3-37048557-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PP3_Strong
The NM_000249.4(MLH1):c.1937A>G(p.Tyr646Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,613,774 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000249.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.0000526 AC: 8AN: 151998Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251332Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135824
GnomAD4 exome AF: 0.0000602 AC: 88AN: 1461776Hom.: 0 Cov.: 31 AF XY: 0.0000605 AC XY: 44AN XY: 727202
GnomAD4 genome 0.0000526 AC: 8AN: 151998Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74242
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:4
This missense variant replaces tyrosine with cysteine at codon 646 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 conflicting results with regard to the variant's impact on MLH1 protein interaction with PMS2 protein (PMID: 16083711, 16724012, 22753075). Multiple studies have shown that this variant does not affect mismatch repair activity (PMID: 16083711, 16724012, 20020535, 22753075). This variant has been reported in individuals affected with Lynch syndrome and Lynch syndrome-associated cancer (PMID: 11870161, 16083711, 16724012, 17250665, 21404117, 23047549, 25110875, 30521064). Tumor data from these individuals show conflicting evidence, with variability in microsatellite stability and protein expression via immunohistochemistry analysis (PMID: 11870161, 16083711, 16724012, 17250665, 21404117). This variant has also been observed in individuals affected with breast cancer or gastric cancer (PMID: 31650731, 36627197). This variant has also been identified in 12/282716 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. -
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The p.Y646C variant (also known as c.1937A>G), located in coding exon 17 of the MLH1 gene, results from an A to G substitution at nucleotide position 1937. The tyrosine at codon 646 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been reported in multiple individuals with clinical histories suspicious for Lynch syndrome, although tumor test results have been inconsistent (Scartozzi M et al. J. Clin. Oncol. 2002 Mar;20:1203-8; Hampel H et al. N. Engl. J. Med. 2005 May;352:1851-60; Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49; Belvederesi L et al. Eur. J. Hum. Genet. 2006 Jul;14:853-9; Hardt K et al. Fam. Cancer. 2011 Jun;10:273-84; Ambry internal data). Functional analyses of the p.Y646C variant have produced conflicting results. Two independent studies have shown this alteration to disrupt PMS2 interaction (Belvederesi L et al. Eur. J. Hum. Genet. 2006 Jul;14:853-9; Andersen SD et al. Hum. Mutat. 2012 Dec;33:1647-55), while another supported normal interaction (Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49). Multiple studies have demonstrated normal localization, normal mismatch repair activity, and expression similar to wild type (Andersen SD et al. Hum. Mutat. 2012 Dec;33:1647-55; Belvederesi L et al. Eur. J. Hum. Genet. 2006 Jul;14:853-9; Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49; Drost M et al. Hum. Mutat. 2010 Mar;31:247-53); however, one functional assay in yeast showed an intermediate activity level (Vogelsang M et al. BMC Cancer. 2009 Oct;9:382). 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 conflicting at this time, the clinical significance of this alteration remains unclear. -
not provided Uncertain:3
The MLH1 c.1937A>G (p.Tyr646Cys) variant has been reported in the published literature in individuals affected with colon cancer (PMID: 15872200 (2005), 16724012 (2006), 21404117 (2011), 25110875 (2015), 25980754 (2015), 30521064 (2019)), breast cancer (PMID: 11870161 (2002), 25186627 (2015), 31650731 (2020), 32547938 (2020)), ovarian cancer (PMID: 23047549 (2012)), and prostate cancer (PMID: 29368341 (2018)). In a large scale breast cancer association study, this variant was reported in breast cancer cases as well as in reportedly healthy individuals (PMID: 33471991 (2021), see also LOVD (http://databases.lovd.nl/shared/genes/MLH1)). Functional studies were conflicting particularly when evaluating binding to PMS2 (PMID: 16083711 (2005), 16724012 (2006), 22753075 (2012)). A study in yeast observing mutation rates (PMID: 19863800 (2009)) also suggests pathogenicity. However, mismatch repair activity has been reported to be proficient (PMID: 16083711 (2005), 20020535 (2010)). The frequency of this variant in the general population, 0.00007 (9/129044 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. -
Observed in individuals with Lynch-syndrome associated cancers and/or polyps, with most tumors demonstrating absence of MLH1 protein expression and/or microsatellite instability; however, one tumor also demonstrated MLH1 promoter hypermethylation (PMID: 11870161, 17250665, 21404117, 25110875, 25980754, 32661327, 15256438, 15872200); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31650731, 19389263, 32547938, 22949387, 19863800, 22753075, 16083711, 15256438, 20020535, 23047549, 21120944, 17594722, 25980754, 25372392, 22426235, 17192056, 25186627, 18383312, 18951440, 29368341, 24073290, 15872200, 11870161, 17250665, 21404117, 25110875, 16724012, 30521064, 32068069, 32661327, 34039291, 35467778, 35449176, 34326862, 32756484, 12799449, 20533529, 31830689, 36627197) -
