3-37050628-T-C
Variant summary
Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000249.4(MLH1):c.2246T>C(p.Leu749Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L749V) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000249.4 missense
Scores
Clinical Significance
Conservation
Publications
- Lynch syndromeInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, ClinGen, Orphanet
- Lynch syndrome 2Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp
- Muir-Torre syndromeInheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Ambry Genetics, G2P, Orphanet
- mismatch repair cancer syndrome 1Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
- Lynch syndrome 1Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- ovarian cancerInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- malignant pancreatic neoplasmInheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
- rhabdomyosarcomaInheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
- prostate cancerInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- breast cancerInheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics
- hereditary breast carcinomaInheritance: AD Classification: NO_KNOWN Submitted by: ClinGen
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ACMG classification
Our verdict: Pathogenic. The variant received 18 ACMG points.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MLH1 | NM_000249.4 | c.2246T>C | p.Leu749Pro | missense_variant | Exon 19 of 19 | ENST00000231790.8 | NP_000240.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MLH1 | ENST00000231790.8 | c.2246T>C | p.Leu749Pro | missense_variant | Exon 19 of 19 | 1 | NM_000249.4 | ENSP00000231790.3 |
Frequencies
GnomAD3 genomes
GnomAD4 exome Cov.: 31
GnomAD4 genome
ClinVar
Submissions by phenotype
Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:3
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This variant is considered pathogenic. Functional studies indicate this variant impacts protein function [PMID: 23403630, 22736432, 20533529]. 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]. -
The missense variant c.2246T>C (p.Leu749Pro) in the MLH1 gene has been reported previously in a heterozygous state in individuals affected with Lynch syndrome (Dudley et al., 2015). Experimental studies have shown that this missense change affects MLH1 function (Kosinski et al., 2010; Borràs et al., 2012). This variant is absent in the gnomAD. It is submitted to ClinVar with varying interpretations as Pathogenic/ Likely Pathogenic. The amino acid Leucine at position 749 is changed to a Proline changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted as damaging by SIFT. The amino acid change p.Leu749Pro in MLH1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -
not provided Pathogenic:3
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Published functional studies demonstrate a damaging effect: reduced mismatch repair activity compared to wild-type and decreased PMS2 levels suggesting a defect in the MLH1-PMS2 heterodimer, with inconsistent results with respect to MLH1 protein expression (PMID: 20533529, 22736432, 23403630); Not observed at significant frequency in large population cohorts (gnomAD); 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: 25871621, 22290698, 21286667, 20864636, 20533529, 26557847, 18205192, 23752102, 17473388, 18383312, 16181381, 24362816, 22949387, 17192056, 14504054, 17505997, 22736432, 23403630, 30787465, 12799449, 22753075, 33939675) -
Hereditary cancer-predisposing syndrome Pathogenic:2
The p.L749P pathogenic mutation (also known as c.2246T>C) is located in coding exon 19 of the MLH1 gene. This results from a T to C substitution at nucleotide position 2246 which is 25 nucleotides from the end of the protein. The leucine at codon 749 is replaced by proline, an amino acid with a few similar properties. This pathogenic mutation has been identified in multiple patients with Lynch syndrome whose tumors all exhibited MSI instability, but the absence of MLH1 staining on IHC was not always noted (Dudley B et al. Am. J. Surg. Pathol. 2015 Aug;39(8):1114-20; Perera S et al. J Mol Diagn. 2010 Nov; 12(6): 757-64; Colombino M et al. Ann Oncol. 2003 Oct; 14(10):1530-6; Losi L et al. Am J Gastroenterol. 2005 Oct; 100(10):2280-7; Pedroni M et. al. Dis. Markers. 