Submissions for variant NM_000249.4(MLH1):c.1474G>A (p.Ala492Thr)

gnomAD frequency: 0.00004  dbSNP: rs63751145

Total submissions: 9

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000132236	SCV000187319	uncertain significance	Hereditary cancer-predisposing syndrome	2023-11-16	criteria provided, single submitter	clinical testing	The p.A492T variant (also known as c.1474G>A), located in coding exon 13 of the MLH1 gene, results from a G to A substitution at nucleotide position 1474. The alanine at codon 492 is replaced by threonine, an amino acid with similar properties. This alteration has been observed in at least one individual whose Lynch-related tumor demonstrated loss of MLH1/PMS2 expression on immunohistochemistry (IHC) (Ambry internal data). This alteration was reported in an individual with sporadic, MSI-H rectal cancer diagnosed at age 41 years (Moslein G et al. Hum. Mol. Genet. 1996 Sep; 5(9):1245-52). This alteration has also been detected in conjunction with a pathogenic mutation in MSH6 in an individual with MSI-H and MSH6 absent colon cancer at age 39 years (Steinke V et al. Eur. J. Hum. Genet. 2008 May; 16(5):587-92). This alteration was not detected in two studies of Asian populations with sporadic colon cancer and healthy controls (Kim JC et al. Fam. Cancer 2004; 3(2):129-37; Mei Q et al. Cancer Genet. Cytogenet. 2006 Nov; 171(1):17-23). Several groups have performed functional studies on this alteration, mostly in yeast, primarily yielding inconsistent results relating to this alteration’s possible effect on protein function (Shimodaira H et al. Nat. Genet. 1998 Aug; 19(4):384-9; Kondo E et al. Cancer Res. 2003 Jun; 63(12):3302-8; Takahashi M et al. Cancer Res. 2007 May; 67(10):4595-604; Ou J et al. Hum. Mutat. 2007 Nov; 28(11):1047-54). This alteration was classified as likely benign by one study that evaluated multiple lines of evidence, including population data, functional evidence, in silico prediction models, segregation with disease and clinical phenotype including tumor characteristics (Tsai GJ et al. Genet Med, 2019 06;21:1435-1442). 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.
GeneDx	RCV000212538	SCV000211105	uncertain significance	not provided	2023-07-11	criteria provided, single submitter	clinical testing	Not observed at a 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: intact PMS2 & EXO1 binding, sufficient MMR repair activity, normal MLH1 expression and stability, and reduced dominant mutator effect (Shimodaira et al., 1998; Kondo et al., 2003; Takahashi et al., 2007); Observed in several individuals with early onset colorectal cancer, one of whom also carried a pathogenic MSH6 variant (Moslein et al., 1996; Steinke et al., 2008; Stojcev et al., 2013); This variant is associated with the following publications: (PMID: 18383312, 12810663, 17510385, 18301448, 17594722, 9697702, 8872463, 8895729, 15340264, 17074586, 16995940, 17192056, 11948175, 21404117, 18373977, 23741719, 30374176, 22290698, 12799449, 20533529, 22753075)
Invitae	RCV000524241	SCV000254350	uncertain significance	Hereditary nonpolyposis colorectal neoplasms	2024-01-26	criteria provided, single submitter	clinical testing	This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 492 of the MLH1 protein (p.Ala492Thr). This variant is present in population databases (rs63751145, gnomAD 0.004%). This missense change has been observed in individual(s) with colon and/or rectal cancer (PMID: 8872463, 8895729, 18301448). ClinVar contains an entry for this variant (Variation ID: 89750). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MLH1 protein function. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on MLH1 function (PMID: 9697702, 12810663, 17192056, 17510385, 18373977). 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	RCV000132236	SCV000689816	uncertain significance	Hereditary cancer-predisposing syndrome	2023-05-26	criteria provided, single submitter	clinical testing	This missense variant replaces alanine with threonine at codon 492 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have reported this variant caused no significant impact on MLH function in an in vitro MMR assay (PMID: 17510385) or on binding to PMS2 and EXO1 (PMID: 12810663), and there have been conflicting results regarding the variant's impact on the dominant mutator effect in yeast (PMID: 9697702, 17510385). This variant has been reported in individuals affected with colorectal cancer (PMID: 8872463, 18301448, 21404117). One of these probands also carried a pathogenic variant in the MSH6 gene, which could explain the observed phenotype (PMID: 18301448). This variant has been identified in 6/282896 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.
