3-36996702-G-A

Position:

chr3-36996702-G-A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2PM5PP3_StrongPP5_Very_Strong

The NM_000249.4(MLH1):c.200G>A(p.Gly67Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,626 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging 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. G67R) has been classified as Pathogenic.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

MLH1
NM_000249.4 missense

Scores

Clinical Significance

Pathogenic reviewed by expert panel P:8

Conservation

PhyloP100: 9.51

Variant links:

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]

MLH1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 16 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr3-36996701-G-A is described in Lovd as [Pathogenic].

PP3

MetaRNN computational evidence supports a deleterious effect, 0.994

PP5

Variant 3-36996702-G-A is Pathogenic according to our data. Variant chr3-36996702-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 17106.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-36996702-G-A is described in Lovd as [Pathogenic]. Variant chr3-36996702-G-A is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4 linkuse as main transcript	c.200G>A	p.Gly67Glu	missense_variant	2/19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8 linkuse as main transcript	c.200G>A	p.Gly67Glu	missense_variant	2/19	1	NM_000249.4	ENSP00000231790	P1	P40692-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000137

AC:

AN:

1459626

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

726322

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000180

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

not provided

Pathogenic:3

Pathogenic, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jan 31, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 15, 2023	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; Segregates with disease in several families meeting Amsterdam criteria, with tumor studies from some individuals demonstrating microsatellite instability (MSI) and/or loss of MLH1 protein expression (Terdiman et al., 2001; Barnetson et al., 2006; Barnetson et al., 2008; Clyne et al., 2009; Yu et al., 2009; Chubb et al., 2015; Frolova et al., 2015); This variant is associated with the following publications: (PMID: 20459533, 24878972, 23510156, 23741719, 16807412, 15475387, 19142183, 22290698, 22949387, 24362816, 11208710, 16995940, 17939062, 17192056, 19493351, 18033691, 25559809, 20068152, 20668451, 22516243, 29887214, 32081490, 30877237, 30787465, 25617771, 22753075, 16083711, 21120944) -

Hereditary cancer-predisposing syndrome

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	May 24, 2024	The p.G67E pathogenic mutation (also known as c.200G>A), located in coding exon 2 of the MLH1 gene, results from a G to A substitution at nucleotide position 200. The glycine at codon 67 is replaced by glutamic acid, an amino acid with similar properties. This alteration is observed in several individuals whose Lynch-related tumors demonstrated high microsatellite instability and/or loss of MLH1 or MLH1 and PMS2 expression on immunohistochemistry (IHC), and MLH1 promoter hypermethylation was negative (Ambry internal data; Barnetson RA et al. Hum Mutat. 2008 Mar;29(3):367-74). This alteration segregated with disease in multiple colon cancer families, and in one family with many cancers that are atypical for Lynch syndrome (Barnetson RA et al. Hum Mutat. 2008 Mar;29(3):367-74; Clyne M et al. Br J Cancer. 2009 Jan 27;100(2):376-80). In vitro yeast studies indicated that G67E is stably expressed but showed inhibition of protein activity during MMR and was therefore categorized as a loss of function allele (Clyne M et al. Br J Cancer. 2009 Jan 27;100(2):376-80). Based on internal structural analysis using published crystal structures, p.G67E is anticipated to result in a significant decrease in structural stability (Wu H et al. Acta Crystallogr F Struct Biol Commun. 2015 Aug;71:981-5; Ambry internal data). 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 supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Aug 05, 2020	This missense variant replaces glycine with glutamic acid at codon 67 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 protein impairs DNA mismatch repair activity in yeast-based assays (PMID: 15475387, 19142183). This variant has been reported in individuals affected with colorectal cancer (PMID: 16807412, 18033691), endometrial cancer (PMID: 25617771), prostate cancer (PMID: 18033691), breast cancer (PMID: 18033691, 19142183, 32081490), uveal melanoma (PMID: 32081490), and leiomyosarcoma (PMID: 19142183, 32659967). It has also been reported that this variant segregates with Lynch syndrome-associated cancers in multiple families (PMID: 18033691). 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. -

Colorectal cancer, hereditary nonpolyposis, type 2

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 27, 2009

- -

Lynch syndrome

Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

Multifactorial likelihood analysis posterior probability >0.99 -

Hereditary nonpolyposis colorectal neoplasms

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 15, 2023

This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 67 of the MLH1 protein (p.Gly67Glu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Lynch syndrome (PMID: 16807412, 18033691, 19142183). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 17106). 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) performed at Invitae indicates that this missense variant is expected to disrupt MLH1 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects MLH1 function (PMID: 15475387, 19142183, 24362816). This variant disrupts the p.Gly67 amino acid residue in MLH1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8521398, 18337503, 19142183). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

1.0

BayesDel_addAF

Pathogenic

0.59

BayesDel_noAF

Pathogenic

0.62

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Pathogenic

0.97

Eigen

Pathogenic

0.95

Eigen_PC

Pathogenic

0.92

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Pathogenic

1.0

M_CAP

Pathogenic

0.50

MetaRNN

Pathogenic

0.99

MetaSVM

Pathogenic

0.90

MutationAssessor

Pathogenic

5.0

MutationTaster

Benign

1.0

A;A;A;A;A;A

PrimateAI

Pathogenic

0.80

PROVEAN

Pathogenic

-7.2

REVEL

Pathogenic

0.99

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

1.0

Vest4

0.97

MutPred

0.99

Loss of catalytic residue at G67 (P = 0.0921);

MVP

0.99

MPC

0.46

ClinPred

1.0

GERP RS

5.8

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.0

Varity_R

0.99

gMVP

0.95

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over