2007; 23(3):179-87). In one study, authors performed multiple independent transfection experiments and reproducibly showed MLH1 expression levels similar to wild type but corresponding PMS2 levels were similar to those achieved when PMS2 was expressed in the absence of MLH1 (reduction was statistically significant p>0.05). They demonstrated this alteration disturbs MLH1-PMS2 dimerization, as it is located within the proposed dimerization interface, a conserved hydrophobic surface area. Authors suggest the pathogenic effect of this mutation is due to direct interference with dimerization and severely compromised mismatch repair activity (Kosinski J et al. Hum Mutat. 2010 Aug; 31(8):975-82). In another study, cells with the MLH1 p.L749P pathogenic mutation had protein expression levels of greater than 70% when compared to wild-type; however the repair activity was less than 30% when compared to wild-type (Hinrichsen I et al. Clin Cancer Res. 2013 May; 19(9):2432-41). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as a disease-causing mutation. -
This missense variant replaces leucine with proline at codon 749 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 decreases protein stability and impairs DNA mismatch repair activity (PMID: 20533529, 22736432, 23403630, 28767177). This variant has been reported in individuals affected with Lynch Syndrome and colorectal cancer (PMID: 14504054, 16181381, 20864636, 21286667, 23752102, 25871621, 26557847). 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. -
Carcinoma of colon Pathogenic:1
The MLH1 p.Leu749Pro variant was identified in 5 of 7124 proband chromosomes (frequency: 0.001) from individuals or families with colorectal cancer, or adrenocortical carcinoma (Colombino 2003, Dudley 2015, Pedroni 2007, Raymond 2013). The variant was also identified in dbSNP (ID: rs267607894) as “With Pathogenic allele”, in ClinVar (classified as pathogenic by Ambry Genetics, GeneDx, InSight; as likely pathogenic by Invitae), Mismatch Repair Genes Variant Database, and Insight Hereditary Tumors Database (9x pathogenic). The variant was not identified in Cosmic, MutDB, UMD-LSDB, Zhejiang University Database, or the MMR Gene Unclassified Variants Database. The variant was not identified in the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Leu749 residue is conserved across mammals and other organisms, and 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 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. The variant caused decreased co-expression of PMS2, which is unstable in the absence of interaction with MLH1, suggesting that this alteration may confer a pathogenic effect (Kosinski 2010, Borras 2012, Dudley 2015). The variant also severely compromised mismatch repair activity (Kosinski 2010). However, the study on allelic expression by Perera (2010) discovered that this variant is not associated with an allelic imbalance; it is likely that this variant affects heterodimerization of MLH1 rather than its expression or stability. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic. -
Lynch syndrome Pathogenic:1
Multifactorial likelihood analysis posterior probability >0.99 -
MLH1-related disorder Pathogenic:1
The MLH1 c.2246T>C variant is predicted to result in the amino acid substitution p.Leu749Pro. This variant was reported in multiple individuals with colorectal cancer (Colombino et al. 2003. PubMed ID: 14504054; Perera S et al. 2010. PubMed ID: 20864636; Raymond VM et al. 2013. PubMed ID: 23752102; Losi L et al. 2005. PubMed ID: 16181381; Colombino M et al. 2011. PubMed ID: 21286667; Magnani G et al. 2015. PubMed ID: 26557847). Functional studies have shown this variant negatively impacts protein function (Kosinski J et al. 2010. PubMed ID: 20533529; Hinrichsen I et al. 2013. PubMed ID: 23403630; Borràs E et al. 2012. PubMed ID: 22736432). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is classified as pathogenic in ClinVar with multiple submitters in agreement (https://www.ncbi.nlm.nih.gov/clinvar/variation/90097/). This variant is interpreted as pathogenic. -
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 749 of the MLH1 protein (p.Leu749Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of Lynch syndrome and/or Lynch syndrome (PMID: 14504054, 16181381, 20864636, 21286667, 23752102, 26557847; internal data). 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: 90097). Invitae Evidence Modeling incorporating data from in vitro experimental studies (internal data) indicates that this missense variant is expected to disrupt MLH1 function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects MLH1 function (PMID: 20533529, 22736432, 23403630). For these reasons, this variant has been classified as Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at