3-37017508-C-T
Variant names:
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2PM5PP3_StrongPP5_Very_Strong
The NM_000249.4(MLH1):c.793C>T(p.Arg265Cys) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,428 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R265H) has been classified as Likely pathogenic.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
MLH1
NM_000249.4 missense, splice_region
NM_000249.4 missense, splice_region
Scores
17
1
1
Clinical Significance
Conservation
PhyloP100: 7.28
Genes affected
MLH1 (HGNC:7127): (mutL homolog 1) The protein encoded by this gene can heterodimerize with mismatch repair endonuclease PMS2 to form MutL alpha, part of the DNA mismatch repair system. When MutL alpha is bound by MutS beta and some accessory proteins, the PMS2 subunit of MutL alpha introduces a single-strand break near DNA mismatches, providing an entry point for exonuclease degradation. The encoded protein is also involved in DNA damage signaling and can heterodimerize with DNA mismatch repair protein MLH3 to form MutL gamma, which is involved in meiosis. This gene was identified as a locus frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 16 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr3-37017509-G-A is described in Lovd as [Likely_pathogenic].
PP3
MetaRNN computational evidence supports a deleterious effect, 0.986
PP5
Variant 3-37017508-C-T is Pathogenic according to our data. Variant chr3-37017508-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 29654.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37017508-C-T is described in Lovd as [Pathogenic]. Variant chr3-37017508-C-T is described in Lovd as [Benign]. Variant chr3-37017508-C-T is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461428Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727036
GnomAD4 exome
AF:
AC:
1
AN:
1461428
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
727036
Gnomad4 AFR exome
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Gnomad4 AMR exome
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Gnomad4 ASJ exome
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Gnomad4 EAS exome
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Gnomad4 SAS exome
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Gnomad4 FIN exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
32
Bravo
AF:
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:23Uncertain:1Other:1
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
not provided Pathogenic:7Uncertain:1
| Pathogenic, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
| Uncertain significance, no assertion criteria provided | research | Biesecker Lab/Clinical Genomics Section, National Institutes of Health | Jul 13, 2012 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 05, 2024 | Published functional studies demonstrate a damaging effect: aberrant splicing and reduced mRNA and protein expression as well as deceased protein stability and reduced binding of MLH1 to PMS2 (PMID: 12386821, 15713769, 18205192, 20864636, 22753075, 21952876, 26761715); Observed in individuals with personal or family histories consistent with pathogenic variants in MLH1 and concordant tumor studies (PMID: 10495924, 12011148, 12386821, 12547705, 15849733, 15926618, 17312306, 19526325, 19698169, 19419416, 20045164, 20587412, 20682701, 21642682, 21404117, 21952876, 24710284, 26248088, 26202870, 30521064, 35534704); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 17210669, 20020535, 18561205, 22824075, 20045164, 21404117, 20682701, 19224586, 21681552, 20864636, 28127413, 15731775, 21952876, 11781295, 11555625, 17594722, 22736432, 22949387, 22753075, 17135187, 23760103, 10495924, 16995940, 15849733, 12547705, 19698169, 26247049, 22843852, 24710284, 21642682, 16216036, 19526325, 20587412, 25345868, 17312306, 21155023, 26053027, 26248088, 17192056, 15926618, 12011148, 26202870, 23741719, 16830052, 15713769, 12386821, 17510385, 26761715, 25081409, 11948175, 28445943, 30274973, 31589614, 32849802, 31332305, 18205192, 33260537, 29758216, 24362816, 31447099, 30787465, 30521064, 31830689, 19419416, 35534704, 31391288) - |
| Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics and Genomics, Karolinska University Hospital | Sep 22, 2014 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Mar 26, 2024 | The MLH1 c.793C>T (p.Arg265Cys) variant has been reported in the published literature in multiple individuals and families with Lynch syndrome (PMIDs: 28445943 (2017), 20587412 (2010), 19419416 (2009), 15713769 (2005), and 12386821 (2002)). It was also found in a breast cancer case in a large scale breast cancer association study (PMID: 33471991 (2021), see also LOVD (http://databases.lovd.nl/shared/genes/MLH1)). Splicing studies indicate that the variant results in exon skipping and premature termination of the MLH1 protein (PMIDs: 18561205 (2008), 15713769 (2005), 12386821 (2002), and 26247049 (2015)). Functional studies suggest reduced expression, protein stability, and mismatch repair activity of the variant protein (PMIDs: 17510385 (2007), 17135187 (2006), and 11555625 (2001)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). 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, this variant is classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Dec 07, 2023 | The MLH1 c.793C>T; p.Arg265Cys variant (rs63751194) is reported in the literature in multiple individuals affected with hereditary nonpolyposis colorectal cancer (HNPCC; Hardt 2011, Jiang 2019, Zhang 2017). This variant is reported in ClinVar (Variation ID: 29654), and is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. In vitro functional analyses demonstrate an effect on splicing at the transcript level (van der Klift 2014) and a loss of mismatch repair activity at the protein level (Drost 2010). Additionally, other amino acid substitutions at this codon (Ser, Gly, His, Pro) have been reported in individuals with HNPCC (Hardt 2011, Mork 2019, Tanyi 2014, Viel 1997). Based on available information, the p.Arg265Cys variant is considered to be pathogenic. References: Drost M et al. A cell-free assay for the functional analysis of variants of the mismatch repair protein MLH1. Hum Mutat. 