ClinVar Miner

Submissions for variant NM_000249.3(MLH1):c.306G>T (p.Glu102Asp) (rs63751665)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) RCV000075637 SCV000106639 uncertain significance Lynch syndrome 2018-06-13 reviewed by expert panel curation G>non-G at last base of exon with first 6 bases of the intron not GTRRGT; Insufficient evidence
GeneDx RCV000115480 SCV000149389 pathogenic not provided 2018-07-13 criteria provided, single submitter clinical testing This variant is denoted MLH1 c.306G>T at the cDNA level. Located at the last nucleotide of exon 3, it is predicted to damage or destroy the natural splice donor site and cause abnormal splicing. RNA analysis of an alternate nucleotide change at the same location, MLH1 c.306G>C, demonstrated skipping of exon 3 (Borras 2012, Buchanan 2014). MLH1 c.306G>T has been observed in an individual with synchronous colorectal cancers showing microsatellite instability (MSI-H) and loss of MLH1 protein expression and in at least four other individuals with suspected Lynch syndrome whose tumors demonstrated microsatellite instability (Whitworth 2016, Borras 2017). In vitro studies found this variant to exhibit mildly deficient mismatch repair (MMR) activity (Takahashi 2007). Although the nucleotide substitution results in the change of a Glutamic Acid to an Aspartic Acid at codon 102, and is called Glu102Asp in the literature, we are using only the nucleotide nomenclature to refer to the variant since the defect is determined to be one of splicing rather than a resulting missense variant. MLH1 c.306G>T was not observed at a significant allele frequency in large population cohorts (Lek 2016). Based on currently available evidence, we consider MLH1 c.306G>T to be pathogenic.
Ambry Genetics RCV000216647 SCV000275253 pathogenic Hereditary cancer-predisposing syndrome 2018-12-06 criteria provided, single submitter clinical testing <span style="font-family:arial,helvetica,sans-serif">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 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 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 immunohistochemistry (IHC) due to the high levels of protein expression (Takahashi et al. Cancer Res. 2007. 67(10): 4595-4604). This alteration has been detected in multiple individuals whose families meet Amsterdam II criteria (Ambry internal data). 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<span style="font-family:arial,helvetica,sans-serif"> is interpreted as a disease-causing mutation.
Invitae RCV000524291 SCV000543564 likely pathogenic Hereditary nonpolyposis colorectal neoplasms 2020-09-30 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid with aspartic acid at codon 102 of the MLH1 protein (p.Glu102Asp). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and aspartic acid. This variant also falls at the last nucleotide of exon 3 of the MLH1 coding sequence, which is part of the consensus splice site for this exon. This variant is present in population databases (rs63751665, ExAC 0.01%). This variant has been reported in individuals affected with colon cancer and/or colon polyps (PMID: 26681312), and an individual with cecal and sigmoid colon cancers (PMID: 26659639). Additionally, this variant has been reported in individuals with MLH1-related disease in the Leiden Open-source Variant Database (PMID: 21520333) and the Universal Mutation Database (PMID: 23729658). ClinVar contains an entry for this variant (Variation ID: 90151). Experimental in vitro studies have shown that this missense change results in a small reduction of mismatch repair activity of the MLH1 protein (PMID: 17510385). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. A different variant affecting this nucleotide (c.306G>C) has been determined to be pathogenic (PMID: 22736432). This suggests that this nucleotide is important for normal RNA splicing, and that other variants at this position may also be pathogenic. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Color Health, Inc RCV000216647 SCV000689874 likely pathogenic Hereditary cancer-predisposing syndrome 2020-09-14 criteria provided, single submitter clinical testing 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.
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology RCV000851292 SCV000993564 pathogenic Lynch syndrome II 2018-09-21 criteria provided, single submitter research
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV000851292 SCV001161675 likely pathogenic Lynch syndrome II 2020-01-09 criteria provided, single submitter clinical testing 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.
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001353746 SCV000592349 pathogenic Carcinoma of colon no assertion criteria provided clinical testing 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.

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