rs72481822

chr3-36993550-G-Achr3-36993550-G-T

Variant summary

Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PVS1 PS1_Moderate PM2 PP5_Very_Strong

The NM_000249.4(MLH1):c.3G>A(p.Met1?) variant causes a start lost change. 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 (★★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MLH1 NM_000249.4 start_lost
• Clinical Significance: Pathogenic reviewed by expert panel P:6
• Conservation: PhyloP100: 5.98

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 20 ACMG points.

• PVS1: Start lost variant, no new inframe start found.
• PS1: Another start lost variant in NM_000249.4 (MLH1) was described as [Pathogenic] in ClinVar as 90134
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-36993550-G-A is Pathogenic according to our data. Variant chr3-36993550-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 90211.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-36993550-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.3G>A	p.Met1?	start_lost	1/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.3G>A	p.Met1?	start_lost	1/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jun 21, 2021	The p.M1? pathogenic mutation (also known as c.3G>A) is located in coding exon 1 of the MLH1 gene and results from a G to A substitution at nucleotide position 3. This alters the methionine residue at the initiation codon (ATG). The N-terminus of the MLH1 protein is known to be functionally/structurally important (Internal analysis; Tempel W et al. Structural Genomics Consortium. PDB ID: 4P7A Crystal Structure of human MLH1). This mutation has been reported in several individuals meeting Amsterdam criteria (Guillem JG et al. Ann Surg. 2007 Apr;245(4):560-5; Ambry internal data) and was also identified in an individual diagnosed with MSI-H ascending colon cancer at age 39, whose tumor demonstrated absence of MLH1 by IHC (Barnetson RA et al, N. Engl. J. Med. 2006 Jun; 354(26):2751-63). In addition to the clinical data presented in the literature, sequence variations that modify the initiation codon are expected to result in either loss of translation initiation, N-terminal truncation, or cause a shift in the mRNA reading frame. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 16, 2023	This variant results in the loss of the translation start codon (methionine at codon 1) of the MLH1 gene. This variant is expected to disrupt the expression of the full-length MLH1 protein. A functional study has shown that downstream in-frame methionine at codon 35 may be used as an alternative translation start site (PMID: 24302565). However, MLH1 protein lacking p.1-34 showed a significantly reduced mismatch DNA repair activity (~25% of wild type), at a level equivalent to a known pathogenic mutation in a cell-free mismatch repair assay (PMID: 24302565). This variant has been reported in individuals affected with Lynch syndrome or suspected of having Lynch syndrome (PMID: 16807412, 17414604, 25430799). This variant has also been reported in an individual with a personal and/or family history of cancer (PMID: 28514183). 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 Likely Pathogenic. -

Hereditary nonpolyposis colon cancer Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Feb 03, 2021

Variant summary: MLH1 c.3G>A (p.Met1Ile) alters the initiation codon and is predicted to result either in absence of the protein or truncation of the encoded protein due to translation initiation at a downstream codon. Three of four in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251482 control chromosomes (gnomAD). c.3G>A has been reported in the literature in individuals affected with Hereditary Nonpolyposis Colorectal Cancer (e.g. Barnetson_2006, Guillem_2007, Goldberg_2015, Espenschied_2017). MSI-H status and absence of MLH1 by immunohistochemical analysis was reported following tumor testing in one of the affected individuals (Barnetson_2006). These data indicate that the variant is likely to be associated with disease. Three ClinVar submitters including an expert panel (InSiGHT) (evaluation after 2014) cite the variant as pathogenic/likely pathogenic. Other variants affecting the MLH1 start codon are cited in HGMD and ClinVar databases as disease associated/pathogenic (e.g. c.1A>C, c.1A>G, c.1A>T, c.2T>A, c.2T>G, c.3G>T). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Lynch syndrome 1 Pathogenic:1

Pathogenic, reviewed by expert panel

curation

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Jun 30, 2017

meets criteria for Class 5 -

not provided Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

- -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Aug 17, 2023

This sequence change affects the initiator methionine of the MLH1 mRNA. The next in-frame methionine is located at codon 35. This variant is not present in population databases (gnomAD no frequency). Disruption of the initiator codon has been observed in individual(s) with Lynch syndrome (PMID: 11112663, 16807412, 24302565, 28944238). ClinVar contains an entry for this variant (Variation ID: 90211). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that disruption of the initiator codon affects MLH1 function (PMID: 24302565). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.43
Cadd	Pathogenic	26
Dann	Uncertain	1.0
DEOGEN2	Benign	0.32	T
Eigen	Pathogenic	0.69
Eigen_PC	Pathogenic	0.72
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.90	D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	0.82	D
MutationTaster	Benign	1.0	D
PROVEAN	Benign	-0.50	N
REVEL	Pathogenic	0.74
Sift	Pathogenic	0.0	D
Sift4G	Benign	0.12	T
Polyphen		0.94	P
Vest4		0.97
MutPred		0.99		Loss of disorder (P = 0.0854);
MVP		0.98
ClinPred		1.0	D
GERP RS		5.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.93
gMVP		0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs72481822; hg19: chr3-37035041;