rs876659681

chr3-37048984-C-CTT

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000249.4(MLH1):c.2070_2071insTT(p.Ile691LeufsTer93) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. Y690Y) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 frameshift
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:7
• Conservation: PhyloP100: -0.219

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.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 113 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-37048984-C-CTT is Pathogenic according to our data. Variant chr3-37048984-C-CTT is described in ClinVar as [Likely_pathogenic]. Clinvar id is 232298.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.2070_2071insTT	p.Ile691LeufsTer93	frameshift_variant	18/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.2070_2071insTT	p.Ile691LeufsTer93	frameshift_variant	18/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Center for Human Genetics, Inc, Center for Human Genetics, Inc	Nov 01, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 19, 2021	- -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Apr 24, 2019	The c.2070_2071insTT pathogenic mutation, located in coding exon 18 of the MLH1 gene, results from an insertion of two nucleotides at position 2070, causing a translational frameshift with a predicted alternate stop codon (p.I691Lfs*93). This frameshift, which occurs at the 3' terminus of MLH1, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 66 amino acids of the protein in addition to elongating the protein by 26 amino acids. Structural analysis shows that this alteration perturbs a known functional domain responsible for binding to and stabilizing PMS2 and removes a cysteine residue shown to be involved in metal binding as part of a functional domain in PMS2 (Ambry internal data; Mohd AB et al. DNA Repair (Amst.) 2006 Mar;5(3):347-61; Smith CE et al. PLoS Genet. 2013 Oct;9(10):e1003869). A similar alteration, MLH1 c.2269-2270insT located in the last codon of the gene is predicted to displace the termination codon downstream and extends the protein by 33 amino acids. Based on haplotype analysis, this alteration is considered an Italian founder mutation. The vast majority of tumors from mutation carriers demonstrated microsatellite instability and loss of MLH1 on immunohistochemical staining. There was also complete segregation with Lynch-related cancers in all informative families, nearly all of whom fulfilled Amsterdam criteria (Caluseriu O et al. J. Med. Genet. 2004 Mar;41(3):e34; Ambry internal data). The c.2070_2071insTT mutation has been detected in multiple individuals whose families meet Amsterdam criteria, and whose tumors show microsatellite instability and/or absence of MLH1 and PMS2 on immunohistochemical staining (Ambry internal data). 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	Apr 19, 2023	This variant inserts 2 nucleotides in exon 18 of the MLH1 gene, creating a frameshift predicted to result in an alternate stop codon. This variant is expected to escape nonsense mediated decay, and impacts the last 66 amino acids of the MLH1 protein and extends the protein by 26 amino acids. Although functional studies have not been reported for the variant, it is expected to disrupt the PMS2/MLH3/PMS1 interacting domain (PMID: 12799449, 16338176, 20533529). This variant has been reported in individuals affected with Lynch syndrome (ClinVar SCV000276394.6) and in an individual affected with colorectal cancer with family history and clinical features suspect of Lynch syndrome (PMID: 28135145). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MLH1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

Lynch syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Jun 08, 2023

This variant inserts 2 nucleotides in exon 18 of the MLH1 gene, creating a frameshift predicted to result in an alternate stop codon. This variant is expected to escape nonsense mediated decay, and impacts the last 66 amino acids of the MLH1 protein and extends the protein by 26 amino acids. Although functional studies have not been reported for the variant, it is expected to disrupt the PMS2/MLH3/PMS1 interacting domain (PMID: 12799449, 16338176, 20533529). This variant has been reported in individuals affected with Lynch syndrome (ClinVar SCV000276394.6) and in an individual affected with colorectal cancer with family history and clinical features suspect of Lynch syndrome (PMID: 28135145). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MLH1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

Oct 06, 2016

- -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Aug 27, 2023

This variant disrupts a region of the MLH1 protein in which other variant(s) (p.Tyr750*, p.Lys732*, p.Ser726*) have been determined to be pathogenic (PMID: 10422993, 10923051, 25197397; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 232298). This variant has not been reported in the literature in individuals affected with MLH1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change results in a frameshift in the MLH1 gene (p.Ile691Leufs*93). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 66 amino acid(s) of the MLH1 protein and extend the protein by 26 additional amino acid residues. -

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: rs876659681; hg19: chr3-37090475;