chr3-37050532-AAC-A

Variant names:

• chr3-37050532-AAC-A
• rs63750971
• NM_000249.4:c.2154_2155delCA

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000249.4(MLH1):​c.2154_2155delCA​(p.Ile719CysfsTer3) 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 Pathogenic (★★★). Synonymous variant affecting the same amino acid position (i.e. H718H) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 frameshift
• Clinical Significance: Pathogenic reviewed by expert panel P:3
• Conservation: PhyloP100: 7.72
• 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 18 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 83 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-37050532-AAC-A is Pathogenic according to our data. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37050532-AAC-A is described in CliVar as Pathogenic. Clinvar id is 90072.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.2154_2155delCA	p.Ile719CysfsTer3	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.2154_2155delCA	p.Ile719CysfsTer3	frameshift_variant	Exon 19 of 19	1	NM_000249.4	ENSP00000231790.3

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:3

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Jul 25, 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. -

Lynch syndrome Pathogenic:1

Sep 05, 2013

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: research

Coding sequence variation resulting in a stop codon with functional domain -

Hereditary cancer-predisposing syndrome Pathogenic:1

Mar 27, 2020

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2154_2155delCA pathogenic mutation, located in coding exon 19 of the MLH1 gene, results from a deletion of two nucleotides at nucleotide positions 2154 to 2155, causing a translational frameshift with a predicted alternate stop codon (p.I719Cfs*3). This variant has been reported in one Portuguese family meeting Amsterdam I criteria and in an individual diagnosed with MSI-H colorectal cancer showing loss of MLH1 on immunohistochemistry and having a family history of colorectal cancer (Isidro G et al. Hum. Mutat., 2003 Nov;22:419-20; Bonnet D et al. Dig Liver Dis, 2012 Jun;44:515-22).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

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.7
Mutation Taster		=0/200	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs63750971; hg19: chr3-37092023;