Submissions for variant NM_000249.4(MLH1):c.1633A>G (p.Thr545Ala)

gnomAD frequency: 0.00004  dbSNP: rs267607840

Total submissions: 18

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000130610	SCV000185486	uncertain significance	Hereditary cancer-predisposing syndrome	2022-11-03	criteria provided, single submitter	clinical testing	The p.T545A variant (also known as c.1633A>G), located in coding exon 14 of the MLH1 gene, results from an A to G substitution at nucleotide position 1633. The threonine at codon 545 is replaced by alanine, an amino acid with similar properties. This variant was reported in conjunction with a pathogenic mutation in MSH2 in an individual diagnosed with breast and colon cancer whose family met Amsterdam I criteria (Hardt K et al. Fam Cancer. 2011 Jun;10:273-84). 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 limited at this time, the clinical significance of this alteration remains unclear.
GeneDx	RCV000656863	SCV000211111	uncertain significance	not provided	2023-04-10	criteria provided, single submitter	clinical testing	Published functional studies demonstrate splicing comparable to wild-type in a minigene assay and in patient RNA analysis, but the impact that this variant has on protein function was not evaluated (van der Klift et al., 2015); 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: 21404117, 18566915, 26898890, 28259476, 12799449, 20533529, 22753075, 26247049)
Invitae	RCV000524244	SCV000261240	uncertain significance	Hereditary nonpolyposis colorectal neoplasms	2024-01-31	criteria provided, single submitter	clinical testing	This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 545 of the MLH1 protein (p.Thr545Ala). This variant is present in population databases (rs267607840, gnomAD 0.009%). This missense change has been observed in individual(s) with breast and/or ovarian cancer and/or hereditary non-polyposis colorectal cancer (PMID: 18566915, 21404117, 26898890). ClinVar contains an entry for this variant (Variation ID: 89812). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MLH1 protein function. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (PMID: 26247049; Invitae). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000656863	SCV000601361	uncertain significance	not provided	2021-05-17	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000130610	SCV000684762	uncertain significance	Hereditary cancer-predisposing syndrome	2023-02-14	criteria provided, single submitter	clinical testing	This missense variant replaces threonine with alanine at codon 545 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in two suspected Lynch syndrome families (PMID: 18566915, 26247049) and one diagnosed Lynch syndrome family (Amsterdam II criteria) that has three colon cancer affected members, one of whom also has a pathogenic MSH2 covariant (PMID: 21404117). This variant has also been observed in an individual affected with familial breast cancer (PMID: 26898890). This variant has been identified in 11/282688 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000212542	SCV000919638	uncertain significance	not specified	2024-02-22	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.1633A>G (p.Thr545Ala) 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. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-05 in 251320 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer (4e-05 vs 0.00071), allowing no conclusion about variant significance. c.1633A>G has been reported in the literature in individuals affected with cancer (e.g. Nilbert_2009, Hardt_2011, Caminsky_2016) without strong evidence for causality. These reports do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. A co-occurrence with a pathogenic variant in MSH2 was reported by Hardt_2011 (variant not specified), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 18566915, 21404117, 26247049, 26898890). ClinVar contains an entry for this variant (Variation ID: 89812). Based on the evidence outlined above, the variant was classified as VUS-possibly benign.
St. Jude Molecular Pathology, St. Jude Children's Research Hospital	RCV000606136	SCV002012436	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2021-10-28	criteria provided, single submitter	clinical testing	The MLH1 c.1633A>G (p.Thr545Ala) missense change has a maximum subpopulation frequency of 0.0085% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/3-37081751-A-G). Six of seven in silico tools predict a deleterious effect of this variant on protein function (PP3), but to our knowledge these predictions have not been confirmed by functional assays. This variant has also been observed in an individual with Lynch syndrome who also harbored a pathogenic variant in MSH2 (BP5; PMID: 21404117). It has also been reported in 1/1358 non-cancer control individuals in a study of individuals with multiple primary cancers (PMID: 29641532). In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: PP3, BP5.
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000212542	SCV002552497	uncertain significance	not specified	2023-08-15	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000656863	SCV002585970	uncertain significance	not provided	2022-08-01	criteria provided, single submitter	clinical testing	MLH1: PM2, BP5
Baylor Genetics	RCV000606136	SCV004190649	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2023-08-13	criteria provided, single submitter	clinical testing
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	RCV003492409	SCV004240743	uncertain significance	Breast and/or ovarian cancer	2023-04-25	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003935009	SCV004750418	uncertain significance	MLH1-related disorder	2024-01-17	criteria provided, single submitter	clinical testing	The MLH1 c.1633A>G variant is predicted to result in the amino acid substitution p.Thr545Ala. This variant has been reported as a variant of uncertain significance in an individual with Lynch syndrome (Nilbert et al. 2009. PubMed ID: 18566915) and in an individual with Lynch syndrome that harbored a pathogenic variant in MSH2 (Hardt et al. 2011. PubMed ID: 21404117, Table S1). Results from a minigene study indicates this variant does not impact splicing (Tables 1 and 2, van der Klift et al. 2015. PubMed ID: 26247049). This variant is reported in 0.0085% of alleles in individuals of European (Non-Finnish) descent in gnomAD. It is interpreted as uncertain in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/89812/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
All of Us Research Program, National Institutes of Health	RCV003997116	SCV004843185	uncertain significance	Lynch syndrome	2023-11-28	criteria provided, single submitter	clinical testing	This missense variant replaces threonine with alanine at codon 545 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). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in two suspected Lynch syndrome families (PMID: 18566915, 26247049) and one diagnosed Lynch syndrome family (Amsterdam II criteria) that has three colon cancer affected members, one of whom also has a pathogenic MSH2 covariant (PMID: 21404117). This variant also has been observed in an individual affected with familial breast cancer (PMID: 26898890). This variant has been identified in 11/282688 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.
Mayo Clinic Laboratories, Mayo Clinic	RCV000212542	SCV000691863	uncertain significance	not specified		no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000606136	SCV000734268	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2		no assertion criteria provided	clinical testing
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	RCV000656863	SCV001905788	uncertain significance	not provided		no assertion criteria provided	clinical testing
Clinical Genetics, Academic Medical Center	RCV000656863	SCV001921140	uncertain significance	not provided		no assertion criteria provided	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV000656863	SCV002036328	uncertain significance	not provided		no assertion criteria provided	clinical testing