3-36993651-T-G

Variant names:

• chr3-36993651-T-G
• rs63749906
• NM_000249.4:c.104T>G

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000249.4(MLH1):​c.104T>G​(p.Met35Arg) 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. M35N) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:5
• Conservation: PhyloP100: 7.62

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]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a helix (size 13) in uniprot entity MLH1_HUMAN there are 19 pathogenic changes around while only 8 benign (70%) in NM_000249.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.991
• PP5: Variant 3-36993651-T-G is Pathogenic according to our data. Variant chr3-36993651-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 89631.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-36993651-T-G is described in Lovd as [Pathogenic]. Variant chr3-36993651-T-G is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.104T>G	p.Met35Arg	missense_variant	Exon 1 of 19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.104T>G	p.Met35Arg	missense_variant	Exon 1 of 19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Jul 10, 2023

Myriad Genetics, Inc.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 17510385]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 8521398]. This variant is expected to disrupt protein structure [Myriad internal data]. -

Carcinoma of colon Pathogenic:1

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The p.Met35Arg variant has not been previously identified in our laboratory, but has been reported in the literature in at least 4/245 probands (0.008 frequency) with HNPCC and was absent from 146 controls (Tannergard 1995, Halvarsson 2005, Poley 2007, Lagerstedt Robinson 2007). Of these studies, the variant was found in individuals who either had MLH1 deficient immunohistochemistry or MSI positive tumors (Halvarsson 2005, Poley 2007, Lagerstedt Robinson 2007), increasing the likelihood this variant is pathogenic. In one family, the variant segregated with disease (Tannergard 1995). The p.Met35 residue is conserved across mammals and other vertebrate species, and computational analyses (SIFT, AlignGVGD) predict a deleterious impact on protein function. Although this information is not predictive enough to assume pathogenicity, functional studies have shown that the p.Met35Arg variant showed a reduction in repair capacity compared to the wild-type protein (Lastella 2006, Takahashi_2007_17510385, Shcherbakova_1999_10082584, Kondo_2003_12810663), increasing the likelihood that an alteration to this residue is pathogenic. In addition, this variant has not been observed in more than 1200 proband chromosomes sequenced for the MLH1 gene by our laboratory, increasing the likelihood, this is a rare variant of clinical significance. In summary, based on the above information, this variant is classified as pathogenic. -

Lynch syndrome Pathogenic:1

Sep 05, 2013

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: research

Multifactorial likelihood analysis posterior probability >0.99 -

not provided Pathogenic:1

Apr 20, 2016

Clinical Genetics and Genomics, Karolinska University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Pathogenic:1

Nov 13, 2017

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.M35R pathogenic mutation (also known as c.104T>G), located in coding exon 1 of the MLH1 gene, results from a T to G substitution at nucleotide position 104. The methionine at codon 35 is replaced by arginine, an amino acid with similar properties. This amino acid position is well conserved in available vertebrate species. This mutation, designated Met35>Arg (ATG>AGG), segregated with disease in a Swedish family meeting Amsterdam criteria (Tannergård P et al. Cancer Res. 1995 Dec;55:6092-6) and was identified in an individual with HNPCC whose two adenomas with low grade dysplasia demonstrated absent MLH1 and PMS2 by immunohistochemistry (Halvarsson B et al. Mod. Pathol. 2005 Aug;18:1095-101). In yeast functional assays, the M35R variant showed a mutator phenotype when compared to wild type suggesting inactivation of mismatch repair (Shcherbakova PV et al. Mol. Cell. Biol. 1999 Apr;19:3177-83). In a yeast two-hybrid assay, M35R displayed almost no beta-galactosidase activity similar to known deleterious alterations (Kondo E et al. Cancer Res. 2003 Jun;63:3302-8). Additionally, the M35R variant demonstrated no dominant mutator effect in reporter assays in yeast, which is consistent with pathogenicity (Shimodaira H et al. Nat Genet. 1998 Aug;19(4):384-9; Takahashi M et al. Cancer Res. 2007 May;67:4595-604). This alteration has been classified as pathogenic using the following lines of evidence: in silico prediction models, segregation with disease, clinical phenotype including tumor characteristics, mutation co-occurrence, and functional studies (Thompson BA et al. Hum. Mutat. 2013 Jan;34:200-9; Thompson BA et al. Nat. Genet. 2014 Feb;46:107-15; available at [www.insight-group.org/variants/classifications/]). In addition, this alteration is predicted to be deleterious by in silico analysis. In addition, this alteration is predicted to be deleterious by MAPP-MMR in silico analyses (Chao EC et al. Hum. Mutat. 2008 Jun;29:852-60). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.43
CADD	Pathogenic	32
DANN	Uncertain	0.98
DEOGEN2	Pathogenic	0.95	D
Eigen	Uncertain	0.58
Eigen_PC	Uncertain	0.63
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	0.98	D
M_CAP	Pathogenic	0.34	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Uncertain	0.045	D
MutationAssessor	Uncertain	2.7	M
PrimateAI	Pathogenic	0.83	D
PROVEAN	Uncertain	-4.0	D
REVEL	Pathogenic	0.90
Sift	Uncertain	0.0010	D
Sift4G	Uncertain	0.0020	D
Polyphen		0.98	D
Vest4		0.99
MutPred		0.96		Gain of ubiquitination at K33 (P = 0.0931);
MVP		0.99
MPC		0.46
ClinPred		1.0	D
GERP RS		6.0
Varity_R		0.99
gMVP		0.97

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs63749906; hg19: chr3-37035142;