2010;31(3):247-253. Hardt K et al. Missense variants in hMLH1 identified in patients from the German HNPCC consortium and functional studies. Fam Cancer. 2011;10(2):273-284. Jiang W. Universal screening for Lynch syndrome in a large consecutive cohort of Chinese colorectal cancer patients: High prevalence and unique molecular features. Int J Cancer. 2019 May 1;144(9):2161-2168. PMID: 30521064. Mork ME et al. Outcomes of disease-specific next-generation sequencing gene panel testing in adolescents and young adults with colorectal cancer. Cancer Genet. 2019;235-236:77-83. Tanyi M et al. MLH1 and MSH2 mutation screening in HNPCC families of Hungary - Two new MMR gene mutations. Eur J Surg Oncol. 2014;40(11):1445-1452. van der Klift HM et al. Splicing analysis for exonic and intronic mismatch repair gene variants associated with Lynch syndrome confirms high concordance between minigene assays and patient RNA analyses. Mol Genet Genomic Med. 2015;3(4):327-345. Viel A et al. Characterization of MSH2 and MLH1 mutations in Italian families with hereditary nonpolyposis colorectal cancer. Genes Chromosomes Cancer. 1997;18(1):8-18. Zavodna K et al. Novel and recurrent germline alterations in the MLH1 and MSH2 genes identified in hereditary nonpolyposis colorectal cancer patients in Slovakia. Neoplasma. 2006;53(4):269-276. Zhang J et al. A molecular inversion probe-based next-generation sequencing panel to detect germline mutations in Chinese early-onset colorectal cancer patients. Oncotarget. 2017 Apr 11;8(15):24533-24547. PMID: 28445943. - |
Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:6
| Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2009 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Neuberg Centre For Genomic Medicine, NCGM | Feb 14, 2023 | The missense c.793C>T(p.Arg265Cys) variant in MLH1 gene has been reported in heterozygous state in multiple individuals affected with colorectal cancer (Tang R, et. al., 2009; Choi YH, et. al., 2009). This variant has been observed to segregate with disease (Tang R, et. al., 2009). Functional studies demonstrate skipping of exon 9-10, aberrant splicing, reduced mRNA and protein expression as well as deceased protein stability, hence proving a damaging effect (Fan Y, et. al., 2012; Casey G, et. al., 2005). The p.Arg265Cys variant is novel (not in any individuals) in both gnomAD Exomes and 1000 Genomes databases. This variant has been reported to the ClinVar database as Uncertain Significance / Pathogenic (multiple submissions). The amino acid change p.Arg265Cys in MLH1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 265 is changed to a Cys changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Nov 19, 2023 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Mar 02, 2017 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | May 06, 2019 | - - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Mar 16, 2023 | This variant is considered likely pathogenic. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 25085752]. This variant is expected to disrupt protein structure [Myriad internal data]. - |
Lynch syndrome Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 21, 2016 | Variant summary: Variant affects a conserved nucleotide and results in a replacement of a large size and basic Arginine (R) with a medium size and polar Cysteine (C). 4/4 in silico tools predict the variant to be disease causing (SNPs&GO was not capture due to low reliability index). The variant is absent from the large and broad cohorts of the ExAC project while it was observed in several HNPCC patients indicating pathogenicity. Moreover, the variant is considered to be a founder mutation in populations of Chinese/Taiwanese origin. Functional studies report the variant to result in exon skipping and a partial MMR defect which in combination likely result in a pathogenic impact. Furthermore, a clinical laboratory and databases cite variant as Pathogenic. Considering all evidence, the variant was classified as a Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 17, 2016 | The p.Arg265Cys variant in MLH1 is absent from large population studies but has been reported in >30 individuals with Lynch Syndrome (Casey 2005, Hardt 2011, Ta ng 2009, InSiGHT database: http://chromium.lovd.nl/LOVD2/colon_cancer/variants.p hp). It segregated with disease in at least 12 family members (Hardt 2011, Tang 2009). Functional studies using patient mRNA showed that the variant leads to ex on skipping and protein truncation (Casey 2005). Additionally, this variant has been classified as pathogenic on Sept 5, 2013 by the ClinGen-approved InSiGHT pa nel (ClinVar SCV000106886.2). In summary, this variant meets criteria to be clas sified as pathogenic for Lynch Syndrome in an autosomal dominant manner based up on segregation studies and the impact of the variant on the protein. - |
| Pathogenic, reviewed by expert panel | research | International Society for Gastrointestinal Hereditary Tumours (InSiGHT) | Sep 05, 2013 | Variant causes aberrant splicing leading to truncated protein: full inactivation of variant allele. - |