University of Washington Department of Laboratory Medicine, University of Washington	RCV000075224	SCV000788235	likely benign	Lynch syndrome	2018-04-01	criteria provided, single submitter	research	The MLH1 variant designated as NM_000249.3: c.1474G>A (p.Ala492Thr) is classified as likely benign. Pretest probability for pathogenicity was less than 0.1 based on computer prediction with PolyPhen2 of 0.033 and MAPP of 2.75 (Thompson et al. 2013, PMID:12900794). Family history analysis of one observed family revealed no Lynch syndrome-associated cancers in multiple individuals tested to have the variant. Cosegregation analysis of the same observed family was performed using analyze.myvariant.org (Rañola et al, 2018, PMID:28965303) and gives a likelihood ratio of 0.19 to 1 that this allele explains cancers in the family (Thompson et al. 2003, PMID:1290079), which provides evidence against pathogenicity. Bayesian analysis integrating all of this data (Tavtigian et al, 2018, PMID:29300386) gives 2% probability of pathogenicity, which is consistent with a classification of likely benign. This variant is not predicted to alter MLH1 function or modify cancer risk. This analysis was performed in conjunction with the family studies project as part of the University of Washington Find My Variant Study.
Sema4, Sema4	RCV000132236	SCV002528653	uncertain significance	Hereditary cancer-predisposing syndrome	2021-10-15	criteria provided, single submitter	curation
Baylor Genetics	RCV003474657	SCV004195029	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2023-10-26	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV003478994	SCV004222964	uncertain significance	not specified	2023-11-03	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.1474G>A (p.Ala492Thr) results in a non-conservative amino acid change located in the region responsible for the interaction of MLH1 with PMS2 (aa 492-756) of the encoded protein sequence (Hardt_2011). Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.6e-05 in 251482 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1474G>A has been reported in the literature in individuals affected with Lynch Syndrome, HNPCC and different types of cancer as well as in at least one healthy individual (Moslein_1996, Thibodeau_1996, Lucci-Cordisco_2006, Steinke_2008, Hardt_2011, Tsai_2018). These reports do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. At least one co-occurrence with another pathogenic variant has been reported (MSH6 c.467C>G, p.Ser156X), providing supporting evidence for a benign role (Steinke_2008). Functional studies report experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (Shimodaira_1998, Kondo_ 2003, Lucci-Cordisco_2006, Takahashi_2007, Zhao_2008). The following publications have been ascertained in the context of this evaluation (PMID: 9699680, 21404117, 12810663, 17192056, 8872463, 17594722, 9697702, 18301448, 17510385, 8895729, 30374176, 18373977). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified this variant as likely benign (n=1) and uncertain significance (n=5). Based on the evidence outlined above, the variant was classified as uncertain significance.
All of Us Research Program, National Institutes of Health	RCV000075224	SCV004841019	uncertain significance	Lynch syndrome	2024-01-11	criteria provided, single submitter	clinical testing	This missense variant replaces alanine with threonine at codon 492 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have reported this variant caused no significant impact on MLH function in an in vitro MMR assay (PMID: 17510385) or on binding to PMS2 and EXO1 (PMID: 12810663), and there have been conflicting results regarding the variant's impact on the dominant mutator effect in yeast (PMID: 9697702, 17510385). This variant has been reported in individuals affected with colorectal cancer (PMID: 8872463, 18301448, 21404117). One of these probands also carried a pathogenic variant in the MSH6 gene, which could explain the observed phenotype (PMID: 18301448). This variant has been identified in 6/282896 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.