3-37047553-C-A

Variant names:

• chr3-37047553-C-A
• rs63750016
• NM_000249.4:c.1766C>A

Variant summary

Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PM1 PM2 PP3_Strong PP5_Very_Strong

The NM_000249.4(MLH1):​c.1766C>A​(p.Ala589Asp) variant causes a missense 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. Variant has been reported in ClinVar as Likely pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A589S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:2
• Conservation: PhyloP100: 7.70
• Publications: 15 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 16 ACMG points.

• PM1: In a hotspot region, there are 10 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 39 uncertain in NM_000249.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.952
• PP5: Variant 3-37047553-C-A is Pathogenic according to our data. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047553-C-A is described in CliVar as Likely_pathogenic. Clinvar id is 89884.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.1766C>A	p.Ala589Asp	missense_variant	Exon 16 of 19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.1766C>A	p.Ala589Asp	missense_variant	Exon 16 of 19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

Alfa AF: 0.00000505 Hom.: 0

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Jul 21, 2023

Myriad Genetics, Inc.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 20020535, 31784484]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 16083711, 21404117]. This variant is expected to disrupt protein structure [Myriad internal data]. -

Lynch syndrome Pathogenic:1

Jun 21, 2019

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Likely pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

Abrogated function (reduced expression in 2 independent assays) & 2 MSI-H tumours -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.51	D
BayesDel_noAF	Pathogenic	0.50
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.93	D;.;.;.;.;.
Eigen	Uncertain	0.63
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Pathogenic	0.97	D;D;.;.;.;D
M_CAP	Pathogenic	0.39	D
MetaRNN	Pathogenic	0.95	D;D;D;D;D;D
MetaSVM	Uncertain	0.42	D
MutationAssessor	Pathogenic	3.6	H;.;.;.;.;.
PhyloP100		7.7
PrimateAI	Pathogenic	0.80	T
PROVEAN	Pathogenic	-5.0	D;D;D;D;D;D
REVEL	Pathogenic	0.92
Sift	Uncertain	0.0030	D;D;D;D;D;D
Sift4G	Uncertain	0.0060	D;D;D;D;D;D
Polyphen		1.0	D;.;.;.;.;.
Vest4		0.88
MutPred		0.81		Loss of sheet (P = 7e-04);.;.;.;.;.;
MVP		0.97
MPC		0.48
ClinPred		1.0	D
GERP RS		5.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.97
gMVP		0.95
Mutation Taster		=0/100	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: rs63750016; hg19: chr3-37089044;