rs63751642

Positions:

• chr3-37000955-AAAG-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2 PM4_Supporting PP3 PP5_Very_Strong

The NM_000249.4(MLH1):​c.213_215del​(p.Glu71del) variant causes a inframe deletion, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 inframe_deletion, splice_region
• Clinical Significance: Pathogenic reviewed by expert panel P:8
• Conservation: PhyloP100: 9.42

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 12 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_000249.4. Strenght limited to Supporting due to length of the change: 1aa.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 3-37000955-AAAG-A is Pathogenic according to our data. Variant chr3-37000955-AAAG-A is described in ClinVar as [Pathogenic]. Clinvar id is 90067.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37000955-AAAG-A is described in Lovd as [Pathogenic]. Variant chr3-37000955-AAAG-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4	c.213_215del	p.Glu71del	inframe_deletion, splice_region_variant	3/19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.213_215del	p.Glu71del	inframe_deletion, splice_region_variant	3/19	1	NM_000249.4	ENSP00000231790	P1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Feb 01, 2006	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Aug 20, 2023	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 14, 2022	In-frame deletion of one amino acid in a non-repeat region; Observed in several individuals with personal or family history consistent with Lynch syndrome (Overbeek 2007, Chong 2009, Shigeyasu 2014, Yang 2021); Published functional studies demonstrate a damaging effect: decreased MLH1 protein expression and interaction with PMS2 as well as defective mismatch repair activity in vitro (Raevaara 2002, Raevaara 2005); RT-PCR and mRNA-based assays have found this variant causes skipping of exon 3 due to disruption of an exonic splice enhancer (McVety 2006, Shigeyasu 2014); In silico analysis supports a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Also known as c.209_211delAAG or c.211_213delGAA; This variant is associated with the following publications: (PMID: 17453009, 19459153, 27829276, 23896635, 21120944, 18561205, 17594722, 16216036, 25504677, 24362816, 22753075, 34178123, 12362032, 16083711, 15923275) -
Pathogenic, no assertion criteria provided	research	Mayo Clinic Laboratories, Mayo Clinic	-	- -

See cases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University Hospital Muenster

Dec 12, 2021

ACMG categories: PS3,PM1,PM2,PM4,PP4,PP5 -

Lynch syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

Variant allele causes in-frame splicing aberration interrupting ATPase domain: full inactivation of variant allele -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 27, 2023

This variant, c.213_215del, results in the deletion of 1 amino acid(s) of the MLH1 protein (p.Glu71del), but otherwise preserves the integrity of the reading frame. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. Studies have shown that this variant results in skipping of exon 3, but is expected to preserve the integrity of the reading-frame (PMID: 15923275, 18561205, 23896635). Experimental studies have shown that this variant affects MLH1 function (PMID: 12362032, 16083711). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 90067). This variant is also known as 71del and c.209_211delAAG in the literature. This variant has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 12362032, 16216036, 17453009, 19459153, 23896635). It has also been observed to segregate with disease in related individuals. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 20, 2021

The c.213_215delAGA pathogenic mutation (also known as p.E71del) is located in coding exon 3 of the MLH1 gene. This pathogenic mutation results from an in-frame AGA deletion of three nucleotides between nucleotide positions 213 and 215, resulting in the in frame deletion of one amino acid (glutamate) at codon 71. This mutation has been reported in numerous individuals with Lynch syndrome (Chong G et al, Hum. Mutat. 2009 Aug; 30(8):E797-812; Kansikas M et al, Hum. Mutat. 2011 Jan; 32(1):107-15; McVety S et al, J. Med. Genet. 2006 Feb; 43(2):153-6; Mangold E et al, J. Pathol. 2005 Dec; 207(4):385-95; Overbeek LI et al, Br. J. Cancer 2007 May; 96(10):1605-12; Raevaara TE et al, Gastroenterology 2005 Aug; 129(2):537-49). cDNA sequencing indicated that this alteration causes exon 3 skipping during mRNA splicing, suggesting the presence of an exon splicing enhancer (ESE) at the 5' end of exon 3, and inclusion of exon 3 in the mRNA is ESE dependent (McVety S et al. J Med Genet. 2006 Feb;43(2):153-6). Further, multiple functional analyses of this mutation have shown significantly reduced DNA repair efficiency compared to wild type (Raevaara et al. J Med Genet. 2002 Oct;39(10):747-50; Raevaara et al. Gastroenterology. 2005 Aug;129(2):537-49; Ou et al. Hum Mutat. 2007 Nov;28(11):1047-54; Kansikas et al. Hum Mutat. 2011 Jan;32(1):107-15). Of note, this alteration is also designated as c.209_211delAAG and c.211_213delGAA in published literature. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.54		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.54		Position offset: 0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs63751642; hg19: chr3-37042446;