Submissions for variant NM_000249.4(MLH1):c.1420C>T (p.Arg474Trp)

dbSNP: rs147939838

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
PreventionGenetics, part of Exact Sciences	RCV000679267	SCV000805949	uncertain significance	not provided	2016-12-22	criteria provided, single submitter	clinical testing
University of Washington Department of Laboratory Medicine, University of Washington	RCV000075209	SCV000887319	uncertain significance	Lynch syndrome	2018-05-01	criteria provided, single submitter	clinical testing	MLH1 NM_000249.3:c.1420C>T has a 59.6% probability of pathogenicity based on combining prior probability from public data with a likelihood ratio of 0.16 to 1, generated from evidence of seeing this as a somatic mutation in a tumor with loss of heterozygosity at the MLH1 locus. See Shirts et al 2018, PMID 29887214.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000820563	SCV000961280	likely benign	Hereditary nonpolyposis colorectal neoplasms	2025-02-02	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV001011503	SCV001171830	uncertain significance	Hereditary cancer-predisposing syndrome	2022-12-01	criteria provided, single submitter	clinical testing	The p.R474W variant (also known as c.1420C>T), located in coding exon 13 of the MLH1 gene, results from a C to T substitution at nucleotide position 1420. The arginine at codon 474 is replaced by tryptophan, an amino acid with dissimilar properties. This variant demonstrated no effect on splicing in one ex vivo assay (Tournier I et al. Hum. Mutat. 2008 Dec;29:1412-24). This variant was also observed in 1/3251 individuals who met eligibility criteria for hereditary breast and ovarian cancer syndrome (Lerner-Ellis J et al. J Cancer Res Clin Oncol, 2021 Mar;147:871-879). 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.
Color Diagnostics, LLC DBA Color Health	RCV001011503	SCV001343152	uncertain significance	Hereditary cancer-predisposing syndrome	2021-02-15	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with tryptophan at codon 474 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). This variant has been reported to have no impact on splicing and on MLH1 function based on a methylation tolerance assay (PMID: 18561205, 30998989). This variant has been reported in InSiGHT and Leiden Open Variations Databases. This variant has been identified in 7/282820 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.
Baylor Genetics	RCV003460706	SCV004193004	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2024-02-24	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000075209	SCV004841005	uncertain significance	Lynch syndrome	2024-01-11	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with tryptophan at codon 474 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). This variant has been reported to have no impact on splicing and on MLH1 function based on a methylation tolerance assay (PMID: 18561205, 30998989). This variant has been reported in InSiGHT and Leiden Open Variations Databases. This variant has been identified in 7/282820 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	RCV004689443	SCV005185700	uncertain significance	not specified	2024-05-30	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.1420C>T (p.Arg474Trp) results in a non-conservative amino acid change in 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 2.4e-05 in 251410 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1420C>T has been reported in the literature in individuals affected with breast cancer (Pramanik_2024), but was also found in controls (Dorling_2021). These reports do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. In functional studies the variant was found to have no effect on RNA splicing (Tournier_2008), and mismatch repair activity (Bouvet_2019). The following publications have been ascertained in the context of this evaluation (PMID: 30998989, 18561205, 38439815, 33471991). ClinVar contains an entry for this variant (Variation ID: 89735). Based on the evidence outlined above, the variant was classified as VUS-possibly benign.
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre	RCV003460706	SCV005374367	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2024-09-22	criteria provided, single submitter	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000679267	SCV001553805	uncertain significance	not provided		no assertion criteria provided	clinical testing	The MLH1 p.Arg474Trp variant was not identified in the literature nor was it identified in the COGR, MutDB, UMD-LSDB, and in the Zhejiang Colon Cancer Databases. The variant was identified in dbSNP (ID: rs147939838) as with Uncertain significance allele; in the ClinVar database as uncertain significance by InSiGHT; 1X in the Cosmic database from a carcinoma of the large intestine with a confirmed somatic status; 1X in the Insight Colon Cancer Gene Variant database with unknown significance, 1X in the Mismatch Repair Genes Variant Database, and listed 8X in the Insight Hereditary Tumors database. The variant was also identified in the 1000 Genomes Project in 2 of 5000 chromosomes (frequency: 0.0004) and in the NHLBI GO Exome Sequencing Project in 7 of 4406 African American alleles. In addition, the variant was identified in control databases in 7 of 277168 chromosomes at a frequency of 0.00003 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: Latino in 3 of 34420 chromosomes (freq: 0.00009), European Non-Finnish in 1 of 126660 chromosomes (freq: 0.000008), and South Asian in 3 of 30782 chromosomes (freq: 0.0001); it was seen in the African, Other, Ashkenazi Jewish, East Asian, European Finnish populations. An exon inclusion functional study was performed, where the variant was amplified by PCR along with 150bp flanking sequences and inserted into a splicing reporter mini-gene. After transfection into HeLa cells, effects of splicing were evaluated. The p.Arg474Trp variant showed no effect (Tournier 2008). The p.Arg474 residue is conserved in mammals but not in more distantly related organisms however computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out 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. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.