rs1553641362

Positions:

• chr3-37004468-C-A
• chr3-37004468-C-G
• chr3-37004468-C-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PP3_Strong PP5_Very_Strong

The NM_000249.4(MLH1):​c.374C>A​(p.Ala125Glu) 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 Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. A125A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 7.59

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 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM1: In a strand (size 9) in uniprot entity MLH1_HUMAN there are 10 pathogenic changes around while only 3 benign (77%) in NM_000249.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.939
• PP5: Variant 3-37004468-C-A is Pathogenic according to our data. Variant chr3-37004468-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 433851.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-37004468-C-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4	c.374C>A	p.Ala125Glu	missense_variant	4/19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.374C>A	p.Ala125Glu	missense_variant	4/19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Jul 13, 2023

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [Myriad internal data]. This variant is expected to disrupt protein structure [Myriad internal data]. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Sep 30, 2023

This sequence change replaces alanine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 125 of the MLH1 protein (p.Ala125Glu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with colorectal cancer (PMID: 29212164, 30072391). ClinVar contains an entry for this variant (Variation ID: 433851). 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. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Colon cancer Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

Jun 01, 2023

The MLH1 p.Ala125glu variant was identified in 3 individuals with colorectal cancer (Rosty 2015, Raskin 2017, Patel 2018). The above patients include features suspicious of Lynch syndrome including a family history that meets Amsterdam criteria and an MSI-high CRC under age 50 (Raskin 2017), CRC at age 62 with IHC displaying loss of PMS2 (Rosty 2015) and IHC displaying loss of PMS2 along with a second pathogenic MLH1 variant identified on tumour sequencing and a high mutational burden. The variant was also identified in ClinVar (classified as likely pathogenic by Invitae and pathogenic by Ambry Genetics). The variant was not identified in dbSNP. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). The variant was identified by our laboratory in 2 individuals with colorectal cancer, one reports to have loss of PMS2 and MLH1 on IHC. The p.Ala125 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) 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 although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 08, 2023

The p.A125E variant (also known as c.374C>A), located in coding exon 4 of the MLH1 gene, results from a C to A substitution at nucleotide position 374. The alanine at codon 125 is replaced by glutamic acid, an amino acid with dissimilar properties. This alteration was identified in several individuals who met clinical criteria for Lynch syndrome with tumor results revealing loss of MLH1 and/or loss of PMS2 on immunohistochemistry or high microsatellite instability (Rosty C et al. BMJ Open, 2016 Feb;6:e010293; Raskin L et al. Oncotarget, 2017 Nov;8:93450-93463; Patel SA et al. Oncologist, 2018 12;23:1395-1400; Ambry internal data). Based on internal structural analysis, this variant 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). 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.49	D
BayesDel_noAF	Pathogenic	0.46
CADD	Pathogenic	28
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.91	D;.;T
Eigen	Pathogenic	0.72
Eigen_PC	Pathogenic	0.73
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.86	D;D;D
M_CAP	Pathogenic	0.33	D
MetaRNN	Pathogenic	0.94	D;D;D
MetaSVM	Uncertain	0.49	D
MutationAssessor	Pathogenic	3.9	H;.;.
PrimateAI	Uncertain	0.72	T
PROVEAN	Pathogenic	-4.5	D;D;D
REVEL	Pathogenic	0.87
Sift	Uncertain	0.0020	D;D;D
Sift4G	Uncertain	0.0020	D;D;D
Polyphen		1.0	D;.;.
Vest4		0.98
MutPred		0.82		Gain of disorder (P = 0.0399);.;.;
MVP		0.96
MPC		0.34
ClinPred		1.0	D
GERP RS		6.0
Varity_R		0.96
gMVP		0.98

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: rs1553641362; hg19: chr3-37045959;