3-37017509-G-C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000249.4(MLH1):c.794G>C(p.Arg265Pro) 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. R265C) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:5 U:1
• Conservation: PhyloP100: 9.59

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 18 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 17 uncertain in NM_000249.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-37017508-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 29654.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.986
• PP5: Variant 3-37017509-G-C is Pathogenic according to our data. Variant chr3-37017509-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 433856.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37017509-G-C is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.794G>C	p.Arg265Pro	missense_variant	10/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.794G>C	p.Arg265Pro	missense_variant	10/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:5 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:1 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Feb 06, 2024	- -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	- -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Jul 18, 2023

This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 19423266]. Functional studies indicate this variant impacts protein function [PMID: 29520894]. This variant is expected to disrupt protein structure [Myriad internal data]. -

Lynch syndrome 1 Pathogenic:1

Likely pathogenic, reviewed by expert panel

curation

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Jun 13, 2018

Multifactorial likelihood analysis posterior probability > 0.95 (0.969) -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Invitae

Oct 25, 2021

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. Experimental studies have shown that this variant affects MLH1 function (PMID: 29520894). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt MLH1 protein function. ClinVar contains an entry for this variant (Variation ID: 433856). This variant has been observed in individual(s) with Lynch syndrome (PMID: 19423266). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with proline at codon 265 of the MLH1 protein (p.Arg265Pro). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and proline. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 17, 2023

The p.R265P variant (also known as c.794G>C), located in coding exon 10 of the MLH1 gene, results from a G to C substitution at nucleotide position 794. The arginine at codon 265 is replaced by proline, an amino acid with dissimilar properties. This variant was detected in an individual with microsatellite high (MSI-H) colorectal cancer at age 57 who was also diagnosed with synchronous pancreatic cancer and MSI-H sebaceous carcinoma. All three tumors showed absence of the MLH1 protein (Tanyi et al. Eur J Surg Oncol. 2009 Oct; 35 (10): 1128-30; Tanyi et al. Eur J Surg Oncol. 2014 Nov; 40(11):1445-52). This variant was reported in a female patient diagnosed with an endometrioid tumor at age 52 which demonstrated loss of both the MLH1, PMS2 proteins, but MLH1 promoter hypermethylation was also present (Post CCB et al. J Natl Cancer Inst, 2021 Sep;113:1212-1220). This alteration was identified in 1 of 1923 Chinese patients with a personal history of colorectal cancer (Yao J et al. Cancer Biol Med, 2022 Jan;19:707-32). This variant has also been reported in early-onset colorectal cancer cases with diagnoses occurring in the second decade of life (Yang M et al. Ther Adv Med Oncol, 2021 Jun;13:17588359211023290; González-Acosta M et al. J Med Genet, 2020 Apr;57:269-273). In another report, this variant was identified in a male proband diagnosed with colorectal cancer at age 59 which demonstrated microsatellite instability along with loss of both MLH1, PMS2 proteins and two somatic events were also reportedly identified (Guillerm E et al. Eur J Hum Genet, 2020 Nov;28:1624-1628). This variant has also been identified in families meeting Amsterdam I/II criteria for Lynch syndrome (Tanyi et al. Eur J Surg Oncol. 2009 Oct; 35 (10): 1128-30; Tanyi et al. Eur J Surg Oncol. 2014 Nov; 40(11):1445-52; Rossi BM et al. BMC Cancer, 2017 Sep;17:623; Álvarez K et al. J Clin Med, 2020 Jun;9; Ambry internal data). Based on internal structural analysis, R265P is deleterious due to being moderately destabilizing to the local structure (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.60
Cadd	Pathogenic	33
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.90	D;.;.;.;.;.;.
Eigen	Pathogenic	0.83
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Pathogenic	0.99	D;D;.;.;.;D;D
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D;D
MetaSVM	Uncertain	0.79	D
MutationAssessor	Pathogenic	4.8	H;.;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D
PrimateAI	Uncertain	0.69	T
PROVEAN	Pathogenic	-6.7	D;D;D;D;D;D;D
REVEL	Pathogenic	0.98
Sift	Pathogenic	0.0	D;D;D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D
Polyphen		1.0	D;.;.;.;.;.;.
Vest4		0.99
MutPred		0.91		Loss of catalytic residue at R265 (P = 0.0323);.;.;.;.;.;.;
MVP		0.99
MPC		0.48
ClinPred		1.0	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.98
gMVP		0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs63751448; hg19: chr3-37059000;