3-37040276-T-C

Position:

• chr3-37040276-T-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.1649T>C​(p.Leu550Pro) 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 Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L550V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:4
• Conservation: PhyloP100: 7.81

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 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 15 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 chr3-37040276-T-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1777213.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.974
• PP5: Variant 3-37040276-T-C is Pathogenic according to our data. Variant chr3-37040276-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 89818.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37040276-T-C is described in Lovd as [Pathogenic]. Variant chr3-37040276-T-C is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.1649T>C	p.Leu550Pro	missense_variant	14/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.1649T>C	p.Leu550Pro	missense_variant	14/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Jul 21, 2023

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

Lynch syndrome 1 Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Nov 03, 2016

Segregation LR = 12.25. Abrogated function (reduced expression in 2 inpedendent assays) & 2 MSI-H tumours -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 17, 2022

ClinVar contains an entry for this variant (Variation ID: 89818). 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 missense change affects MLH1 function (PMID: 16083711, 18999873, 20020535, 21120944, 21404117, 22753075, 31784484). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MLH1 protein function. This missense change has been observed in individuals with clinical features of Lynch syndrome (PMID: 16083711, 16216036, 21404117, 32658311; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 550 of the MLH1 protein (p.Leu550Pro). -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 11, 2020

The p.L550P pathogenic mutation (also known as c.1649T>C), located in coding exon 14 of the MLH1 gene, results from a T to C substitution at nucleotide position 1649. The leucine at codon 550 is replaced by proline, an amino acid with similar properties. This alteration has been observed in multiple individuals whose colorectal tumors demonstrated high microsatellite instability and loss of MLH1 expression on immunohistochemistry (IHC), and have family histories consistent with Lynch syndrome (Ambry internal data; Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49; Drost M et al. Hum. Mutat. 2010 Mar;31:247-53; Kansikas M et al. Hum. Mutat. 2011 Jan;32:107-15; Hardt K et al. Fam. Cancer. 2011 Jun;10:273-84). This variant co-segregated with disease in one family tested in our laboratory (Ambry internal data). In multiple functional studies, this alteration has been shown to result in reduced MMR activity, reduced protein expression, and deficient interaction with PMS2 (Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49; Drost M et al. Hum. Mutat. 2010 Mar;31:247-53; Kansikas M et al. Hum. Mutat. 2011 Jan;32:107-15; Hardt K et al. Fam. Cancer. 2011 Jun;10:273-84; Andersen SD et al. Hum. Mutat. 2012 Dec;33:1647-55). This variant was not reported in population-based 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 supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.45	D
BayesDel_noAF	Pathogenic	0.41
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.90	D;.;.;.;.;.;D
Eigen	Benign	0.075
Eigen_PC	Benign	0.075
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.95	D;D;.;.;.;D;D
M_CAP	Uncertain	0.22	D
MetaRNN	Pathogenic	0.97	D;D;D;D;D;D;D
MetaSVM	Benign	-0.34	T
MutationAssessor	Uncertain	2.6	M;.;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D
PrimateAI	Pathogenic	0.86	D
PROVEAN	Uncertain	-4.1	D;D;D;D;D;D;D
REVEL	Pathogenic	0.78
Sift	Benign	0.039	D;D;D;D;D;D;D
Sift4G	Uncertain	0.059	T;D;D;D;D;T;D
Polyphen		1.0	D;.;.;.;.;.;.
Vest4		0.96
MutPred		0.95		Loss of stability (P = 0.0036);.;.;.;.;.;.;
MVP		1.0
MPC		0.49
ClinPred		0.98	D
GERP RS		4.6
Varity_R		0.98
gMVP		0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs63750193; hg19: chr3-37081767;