3-37001053-G-T
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Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PP3_StrongPP5_Strong
The NM_001167618.3(MLH1):c.-418G>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.00000629 in 1,430,404 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 Uncertain significance (★★★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000063 ( 0 hom. )
Consequence
MLH1
NM_001167618.3 5_prime_UTR_premature_start_codon_gain
NM_001167618.3 5_prime_UTR_premature_start_codon_gain
Scores
14
4
1
Splicing: ADA: 1.000
2
Clinical Significance
Conservation
PhyloP100: 6.33
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 Likely_pathogenic. Variant got 8 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.985
PP5
Variant 3-37001053-G-T is Pathogenic according to our data. Variant chr3-37001053-G-T is described in ClinVar as [Uncertain_significance]. Clinvar id is 90151.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=8, Likely_pathogenic=3}. Variant chr3-37001053-G-T is described in Lovd as [Likely_pathogenic]. Variant chr3-37001053-G-T is described in Lovd as [Benign]. Variant chr3-37001053-G-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251334Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135846
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GnomAD4 exome AF: 0.00000629 AC: 9AN: 1430404Hom.: 0 Cov.: 26 AF XY: 0.00000981 AC XY: 7AN XY: 713570
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32
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ClinVar
Significance: Uncertain significance
Submissions summary: Pathogenic:12Uncertain:1
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:4
| Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Jul 14, 2023 | This variant is considered 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: 27363726]. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad internal data]. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jan 03, 2024 | - - |
| Pathogenic, criteria provided, single submitter | research | HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology | Sep 21, 2018 | - - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics | Jan 09, 2020 | The heterozygous missense substitution c.306G>T (p.Glu102Asp) lies in exon 3 of the MLH1 gene and alters a conserved residue in the protein. The variant is predicted to be damaging by SIFT, LRT, Mutation Taster, Mutation Assessor and FATHMM. The variant lies in the ATPase domain (residues 25-207) of the protein, which is crucial for the MMR activity of the MLH1 protein (PMID: 26249686). In silico splice prediction tools (ASSP, NNSPLICE and MaxEntScan) suggests that this variant might affect splicing or create alternate cryptic splice site. The variant has been reported as Likely pathogenic in the ClinVar database. In summary, the variant meets our criteria to be classified as likely pathogenic. - |
Hereditary cancer-predisposing syndrome Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2022 | The c.306G>T pathogenic mutation (also known as p.E102D), located in coding exon 3 of the MLH1 gene, results from a G to T substitution at nucleotide position 306. The glutamate at codon 102 is replaced by aspartate, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 3, which makes it likely to have some effect on normal mRNA splicing. This alteration has been detected in multiple individuals whose families meet Amsterdam II criteria (Ambry internal data). In addition, this alteration has previously been reported in a male diagnosed with colon cancer and squamous carcinoma, as well as a family history of colon cancer. The colon tumors exhibited microsatellite instability and were absent for MLH1 and PMS2 protein on immunohistochemistry (IHC) analysis (Whitworth J et al. JAMA Oncol. 2016;2(3):373-379). This alteration also showed a dominant mutator effect in three different yeast functional assays, decreased mismatch repair (MMR) activity in an in vitro MMR assay, but normal MLH1 expression in transfected HCT116 cells. Given this information, the authors predicted this alteration to be pathogenic but possibly leading to intact MLH1 staining by IHC due to the high levels of protein expression (Takahashi et al. Cancer Res. 2007. 67(10): 4595-4604). A case study has been recently described in an individual diagnosed with colorectal, endometrial cancer and intact IHC (Nagabhushana et al. Gynecol. Oncol. Rep. 2021. Aug;37:100854). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Sep 14, 2020 | This missense variant replaces glutamic acid with aspartic acid at codon 102 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). This variant alters the last nucleotide of exon 3, and splice site prediction tools suggest that this variant may impact RNA splicing. A functional study has shown that the mutant protein retained dominant mutator effect in yeast, partially reduced in vitro MMR activity (56%), and near normal MLH1 expression (>75%) when transiently expressed in a human cell line (PMID: 17510385). This variant has been observed in multiple individuals affected with Lynch syndrome (PMID: 21671081, 22736432), Muir Torre syndrome (PMID 26743599), colon cancer or colon polyps (PMID; 26681312) and pancreatic cancer (PMID 25479140). This variant has been identified in 3/251334 chromosomes in the general population by the Genome Aggregation Database (gnomAD). A different variant occurring at the same nucleotide position has been shown to impact splicing and cause exon 3 skipping (r.208_306del) and in-frame deletion of 33 amino acids (p.K70_E102del) in the ATPase domain of the MLH1 protein (PMID: 22736432). Based on the available evidence, this variant is classified as Likely Pathogenic. - |
Carcinoma of colon Pathogenic:1
| Pathogenic, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The p.Glu102Asp variant has been previously reported in the literature and by our laboratory. Takahashi (2007) reported this variant in 1/202 proband chromosomes; however, the proband in this case was not informative for HNPCC. In-vitro mismatch repair analysis demonstrated that the p.Glu102Asp variant had 56.1% activity and >75% relative MLH1 expression (Takahashi 2007). In addition, this variant has previously been reported by our laboratory in one family where segregation of this variant was observed with Lynch related cancers in 3 individuals and both MLH1 deficiency and MSI tumours were demonstrated in more than one case, increasing the likelihood that this variant is pathogenic. In addition, the p.Glu102 residue is conserved across mammals, lower species and computational analyses (PolyPhen-2, MAPP, AlignGVGD) suggest that the p.Glu102Asp variant may impact the protein. The p.Glu102Asp (c.306G>T) variant occurs in the last base of the exon and this