Carcinoma of colon Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | 3DMed Clinical Laboratory Inc | Feb 10, 2018 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The p.Arg265Cys variant has been previously reported in the literature and by our laboratory. It is also reported in dbSNP from a clinical source (dbSNP#:rs63751194). In one study, this variant was reported in 2 different families and was associated with skipping of exons 9 and 10 from cDNA (Casey 2005). In another report, including probands who met Amsterdam criteria for HNPCC or who had a family history, this variant was found to reduce exon inclusion. This variant has been tested in different functional assays at the protein level, with results that were not always consistent; the p.Arg265Cys was associated with a mild reduction of mismatch repair efficiency in four studies (Plotz 2006; Ellison 2001; Wanat 2007; Takahashi 2007) but not in a fifth one (Trojan 2002) (Tournier 2007). One large study of Tawainese patients demonstrated that the p.Arg265Cys variant was identified in 13 out of 93 unrelated families. In total, 93 cancers were noted in these 13 families including 66 with cases of colon cancer, 6 cases of rectal cancer, 3 cases of endometrial cancer, 6 cases of gastric cancer, 1 case of ovarian cancer and 11 cases of other types of cancer (Tang 2009). In another report, deficient MLH1 IHC status and MSI-H tumor was noted in an individual with this variant who developed colorectal cancer at age 55 (Perera 2010). In summary, based on the above information this variant is classified as pathogenic. - |
Hereditary cancer-predisposing syndrome Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 17, 2024 | The c.793C>T pathogenic mutation (also known as p.R265C), located in coding exon 10 of the MLH1 gene, results from a C to T substitution at nucleotide position 793. The arginine at codon 265 is replaced by cysteine, an amino acid with highly dissimilar properties. This mutation has been identified in several individuals who met Amsterdam I/II criteria for Lynch syndrome (Trojan J et al. Gastroenterology. 2002 Jan;122:211-9; Wolf B et al. Wien. Klin. Wochenschr. 2005 Apr;117:269-77; Woods MO et al. Gut. 2010 Oct;59:1369-77; Hardt K et al. Fam. Cancer. 2011 Jun;10:273-84; Ambry internal data). In addition, this mutation has been identified in multiple probands whose Lynch syndrome-associated tumor demonstrated high microsatellite instability and/or loss of MLH1/PMS2 expression by immunohistochemistry (Li S et al. J. Med. Genet. 2020 Jan;57:62-69; Ambry internal data). This mutation has been associated with exon-skipping, premature protein truncation, and low expression of the variant allele (Casey G et al. JAMA. 2005 Feb;293:799-809; Tournier I et al. Hum. Mut. 2008 Dec;29:1412-24; van der Klift HM et al. Mol. Genet. Genomic Med. 2015 Jul;3:327-45). This mutation has also been shown to segregate with disease in several families meeting Amsterdam I/II criteria (De Jong AE et al. Gastroenterology. 2004 Jan;126:42-8; Tang R et al. Clin. Genet. 2009 Apr;75:334-45; Sjursen W et al. J. Med. Genet. 2010 Sep;47:579-85). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. This amino acid position is highly conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive. However, RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). In addition, as a missense substitution this is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Jan 01, 2022 | This missense variant replaces arginine with cysteine at codon 265 in the MutS interacting domain 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 significantly decreases MLH1 protein stability (PMID: 18205192) and the ability of MLH1 protein to bind PMS2 (PMID: 21952876). This variant has also been shown to affect mRNA splicing (PMID: 12386821, 15713769, 18561205). This variant has been reported in individuals affected with Lynch syndrome or colorectal cancer (PMID: 12386821, 15713769, 19419416, 20587412, 20864636). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. - |
Lynch syndrome 1 Pathogenic:1Other:1
| not provided, no classification provided | literature only | GeneReviews | - | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Ding PR Lab, Sun Yat-sen University Cancer Center | - | - - |
Muir-Torré syndrome;C1333991:Colorectal cancer, hereditary nonpolyposis, type 2;C5399763:Mismatch repair cancer syndrome 1 Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 06, 2024 | - - |
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 19, 2024 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 265 of the MLH1 protein (p.Arg265Cys). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or altered protein product. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with colorectal cancer or Lynch syndrome (PMID: 12386821, 15713769, 19419416, 20587412, 20864636). It has also been observed to segregate with disease in related individuals. Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this MLH1 variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 1,370,736 individuals referred to our laboratory for MLH1 testing. ClinVar contains an entry for this variant (Variation ID: 29654). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on MLH1 function (PMID: 11555625, 11781295, 17135187, 17510385). Studies have shown that this missense change alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 18561205, 22736432, 26247049; Invitae). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Pathogenic
D;.;.;.;.;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;.;.;.;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
H;.;.;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D;D;D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D;D;D;D;D;D
Sift4G
Pathogenic
D;D;D;D;D;D;D
Polyphen
D;.;.;.;.;.;.
Vest4
MutPred
Loss of disorder (P = 0.0477);.;.;.;.;.;.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at