3-37007064-G-T

Variant names:

• chr3-37007064-G-T
• rs267607750
• NM_000249.4:c.453+1G>T

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1_Moderate PM2 PP5_Very_Strong

The NM_000249.4(MLH1):​c.453+1G>T variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 splice_donor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic reviewed by expert panel P:8
• Conservation: PhyloP100: 9.57
• Publications: 6 publications found

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]

MLH1 Gene-Disease associations (from GenCC):

• Lynch syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, ClinGen, Orphanet
• Lynch syndrome 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp
• Muir-Torre syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Ambry Genetics, G2P, Orphanet
• mismatch repair cancer syndrome 1

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
• Lynch syndrome 1

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• ovarian cancer

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• malignant pancreatic neoplasm

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• rhabdomyosarcoma

  Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
• prostate cancer

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• breast cancer

  Inheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics
• hereditary breast carcinoma

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.03214443 fraction of the gene. Cryptic splice site detected, with MaxEntScore 4.5, offset of 9, new splice context is: atgGTacat. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-37007064-G-T is Pathogenic according to our data. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37007064-G-T is described in CliVar as Likely_pathogenic. Clinvar id is 90223.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.453+1G>T		splice_donor_variant, intron_variant	Intron 5 of 18	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.453+1G>T		splice_donor_variant, intron_variant	Intron 5 of 18	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:8

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:3

Dec 13, 2016

Counsyl

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -

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 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. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 25085752]. -

Oct 20, 2022

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Lynch syndrome Pathogenic:2

Jun 21, 2019

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Likely pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

Interrupts canonical donor splice site -

Oct 10, 2014

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:1

Sep 18, 2018

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is denoted MLH1 c.453+1G>T or IVS5+1G>T and consists of a G>T nucleotide substitution at the +1 position of intron 5 of the MLH1 gene. The variant destroys a canonical splice donor site and is predicted to cause abnormal gene splicing, leading to either an abnormal message that is subject to nonsense-mediated mRNA decay or to an abnormal protein product. This variant has been reported in at least one individual who was reported to have colon, jejunum and renal cancer all under the age of 50 (Zhang 2015). We consider this variant to be likely pathogenic. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Oct 30, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change affects a donor splice site in intron 5 of the MLH1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and 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). Disruption of this splice site has been observed in individual(s) with Lynch syndrome-related cancer (PMID: 18931482, 23747338, 25892863, 26681312). ClinVar contains an entry for this variant (Variation ID: 90223). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Dec 23, 2024

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.453+1G>T intronic variant results from a G to T substitution one nucleotide after coding exon 5 of the MLH1 gene. This variant has been identified in a proband whose Lynch syndrome-associated tumor demonstrated low microsatellite instability and loss of MLH1/PMS2 expression by immunohistochemistry (Sheng JQ et al. Cytogenet. Genome Res. 2008 Oct;122:22-7; Zhang JX et al. World J. Gastroenterol., 2015 Apr;21:4136-49; de Voer RM et al. Gastroenterology, 2013 Sep;145:544-7). This alteration was also identified in 1/10030 consecutive patients referred for evaluation by an NGS hereditary cancer panel (Susswein LR et al. Genet Med, 2016 08;18:823-32). This variant has been identified in probands whose Lynch syndrome-associated tumor demonstrated high microsatellite instability and/or loss of PMS2 or MLH1/PMS2 expression by immunohistochemistry (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site; however, direct evidence is insufficient at this time (Ambry internal data). Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.43
CADD	Pathogenic	35
DANN	Uncertain	0.99
Eigen	Pathogenic	1.3
Eigen_PC	Pathogenic	1.2
FATHMM_MKL	Pathogenic	1.0	D
PhyloP100		9.6
GERP RS		6.2
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.94
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.23		Position offset: 8
DS_DL_spliceai		1.0		Position offset: -1

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

Other links and lift over

dbSNP: rs267607750; hg19: chr3-37048555;