position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In-silico or computational prediction software (SpliceSiteFinder, MaxEntScan, NNSPLICE, HumanSpliceFinder) predicts a greater than 10% difference in splicing in 4 of 4 different programs, increasing the likelihood this variant may have clinical significance. However, this in-silico and conservation information is not predictive enough to assume pathogenicity. Another variant at the same amino acid residue, p.Glu102Lys, has been identified in 1/42 proband chromosomes from the Creighton University Hereditary Cancer Institute in individuals whom satisfied the Bethesda criteria (Chao 2008). An additional study identified the p.Glu102Lys variant in 1/8 proband chromosomes (who met Amsterdam criteria) and demonstrated that the nucleotide change abrogated the splicing pattern of exon 3, resulting in a 5-bp deletion in the transcript (Nagawa 2002). Furthermore, the p.Glu102Lys variant was demonstrated to be a loss of function variant by in-vitro complementation analysis (Ellison 2001). In summary, based on the above information, this variant is classified as pathogenic. - |
Inherited MMR deficiency (Lynch syndrome) Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Genomics and Molecular Medicine Service, East Genomic Laboratory Hub, NHS Genomic Medicine Service | May 14, 2024 | PS3_Supporting,PM3_Supporting,PP1_Moderate,PP4_Very Strong - |
Hereditary nonpolyposis colon cancer Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 22, 2022 | Variant summary: MLH1 c.306G>T (p.Glu102Asp) results in a conservative amino acid change located in the N-terminal domain (IPR002099) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant is located at the last nucleotide of exon 3, therefore can affect splicing. Several computational tools predict a significant impact on normal splicing: three predict the variant weakens a 5' donor site, while three predict the variant weakens/abolishes a cryptic 5' donor site, which is located 5 nucleotides upstream from the canonical splice site. One observation from a patient carrying c.303T>G and c.306G>T in trans showed that allele c.306G>T did not produce any wild-type splice product, strongly suggesting for a pathogenic outcome by defective splicing (poster from Myriad Genetics, 2015 ASHG meeting). A different variant affecting the same nucleotide (i.e. a G>C change) was found to cause a splicing defect (Borras_2012). The variant allele was found at a frequency of 1.2e-05 in 251464 control chromosomes (gnomAD). c.306G>T has been reported in the literature in several individuals affected with Lynch Syndrome associated tumors (e.g. Chao_2008, Kovac_2011, Susswein_2016, Whitworth_2016, Sethi_2016, Kim_2020, Nagabhushana_2021), and in multiple cases loss of MLH1 and PMS2 expression and / or high microsatellite instability was described in the associated tumor, although in a few cases retained MMR protein expression was also noted. These data indicate that the variant is likely to be associated with disease. An in vitro study, examining the protein level effects of this missense change demonstrated that the variant resulted in retained protein expression (>75% of wild-type) with a somewhat reduced MMR activity (<60% of wild-type; Takahashi_2007), however, authors used an intronless cDNA sequence for mutagenesis, and in light of the (potential) spliceogenic effect, these findings might not reflect the overall in vivo consequences of the variant. Eight submitters, including an expert panel (InSiGHT), have provided clinical-significance assessments for this variant in ClinVar after 2014, and classified the variant as pathogenic (n=4) / likely pathogenic (n=3), while the expert panel called the variant as VUS (n=1). Based on the evidence outlined above, the variant was classified as pathogenic. - |
not provided Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jan 30, 2023 | Exonic splice site variant predicted to cause aberrant splicing leading to in-frame skipping of the adjacent exon in a gene for which loss of function is a known mechanism of disease; 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; Deletions involving coding exons of this gene are a known mechanism of disease (HGMD; other references); This variant is associated with the following publications: (PMID: 25525159, 28765196, 28912153, 24362816, 26659639, 22290698, 24323032, 17510385, 22736432, 26681312, 30720243, 16083711, 21120944, 22753075, 32809219, 29922827, 34504932) - |
Muir-Torré syndrome Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Neuberg Centre For Genomic Medicine, NCGM | - | The MLH1 c.306G>T (p.Glu102Asp) variant has been reported in individuals affected with colon cancer and/or colon polyps (Susswein LR et al., 2016), and an individual with cecal and sigmoid colon cancers (Whitworth J et al., 2016). Experimental studies have shown that this variant exhibits mildly deficient mismatch repair (MMR) activity (Takahashi 2007). The p.Glu102Asp variant is novel (not in any individuals) in 1000 Genomes. It has been submitted to ClinVar with varying interpretations: Pathogenic/ Likely Pathogenic. The amino acid Glu at position 102 is changed to a Asp changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by both SIFT and PolyPhen2. The residue is conserved across species. The amino acid change p.Glu102Asp in MLH1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. - |
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 102 of the MLH1 protein (p.Glu102Asp). RNA analysis indicates that this missense change induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs63751665, gnomAD 0.01%). This missense change has been observed in individual(s) with colon cancer and/or colon polyps (PMID: 21520333, 23729658, 26659639, 26681312). ClinVar contains an entry for this variant (Variation ID: 90151). 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: 17510385). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in skipping of exon 3, but is expected to preserve the integrity of the reading-frame (Invitae). This variant disrupts a region of the MLH1 protein in which other variant(s) (p.Cys77Arg) have been determined to be pathogenic (PMID: 10660333, 11793442, 15475387, 16083711, 17210669, 22736432, 27602174). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. - |
Lynch syndrome Uncertain:1
| Uncertain significance, reviewed by expert panel | curation | International Society for Gastrointestinal Hereditary Tumours (InSiGHT) | Jun 13, 2018 | G>non-G at last base of exon with first 6 bases of the intron not GTRRGT; Insufficient evidence - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
H
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Loss of methylation at R100 (P = 0.1855);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
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