Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000249.4(MLH1):c.1667G>A(p.Ser556Asn) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S556I) has been classified as Pathogenic.
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]
Verdict is Pathogenic. Variant got 18 ACMG points.
PM1
?
PM1 - Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation
In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 15 uncertain in NM_000249.4
PM2
?
PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
PM5
?
PM5 - Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before
Other missense variant is known to change same aminoacid residue: Variant chr3-37040294-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 89825.Status of the report is reviewed_by_expert_panel, 3 stars.
PP3
?
PP3 - Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
PP5
?
PP5 - Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-37040294-G-A is Pathogenic according to our data. Variant chr3-37040294-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 449776.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-37040294-G-A is described in Lovd as [Pathogenic].
Likely pathogenic, criteria provided, single submitter
clinical testing
GeneDx
Sep 10, 2019
Not observed in large population cohorts (Lek 2016); Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Whitworth 2015, Sjursen 2016, Yurgelun 2017); This variant is associated with the following publications: (PMID: 25248401, 27064304, 22949387, 28135145, 30521064, 30720243) -
Likely pathogenic, criteria provided, single submitter
clinical testing
CeGaT Center for Human Genetics Tuebingen
Apr 01, 2023
MLH1: PM1, PM2, PS4:Moderate, PP1 -
Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1
Likely pathogenic, criteria provided, single submitter
clinical testing
Baylor Genetics
Apr 20, 2022
- -
Lynch-like syndrome Pathogenic:1
Likely pathogenic, no assertion criteria provided
clinical testing
Constitutional Genetics Lab, Leon Berard Cancer Center
This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 556 of the MLH1 protein (p.Ser556Asn). This variant also falls at the last nucleotide of exon 14, which is part of the consensus splice site for this exon. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This missense change has been observed in individuals with colorectal cancer and clinical features of Lynch syndrome (PMID: 27064304, 28135145; Invitae; externalcommunication). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 449776). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -
The c.1667G>A pathogenic mutation (also known as p.S556N), located in coding exon 14 of the MLH1 gene, results from a G to A substitution at nucleotide position 1667. The amino acid change results in serine to asparagine at codon 556, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 14, which makes it likely to have some effect on normal mRNA splicing. This alteration has been identified in multiple families fulfilling Amsterdam criteria (Sjursen W et al. Mol Genet Genomic Med. 2016 Mar;4:223-31; Yurgelun MBJ. Clin. Oncol. 2017 Apr;35(10):1086-1095; Jiang W et al. Int J Cancer, 2019 05;144:2161-2168). Another alteration at this same nucleotide position, c.1667G>T, has been shown to result in the use of a cryptic splice site that leads to a frameshift predicted to create a truncated protein (Sharp et al. Hum Mutat. 2004 Sep;24(3):272; Desmet et al. Nucleic Acids Res. 2009 May;37(9):e67). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Lynch syndrome 1 Uncertain:1
Uncertain significance, no assertion criteria provided