rs876659002

chr3-37048994-GA-TC

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1 PM2 PP3

The NM_000249.4(MLH1):c.2080_2081inv(p.Glu694Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E694A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:7
• Conservation: PhyloP100: 9.05

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 Uncertain_significance. Variant got 5 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 16 uncertain in NM_000249.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.2080_2081inv	p.Glu694Ser	missense_variant	18/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.2080_2081inv	p.Glu694Ser	missense_variant	18/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 25, 2023	This variant causes a deletion of GA and insertion of TC at nucleotide positions 2080 and 2081 in exon 18 of the MLH1 gene, which replaces glutamic acid with serine at codon 694 of the MLH1 protein. This substitution changes two basepairs, c.2080G>T and c.2081A>C, which together changes the codon for glutamic acid (GAG) to one for serine (TCG). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with early onset, microsatellite unstable colorectal cancer (PMID: 33753878), as well as in an individual affected with sarcoma who also carried a pathogenic variant in the BRCA2 gene (PMID: 25712765). This variant has not been identified 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 11, 2023	The c.2080_2081delGAinsTC variant (also known as p.E694S), located in coding exon 18 of the MLH1 gene, results from an in-frame deletion of GA and insertion of TC at nucleotide positions 2080 to 2081. This results in the substitution of the glutamic acid residue for a serine residue at codon 694, an amino acid with similar properties. This alteration has been identified in a patient whose colon tumor demonstrated microsatellite instability, absent MLH1 staining by IHC, and loss of heterozygosity (Kim JE et al. Exp Mol Med, 2021 Mar;53:446-456). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be neutral by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Oct 16, 2023

Variant summary: MLH1 c.2080_2081delinsTC (p.Glu694Ser) results in a non-conservative amino acid change located in the C-terminal domain (IPR032189) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. This variant is reported as two separate single nucleotide changes in gnomAD, with both variants found in the same subpopulations with the same number of occurrences, and read data demonstrating that both of these SNPs occurred together in cis, in 3 cases. Therefore the variant allele was found at a frequency of 2e-05 in 251054 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.2080_2081delinsTC has been reported in the literature in an individual affected with sarcoma, who also carried a BRCA2 pathogenic allele (Varga_2015). This report does not provide unequivocal conclusions about association of the variant with Lynch Syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 25712765). Four submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -

Colorectal cancer, hereditary nonpolyposis, type 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Baylor Genetics

Jun 20, 2023

- -

Lynch syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Jan 08, 2024

This variant causes a deletion of GA and insertion of TC at nucleotide positions 2080 and 2081 in exon 18 of the MLH1 gene, which replaces glutamic acid with serine at codon 694 of the MLH1 protein. This substitution changes two basepairs, c.2080G>T and c.2081A>C, which together changes the codon for glutamic acid (GAG) to one for serine (TCG). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with early onset, microsatellite unstable colorectal cancer (PMID: 33753878), as well as in an individual affected with sarcoma who also carried a pathogenic variant in the BRCA2 gene (PMID: 25712765). This variant has not been identified 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. -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Jan 28, 2023

Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this variant does not alter protein structure/function; Observed in an individual with sarcoma who also carried a pathogenic variant in BRCA2 (Varga et al., 2015); This variant is associated with the following publications: (PMID: 23695190, 25712765, 12799449, 20533529, 22753075) -

Hereditary nonpolyposis colorectal neoplasms Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Oct 05, 2022

This sequence change replaces glutamic acid, which is acidic and polar, with serine, which is neutral and polar, at codon 694 of the MLH1 protein (p.Glu694Ser). This variant is present in population databases (no rsID available, gnomAD 0.2%). This missense change has been observed in individual(s) with sarcoma (PMID: 25712765). ClinVar contains an entry for this variant (Variation ID: 455415). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs876659002; hg19: chr3-37090485;