NM_000249.4:c.2250C>G
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_StrongPM2PP5_Strong
The NM_000249.4(MLH1):c.2250C>G(p.Tyr750*) variant causes a stop gained change involving the alteration of a non-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 Uncertain significance (★★★).
Frequency
Consequence
NM_000249.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD4 exome Cov.: 31
GnomAD4 genome
ClinVar
Submissions by phenotype
Lynch syndrome Pathogenic:1Uncertain:1
Insufficient evidence: premature termination codon outside of known functional domain; Nonsense variant after codon 743 in MLH1 = VUS -
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Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation. -
not provided Pathogenic:1
This variant is denoted MLH1 c.2250C>G at the cDNA level and p.Tyr750Ter (Y750X) at the protein level. The substitution creates a nonsense variant, which changes a Tyrosine to a premature stop codon (TAC>TAG). This variant is, the last exon of the gene, and results in protein truncation and loss of 7 amino acids. MLH1 Tyr750Ter has been observed in at least two individuals with colorectal cancer and in at least one HNPCC family (Syngal 1999, Wang 2006, Mueller 2009). In a mouse embryonic fibroblast model, this variant was associated with MLH1 expression levels similar to wild type, but reduced levels of PMS2, which was described as indicating an inability to stabilize PMS2 protein (Mohd 2006). Similar results were also demonstrated in an in vitro human cell line study, which further reported that MLH1 Tyr750Ter was associated with significantly reduced, but not entirely eliminated, mismatch repair activity (Kosinski 2010). We therefore consider MLH1 Tyr750Ter to be a likely pathogenic variant. -
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
This sequence change creates a premature translational stop signal (p.Tyr750*) in the MLH1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 7 amino acid(s) of the MLH1 protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 10422993). ClinVar contains an entry for this variant (Variation ID: 90099). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects MLH1 function (PMID: 20533529). RNA analysis performed to evaluate the impact of this premature translational stop signal on mRNA splicing indicates it does not significantly alter splicing (Invitae). This variant disrupts a region of the MLH1 protein in which other variant(s) (p.Lys751Serfs*3) have been determined to be pathogenic (PMID: 8797773, 12799449, 16338176, 18566915, 18931482, 20533529, 24802709, 27295708). 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. -
Hereditary cancer-predisposing syndrome Pathogenic:1
The p.Y750* pathogenic mutation (also known as c.2250C>G), located in coding exon 19 of the MLH1 gene, results from a C to G substitution at nucleotide position 2250. This changes the amino acid from a tyrosine to a stop codon within coding exon 19 (p.Y750*). This variant occurs at the 3' terminus of theMLH1 gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 7 amino acids of the protein. However, premature stop codons are typically deleterious in nature and the impacted region is critical for protein function based on an internal structural analysis which suggests that this variant perturbs a known functional domain responsible for binding to as well as stabilizing PMS2 and removes a terminal 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; Gueneau E et al. Nat. Struct. Mol. Biol. 2013 Apr;20:461-8). This variant has also been reported in families meeting Amsterdam I/II criteria for Lynch syndrome (Syngal S et al. JAMA, 1999 Jul;282:247-53; Yuan Y et al. Jpn. J. Clin. Oncol., 2004 Nov;34:660-6; Wang XL et al. World J. Gastroenterol., 2006 Jul;12:4074-7; Mueller J et al. Cancer Res., 2009 Sep;69:7053-61). And this variant has been reported in a female diagnosed with pancreatic adenocarcinoma with a family history of colorectal cancer (Shindo K et al. J. Clin. Oncol., 2017 Oct;35:3382-3390). An in vitro mismatch repair (MMR) complementation assay demonstrated compromised relative MMR activity at 16% for this variant and decreased coexpression (23%) of PMS2 by co-immunoprecipitation upon transient expression in HEK293T cells, suggesting that this variant interferes with heterodimerization (Kosinski J et al. Hum. Mutat., 2010 Aug;31:975-82). This alteration is expected to result in loss of function by premature protein truncation. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Computational scores
Source:
Splicing
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