3-37028857-AC-ACC

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.1489dup(p.Arg497ProfsTer6) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,846 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★★). Synonymous variant affecting the same amino acid position (i.e. T495T) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: MLH1 NM_000249.4 frameshift
• Clinical Significance: Pathogenic reviewed by expert panel P:20 O:1
• Conservation: PhyloP100: 0.659

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 undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-37028857-A-AC is Pathogenic according to our data. Variant chr3-37028857-A-AC is described in ClinVar as [Pathogenic]. Clinvar id is 89753.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.1489dup	p.Arg497ProfsTer6	frameshift_variant	13/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.1489dup	p.Arg497ProfsTer6	frameshift_variant	13/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461846 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727226

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:20 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:9

Pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	-	- -
Pathogenic, no assertion criteria provided	research	Mayo Clinic Laboratories, Mayo Clinic	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 29, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Feb 04, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2023	MLH1: PVS1, PM2 -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 09, 2018	This duplication of one nucleotide is denoted MLH1 c.1489dupC at the cDNA level and p.Arg497ProfsX6 (R497PfsX6) at the protein level. The normal sequence, with the base that is duplicated in brackets, is ACCCCC[dupC]GGAG. The duplication causes a frameshift, which changes an Arginine to a Proline at codon 497, and creates a premature stop codon at position 6 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. Also published as MLH1 c.1489_1490insC using alternate nomenclature, this variant has been reported in many individuals and families with Lynch syndrome (Kurzawski 2002, Behrens 2003, Mangold 2005, Wolf 2006, Bonadona 2011, Buchanan 2014, Magnani 2015). MLH1 c.1489dupC has also been reported in at least one individual with a clinical diagnosis of Muir-Torre syndrome (Mangold 2007). Additionally, this variant has been observed in the germline of at least two individuals with breast cancer; one breast tumor demonstrated loss of MLH1 protein on immunohistochemistry and the other breast tumor demonstrated loss of heterozygosity (Lotsari 2012, Pedroni 2014). Lastly, the International Society for Gastrointestinal Hereditary Tumours Incorporated (InSiGHT) classifies this variant as pathogenic (Thompson 2014). Based on currently available evidence, we consider MLH1 c.1489dupC to be pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Dec 01, 2016	- -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Oct 17, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Sep 01, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 15, 2023	This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. -

Lynch syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	Mar 23, 2016	- -
Pathogenic, reviewed by expert panel	research	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Sep 05, 2013	Coding sequence variation resulting in a stop codon -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	May 31, 2023	The c.1489dup (p.Arg497Profs*6) variant of the MLH1 gene creates a frameshift resulting in a premature termination codon that is predicted to lead to absent or truncated protein product. This variant has been reported in multiple individuals (>20) affected with Lynch syndrome associated phenotypes including colorectal cancer, breast cancer, endometrial cancer, small bowel cancer, and hereditary nonpolyposis colorectal cancer (HNPCC) (PMID: 17199584, 15849733, 8872463, 27535758, 15765394, 23695190, 15926618). In addition, this variant has been found in breast ductal tumors demonstrating microsatellite instability and loss of MLH1 protein expression by immunohistochemistry (PMID: 22691310). In vitro yeast two-hybrid assay demonstrated that the predicted truncated protein failed to interact with PMS2 protein (PMID:?12810663). Loss of function variants of the MLH1 gene are known to be pathogenic (PMID: 14635101, 15942939, 16955466, 15713769, 24362816, 33468175). Truncating variants downstream of this variant are reported to be pathogenic in the literature (PMID: 8571956, 12810663, 15849733, 20459533) and by several ClinVar submitters (ClinVar ID: 89754, 89888, 89889, 439171). This variant is absent in the general population database (gnomAD) and classified as pathogenic by expert panel (ClinVar ID: 89753). Therefore, the c.1489dup (p.Arg497Profs*6) variant in the MLH1 gene is classified as pathogenic. -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

CZECANCA consortium

Jun 11, 2019

- -

Hereditary nonpolyposis colon cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Mar 26, 2019

Variant summary: MLH1 c.1489dupC (p.Arg497ProfsX6) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 277234 control chromosomes (gnomAD). c.1489dupC has been reported in the literature in multiple individuals affected with Lynch Syndrome (Kamiza_2015, Kurzawski_2006, Kondo_2003). These data indicate that the variant is very likely to be associated with disease. Experimental evidence evaluating an impact on protein function demonstrated that there was no interaction between the predicted truncated protein and PMS2 (Kondo_2003). Six ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Nov 28, 2023

This sequence change creates a premature translational stop signal (p.Arg497Profs*6) in the MLH1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MLH1 are known to be pathogenic (PMID: 15713769, 24362816). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Lynch syndrome or Lynch syndrome associated cancers (PMID: 1756143, 8872463, 12810663, 15849733, 15926618, 18566915, 21598002, 22691310, 23695190, 24323032, 26053027). ClinVar contains an entry for this variant (Variation ID: 89753). For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 07, 2021

The c.1489dupC pathogenic mutation, located in coding exon 13 of the MLH1 gene, results from a duplication of C at nucleotide position 1489, causing a translational frameshift with a predicted alternate stop codon (p.R497Pfs*6). This mutation has been reported in multiple studies of patients with Lynch syndrome, including those meeting Amsterdam criteria and/or with tumors demonstrating microsatellite instability or loss of MLH1 protein expression by IHC (Moslein G et al. Hum. Mol. Genet., 1996 Sep;5:1245-52; Mangold E et al. Int J Cancer, 2005 Sep;116:692-702; Papp J et al. World J Gastroenterol, 2007 May;13:2727-32; Kast K et al. Arch Gynecol Obstet, 2016 11;294:1299-1303). This mutation was also present in individuals from HNPCC families with Muir-Torre features (Mangold E et al. Br J Dermatol, 2007 Jan;156:158-62), small bowel cancer (Schulmann K et al. Gastroenterology, 2005 Mar;128:590-9), breast cancer (Lotsari JE et al. Breast Cancer Res., 2012 Jun;14:R90), and a neuroendocrine pancreatic tumor (Brieger A et al. Fam Cancer, 2011 Sep;10:591-5). Of note, this mutation is also designated as c.1489_1490insC and 495insC in published literature. In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

Endometrial carcinoma Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

CZECANCA consortium

Feb 21, 2023

- -

Lynch syndrome 1 Other:1

not provided, no classification provided

literature only

GeneReviews

-

- -

Computational scores

Source: dbNSFP v4.3

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: rs63750855; hg19: chr3-37070348;