chr3-37050632-CAA-C

Variant names:

• chr3-37050632-CAA-C
• rs267607901
• NM_000249.4:c.2252_2253delAA

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_Strong PM2 PP5_Very_Strong

The NM_000249.4(MLH1):​c.2252_2253delAA​(p.Lys751SerfsTer3) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,816 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★★).

• 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:11 O:1
• Conservation: PhyloP100: 9.00

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 14 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 4 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-37050632-CAA-C is Pathogenic according to our data. Variant chr3-37050632-CAA-C is described in ClinVar as [Pathogenic]. Clinvar id is 90101.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050632-CAA-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.2252_2253delAA	p.Lys751SerfsTer3	frameshift_variant	Exon 19 of 19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.2252_2253delAA	p.Lys751SerfsTer3	frameshift_variant	Exon 19 of 19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461816 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 727220

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:11 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:4

Mar 15, 2023

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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

Dec 10, 2015

Counsyl

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 12, 2018

Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This c.2252_2253delAA (p.Lys751Serfs*3) variant in the MLH1 gene has been reported in multiple individuals with Lynch syndrome (PMID 8797773, 24802709, 27295708, 28874130). Microsatellite instability (MSI) and protein expression studies in tumors from patients with this variant showed MSI-high mutator phenotype and loss of PMS2 expression (PMID 24802709). This variant is absent from large databases of genetic variation in the general population. Therefore, the c.2252_2253delAA (p.Lys751Serfs*3) variant in the MLH1 gene is classified as pathogenic. -

Dec 09, 2024

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PVS1,PP4_STR,PM2_SUP -

not provided Pathogenic:2

-

Mayo Clinic Laboratories, Mayo Clinic

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Jun 08, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Frameshift variant predicted to result in abnormal protein length as the last 6 amino acids are replaced with 2 different amino acids, and other similar variants have been reported in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 9559627, 18566915, 8797773, 24802709, 29238914, 27295708, 18931482, 15365995, 28874130, 26884312, 27978560, 29151953, 21642682, 25345868, 27606285, 31447099, 30787465, 12799449, 20533529, 22753075, 32782288) -

Lynch syndrome 1 Pathogenic:1 Other:1

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Oct 10, 2014

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: research

Multifactorial likelihood analysis posterior probability >0.99 -

Carcinoma of colon Pathogenic:1

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The MLH1 p.Lys751SerfsX3 variant was identified in 14 of 2728 proband chromosomes (frequency: 0.005) from individuals or families with colorectal cancer, and was not identified in 924 control chromosomes from healthy individuals (Borelli 2014, Han 1996, Nilbert 2009, Shin 2004). The variant was also identified in dbSNP (ID: rs267607907) as “With Pathogenic allele”, “Mismatch Repair Genes Variant Database”, InSiGHT Colon Cancer Gene Variant Database (LOVD), ClinVar database (classified as uncertain significance by InSight, pathogenic by Ambry genetics, likely pathogenic by Mayo clinic). The variant occurs outside of the splicing consensus sequence and 3 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. The c.2252_2253del variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 751 and leads to a premature stop codon 3 codons downstream. This alteration is then predicted to result in a truncated or absent protein and loss of function. Loss of function variants of the MLH1 gene are an established mechanism of disease in Lynch syndrome and this is the type of variant expected to cause the disorder. A study by Borelli (2014) identified 11 patients with colorectal cancer with this variant and showed the MSI-high mutator phenotype with loss of PMS2 expression in all but one tumor. There was also a statistically significant (p = 0.0057) higher frequency of pancreatic tumours compared to families with other MLH1 pathogenic variants. Moreover the clinical features, tissue analysis and co-segregation with disease strongly support the hypothesis that the MLH1 c.2252_2253delAA variant has a pathogenic effect. In addition, in an in silico model study the variant fell in the >99% probability range for known class 5 (pathogenic) variant (Joeri van der Velde 2015). The c-terminus of the MLH1 protein is known to be well conserved and important for PMS2 binding and DNA mismatch repair (Mohd 2006). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Muir-Torré syndrome;C1333991:Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Oct 03, 2016

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Sep 17, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Lys751Serfs*3) in the MLH1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 6 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 Lynch syndrome (PMID: 8797773, 18566915, 18931482, 24802709, 27295708). It is commonly reported in individuals of Italian ancestry (PMID: 24802709). Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this MLH1 variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 1,370,736 individuals referred to our laboratory for MLH1 testing. ClinVar contains an entry for this variant (Variation ID: 90101). RNA analysis performed to evaluate the impact of this premature translational stop signal on mRNA splicing indicates it does not significantly alter splicing (internal data). For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Sep 14, 2021

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2252_2253delAA pathogenic mutation, located in coding exon 19 of the MLH1 gene, results from a deletion of two nucleotides at nucleotide positions 2252 to 2253, causing a translational frameshift with a predicted alternate stop codon (p.K751Sfs*3). This mutation has been identified in numerous individuals with features of Lynch syndrome (Sheng JQ et al, Cytogenet. Genome Res. 2008 ; 122(1):22-7; Nilbert M et al, Fam. Cancer 2009 ; 8(1):75-83; Han HJ et al, J. Natl. Cancer Inst. 1996 Sep; 88(18):1317-9; Cajal AR et al. Medicina (B Aires), 2016;76:180-2). Borelli, et al. describes this as an Italian founder mutation and demonstrates that it segregates with disease in 11 families (10 meeting Amsterdam criteria) with a total of 24 MSI-H tumors (Borelli I et al, Fam. Cancer 2014 Sep; 13(3):401-13).This alteration is expected to result in loss of function by premature protein truncation. As such, this alteration is interpreted as a disease-causing mutation. -

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: rs267607901; hg19: chr3-37092123;