3-37050632-C-G

Position:

• chr3-37050632-C-G

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1_Strong PM2 PP5_Strong

The NM_000249.4(MLH1):​c.2250C>G​(p.Tyr750Ter) 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: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 stop_gained
• Clinical Significance: Uncertain significance reviewed by expert panel P:4 U:1
• Conservation: PhyloP100: 2.33

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 10 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 5 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-37050632-C-G is Pathogenic according to our data. Variant chr3-37050632-C-G is described in ClinVar as [Uncertain_significance]. Clinvar id is 90099.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=1, Pathogenic=3}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4	c.2250C>G	p.Tyr750Ter	stop_gained	19/19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.2250C>G	p.Tyr750Ter	stop_gained	19/19	1	NM_000249.4	ENSP00000231790	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:4 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Lynch syndrome Pathogenic:1 Uncertain:1

Uncertain significance, reviewed by expert panel	curation	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Jun 21, 2019	Insufficient evidence: premature termination codon outside of known functional domain; Nonsense variant after codon 743 in MLH1 = VUS -
Pathogenic, criteria provided, single submitter	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	Jul 05, 2016	- -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Jul 25, 2023

This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Jul 02, 2015

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 cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 28, 2020

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: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.51	D
BayesDel_noAF	Pathogenic	0.50
CADD	Pathogenic	36
DANN	Uncertain	1.0
Eigen	Uncertain	0.68
Eigen_PC	Uncertain	0.53
FATHMM_MKL	Uncertain	0.94	D
MutationTaster	Benign	1.0	D;D;D;D;D;D
Vest4		0.79
ClinPred		1.0	D
GERP RS		3.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.7

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: rs267607893; hg19: chr3-37092123;