The MLH1 p.Tyr646Cys variant was identified in 3 of 6722 proband chromosomes (frequency: 0.0004) from individuals or families with Lynch syndrome, ovarian cancer, and colorectal cancer and was not identified in 870 chromosomes from healthy individuals (Yurgelun 2015, Pal 2012, Hampel 2005). The variant was also identified in the following databases: dbSNP (ID: rs35045067) “With Uncertain significance allele”, ClinVar (classified uncertain significance, reviewed by an expert panel in 2013; submitters: InSIGHT, Ambry Genetics, GeneDx, Invitae, and Laboratory Corporation of America), UMD-LSDB (1x, unclassified variant), and Mismatch Repair Genes Variant Database. The c.1937A>G variant was not identified in COGR, Cosmic, MutDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, or the Insight Hereditary Tumors Database. The variant was identified in control databases in 12 of 277044 chromosomes at a frequency of 0.00004 (Genome Aggregation Database Feb 27, 2017). The variant was identified in the following populations: European in 9 of 126552 chromosomes (freq: 0.00007), African in 1 of 24036 chromosomes (freq: 0.00004), Latino in 1 of 34418 chromosomes (freq: 0.00003), and East Asian in 1 of 18862 chromosomes (freq: 0.00005); it was not observed in the Other, Ashkenazi Jewish, Finnish, or South Asian populations. Functional assays on this variant report conflicting assessments of pathogenicity (Andersen 2012, Belvederesi 2006, Drost 2010, Nakagawa 2004, Raevaara 2005, Vogelsang 2009). The p.Tyr646 residue is conserved across mammals and other organisms and 5 of 5 computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
not specified Uncertain:2
Variant summary: MLH1 c.1937A>G (p.Tyr646Cys) results in a non-conservative amino acid change located in the DNA mismatch repair protein Mlh1, C-terminal domain (IPR032189) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4.4e-05 in 251732 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer (4.4e-05 vs 0.00071), allowing no conclusion about variant significance. c.1937A>G has been reported in the literature in individuals affected with HNPCC, HNPCC-related cancers, or other cancers including prostate cancer and breast cancer, without strong evidence (i.e. segregation data) for causality (e.g. Scartozzi_2002, Nakagawa_2004, Belvederesi_2006, Hardt_2011, Yurgelun_2015, IsaacssonVelho_2018, Jiang_2019, Kwong_2020, Yoo_2020, Nikitin_2020, Xiao_2020, Talbot_2021, Hu_2022, Brady_2022, Zhang_2023, Shtaya_2024). These data do not allow any conclusion about variant significance. A co-occurrence with another pathogenic variant has been reported (BRCA1 c.5266dupC, p.Q1756fs), providing supporting evidence for a benign role (Nikitin_2020). In vitro functional studies provided conflicting results in relation to binding of this MLH1 Y646C mutant with PMS2 (Raevaara_2005, Belvederesi_2006, Drost_2011, Andersen_2012). Localization and expression of this variant and MMR activity of this mutant were found to be normal (Raevaara_2005, Belvederesi_2006, Vogelsang_2009, Drost_2011, Andersen_2012). However, in vitro measurement of mutation rate of this mutant was highly impaired (Vogelsang_2009) and it was also defective in binding with Exo1 protein (Andersen_2012). Thus, based on the functional assays, it is uncertain whether this variant leads to functional impairment. The following publications have been ascertained in the context of this evaluation (PMID: 19389263, 18383312, 15256438, 21120944, 16724012, 17250665, 20020535, 17192056, 16083711, 11870161, 39546165). ClinVar contains an entry for this variant (Variation ID: 36545). Based on the evidence outlined above, the variant was classified as uncertain significance. -
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Colorectal cancer, hereditary nonpolyposis, type 2 Uncertain:2
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Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 646 of the MLH1 protein (p.Tyr646Cys). This variant is present in population databases (rs35045067, gnomAD 0.007%). This missense change has been observed in individuals with clinical features of Lynch syndrome. It has also been observed in unaffected individuals (PMID: 11870161, 30521064; internal data). ClinVar contains an entry for this variant (Variation ID: 36545). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt MLH1 protein function with a positive predictive value of 95%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on MLH1 function (PMID: 16083711, 16724012, 19863800, 20020535, 22753075). For these reasons, this variant has been classified as Pathogenic. -
Lynch syndrome 1 Uncertain:1
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Lynch syndrome Uncertain:1
This missense variant replaces tyrosine with cysteine at codon 646 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 conflicting results with regard to the variant's impact on MLH1 protein interaction with PMS2 protein (PMID: 16083711, 16724012, 22753075). Multiple studies have shown that this variant does not affect mismatch repair activity (PMID: 16083711, 16724012, 20020535, 22753075). This variant has been reported in individuals affected with Lynch syndrome and Lynch syndrome-associated cancer (PMID: 11870161, 16083711, 16724012, 17250665, 21404117, 23047549, 25110875, 30521064). Tumor data from these individuals show conflicting evidence, with variability in microsatellite stability and protein expression via immunohistochemistry analysis (PMID: 11870161, 16083711, 16724012, 17250665, 21404117). This variant has also been observed in individuals affected with breast cancer or gastric cancer (PMID: 31650731, 36627197). This variant has also been identified in 12/282716 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at