffected siblings from this family did not carry this variant. In another family, this variant co-occurred in trans with a different pathogenic variant in the MLH1 gene (PMID: 21404117, 31332305). This variant has also been reported in individuals affected with endometrial cancer (PMID: 26552419) or pancreatic cancer (PMID: 28767289). In a large breast cancer case-control study, this variant was observed in 6/60466 cases and 5/53461 unaffected controls (PMID: 33471991) This variant has been identified in 10/282844 chromosomes 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.
German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne	RCV004760365	SCV005373731	benign	Hereditary breast ovarian cancer syndrome	2024-10-11	criteria provided, single submitter	curation	According to the ClinGen InSiGHT ACMG MLH1 v1.0.0 criteria we chose these criteria: PP3 (supporting pathogenic): Applied prior : 0.72 (thus >0.68 & ≤0.81), BS2 (strong benign): Hardt 2011 (PMID: 21404117): reported to co-occur in trans with a known pathogenic MLH1 variant (H329P, ClinVar ID: 17085) in a patient who did not demonstrate a Constitutive MMR-Deficiency Disease phenotype, BS3 (strong benign): Rath 2022 (PMID: 36054288): OddsPath_Non-functional = 5.00E-2 (thus > 0.48) + Morak 2019 (PMID: 31332305): No effect on splicing. Drost 2019 (PMID: 30504929): study was supportive of neither a pathogenic or benign classification Invitae (Accession: SCV000218899.13): Advanced modeling of protein sequence and biophysical properties [...] performed at Invitae indicates that this missense variant is expected to disrupt MLH1 protein function with a positive predictive value of 80%. Various old functional studies showing conflicting results regarding effect of variant on protein function.
Fulgent Genetics, Fulgent Genetics	RCV005025123	SCV005662492	uncertain significance	Mismatch repair cancer syndrome 1; Muir-Torré syndrome; Colorectal cancer, hereditary nonpolyposis, type 2	2024-04-26	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV005055564	SCV005726069	uncertain significance	not specified	2024-11-21	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.191A>G (p.Asn64Ser) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.6e-05 in 251442 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.191A>G has been reported in the literature in individuals affected with colorectal, endometrial, pancreatic, ovarian cancer, or Lynch Syndrome (e.g. Shindo_2017, Espenschied_2017, Spaepen_2006, Lilyquist_2017, Goodfellow_2015, Wijnen_1997). These data indicate that the variant may be associated with disease. Co-occurrences with other pathogenic variant(s) have been reported (MLH1 c.986A>C, p.His329Pro), providing supporting evidence for a benign role (Morak_2019, Hardt_2011). Multiple publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in moderately reduced MMR activity (e.g. Hardt_2011, Takahashi_2007, Ellison_2004, Drost_2019, Plotz_2006, Wanat_2007). The following publications have been ascertained in the context of this evaluation (PMID: 30504929, 15475387, 28514183, 26552419, 21404117, 28888541, 31332305, 17135187, 28767289, 16736289, 17510385, 17210669, 9311737, 37854294). ClinVar contains an entry for this variant (Variation ID: 89947). Based on the evidence outlined above, the variant was classified as uncertain significance.
PreventionGenetics, part of Exact Sciences	RCV004748556	SCV005361633	uncertain significance	MLH1-related disorder	2024-05-08	no assertion criteria provided	clinical testing	The MLH1 c.191A>G variant is predicted to result in the amino acid substitution p.Asn64Ser. This variant has been reported in individuals with hereditary nonpolyposis colorectal cancer (Wijnen et al. 1997. PubMed ID: 9311737; Hardt et al. 2011. PubMed ID: 21404117) and ovarian cancer (Table S7 in Lilyquist et al. 2017. PubMed ID: 28888541) and pancreatic cancer (Shindo et al. 2017. PubMed ID: 28767289). Functional studies have indicated the p.Asn65Ser variant results in reduced mismatch repair activity and reduced MLH1 expression (Ellison et al. 2004. PubMed ID: 15475387; Wanat et al. 2007. PubMed ID: 17210669; Takahashi et al. 2007. PubMed ID: 17510385). This variant is reported in 0.0070% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant has conflicting interpretations in ClinVar with the majority being uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/89947). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.