3-37050632-CAA-CAAAA

Position:

• chr3-37050632-CAA-CAAAA

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2 PM4 PP5_Strong

The NM_000249.4(MLH1):​c.2252_2253dup​(p.Val752LysfsTer32) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★★★). Synonymous variant affecting the same amino acid position (i.e. Y750Y) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 frameshift
• Clinical Significance: Uncertain significance reviewed by expert panel P:5 U: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 Likely_pathogenic. Variant got 8 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Frameshift in the end of transcript resulting in stoplost. Downstream stopcodon found after 762 codons.
• PP5: Variant 3-37050632-C-CAA is Pathogenic according to our data. Variant chr3-37050632-C-CAA is described in ClinVar as [Uncertain_significance]. Clinvar id is 90102.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=3, Pathogenic=2, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.2252_2253dup	p.Val752LysfsTer32	frameshift_variant	19/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.2252_2253dup	p.Val752LysfsTer32	frameshift_variant	19/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:5 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 17, 2023	The c.2252_2253dupAA variant, located in coding exon 19 of the MLH1 gene, results from a duplication of AA at nucleotide positions 2252 and 2253, causing a translational frameshift with a predicted alternate stop codon (p.Val752Lysfs*32). This alteration occurs only five amino acids prior to the normal termination codon, and is predicted to elongate MLH1 by 26 amino acids. This variant has been identified in HNPCC patients who fulfilled Bethesda and/or Amsterdam II guidelines with tumor analysis revealing MSI-H and loss of MLH1 and/or PMS2 by IHC (Pistorius SR et al. Int J Colorectal Dis. 2000 Nov;15(5-6):255-63; Sheng JQ et al. Cytogenet. Genome Res. 2008;122(1):22-7; Wolf B et al. Wien. Klin. Wochenschr. 2005 Apr;117(7-8):269-77; Mangold E et al. Int. J. Cancer. 2005 Sep;116(5):692-702; Fu L et al. Cell Oncol (Dordr). 2013 Jun;36:225-31; Rossi BM et al. BMC Cancer. 2017 Sep;17:623; Ambry internal data). Structural analysis shows that this alteration perturbs a known functional domain responsible for binding to PMS2 and removes a cysteine residue shown to be involved in metal binding as part of a functional domain in PMS2 (Mohd AB et al. DNA Repair (Amst.) 2006 Mar;5(3):347-61; Smith CE et al. PLoS Genet. 2013 Oct;9(10):e1003869). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jun 28, 2019	This variant inserts 2 nucleotides in exon 19 of the MLH1 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has been reported in multiple hereditary nonpolyposis colorectal cancer (HNPCC) families (PMID: 15849733, 15926618, 18931482). This variant has been reported to segregate with disease (InSiGHT database; http://insight-database.org/classifications/index.html?gene=MLH1&variant=c.2252_2253dup). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Feb 25, 2021

- -

Hereditary nonpolyposis colon cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Jan 23, 2023

Variant summary: MLH1 c.2252_2253dupAA (p.Val752LysfsX32) causes a frameshift which results in an extension of the protein in the carboxy terminal homology domain (Sui_2019). The variant was absent in 251302 control chromosomes. c.2252_2253dupAA has been reported in the literature in multiple individuals affected with Hereditary Nonpolyposis Colorectal Cancer (Dominguez-Valentin_2013, Sheng_2008, Mangold_2005, Wolf_2005, Sui_2019). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four (other) submitters including an expert panel have provided clinical-significance assessments for this variant to ClinVar after 2014, and classified it as pathogenic/likely pathogenic (n=3) or VUS (n=1). 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

Sep 21, 2022

For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the MLH1 protein in which other variant(s) (p.*757Leuext*33) have been determined to be pathogenic (PMID: 8128251, 9697702, 12810663, 14985405). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 90102). This variant is also known as Ins AA at 2254 or c.2253_2254insAA. This variant has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 11151427, 15849733, 15926618, 18931482, 23640085, 24344984). This variant is not present in population databases (gnomAD no frequency). This sequence change results in a frameshift in the MLH1 gene (p.Val752Lysfs*32). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 5 amino acid(s) of the MLH1 protein. -

Lynch syndrome Uncertain:1

Uncertain significance, reviewed by expert panel

curation

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Jun 21, 2019

Insufficient evidence: extends protein by 26 amino acids -

Computational scores

Source: dbNSFP v4.3

Splicing

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;