rs267607791

Positions:

• chr3-37014545-G-GT

Variant summary

Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PVS1 PM2 PP3 PP5_Very_Strong

The ENST00000231790.8(MLH1):​c.790+1_790+2insT variant causes a splice donor, intron 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 ENST00000231790.8 splice_donor, intron
• Clinical Significance: Pathogenic reviewed by expert panel P:7
• Conservation: PhyloP100: 7.68

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 19 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP3: Multiple lines of computational evidence support a deleterious effect 2: max_spliceai, phyloP100way_vertebrate [when was below the threshold]
• PP5: Variant 3-37014545-G-GT is Pathogenic according to our data. Variant chr3-37014545-G-GT is described in ClinVar as [Pathogenic]. Clinvar id is 90361.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4	c.790+2dupT		splice_region_variant, intron_variant		ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.790+1_790+2insT		splice_donor_variant, intron_variant		1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 23

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 09, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Nov 29, 2024	The c.790+2dupT intronic pathogenic mutation, results from a duplication of two nucleotides at nucleotide position 790 after intron 9 of the MLH1 gene. This mutation has been demonstrated to result in exon 9 & exon 9,10 skipping and was identified in multiple probands whose tumors demonstrated loss of MLH1/PMS2 expression by immunohistochemistry and/or met Amsterdam I/II criteria for HNPCC/Lynch syndrome (Liu B et al. Nat. Med. 1996 Feb;2(2):169-74; Kohonen-Corish M et al. Am. J. Hum. Genet. 1996 Oct; 59(4):818-24; Young J et al. Pathology, 2002 Dec;34:529-33; Mangold E et al. Int. J. Cancer 2005 Sep; 116(5):692-702; Southey MC et al. J. Clin. Oncol., 2005 Sep;23:6524-32; Walsh MD et al. Mod. Pathol. 2012 May; 25(5):722-30; Jenkins MA et al. Clin. Gastroenterol. Hepatol., 2006 Apr;4:489-98; Arnold S et al. Hum. Mutat., 2009 May;30:757-70; Ambry internal data). Of note, this alteration is also designated as c.790+2_+3insT, IVS9+2_+3insT, and IVS9+3insT in published literature. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. 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. -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Jul 19, 2023

This variant is considered pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. Functional studies indicate this variant impacts protein function [PMID: 11781295, 8574961]. -

Hereditary nonpolyposis colon cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Dec 06, 2022

Variant summary: MLH1 c.790+2dupT alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Four of four computational tools predict a significant impact on normal splicing, predicting the variant abolishes the canonical 5' splicing donor site. At least two publications report experimental evidence that this variant indeed affects mRNA splicing, producing transcripts skipping exon 9 or both exons 9 and 10 (e.g. Kohonen-Corish_1996, Arnold_2009). The variant was absent in 249450 control chromosomes (gnomAD). c.790+2dupT has been reported in the literature in multiple individuals affected with Hereditary Nonpolyposis Colorectal Cancer, including individuals with tumors with high microsatellite instability and lacking MLH-1 expression, and cosegregation with disease in at least one family who met Amsterdam criteria (e.g. Kohonen-Corish_1996, Liu_1996, Arnold_2009). These data indicate that the variant is very likely to be associated with disease. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Lynch syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

Variant causes splicing aberration interrupting protein function: full inactivation of variant allele. Multifactorial likelihood analysis posterior probability >0.99. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Clinical Genetics Laboratory, Skane University Hospital Lund

May 27, 2022

- -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 08, 2022

This variant is also known as c.790+2_790+3insT and IVS9+_x0001_3insT. For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exons 9-10, but is expected to preserve the integrity of the reading-frame (PMID: 8574961, 8808596, 19267393). Based on a multifactorial likelihood algorithm using genetic, in silico, and/or statistical data, this variant has been determined to have a high probability of being pathogenic (PMID: 22949379). ClinVar contains an entry for this variant (Variation ID: 90361). This variant has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 8574961, 8808596, 15849733, 16616355, 22322191). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 9 of the MLH1 gene. It does not directly change the encoded amino acid sequence of the MLH1 protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.87		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.87		Position offset: -1

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

Publications

LitVar

Other links and lift over

dbSNP: rs267607791; hg19: chr3-37056036;