rs63750693

chr3-37047652-T-Achr3-37047652-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.1865T>A(p.Leu622His) 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. L622P) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 31)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:5 O:1
• 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 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 16 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 chr3-37047652-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 89911.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.983
• PP5: Variant 3-37047652-T-A is Pathogenic according to our data. Variant chr3-37047652-T-A is described in ClinVar as [Pathogenic]. Clinvar id is 29657.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37047652-T-A is described in Lovd as [Pathogenic]. Variant chr3-37047652-T-A is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.1865T>A	p.Leu622His	missense_variant	16/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.1865T>A	p.Leu622His	missense_variant	16/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 10, 2021	The p.L622H pathogenic mutation (also known as c.1865T>A), located in coding exon 16 of the MLH1 gene, results from a T to A substitution at nucleotide position 1865. The leucine at codon 622 is replaced by histidine, an amino acid with similar properties. In one study, this mutation was detected in 12 Spanish families with Lynch-related tumors that demonstrated high microsatellite instability (MSI-H) and/or loss of MLH1 expression on immunohistochemistry (IHC), and met Amsterdam criteria. Haplotype analysis confirmed that all families carried the same ancestral allele, strongly supporting p.L622H as a founder mutation of Spanish origin (Borràs E et al. Cancer Res, 2010 Oct;70:7379-91). This alteration is identified in additional Spanish individuals whose Lynch-related tumors demonstrated MSI-H and/or loss of MLH1 expression on IHC, and family history met Amsterdam criteria (Godino J et al. Hum. Mutat., 2001 Dec;18:549; Pérez-Cabornero L et al. Cancer Prev Res (Phila), 2011 Oct;4:1546-55). Based on internal structural analysis using published crystal structures, L622H is more disruptive to the MLH1 C-terminal domain than nearby internally pathogenic variants (Wu H et al. Acta Crystallogr F Struct Biol Commun, 2015 Aug;71:981-5; Ambry internal data). In two functional studies, this alteration demonstrated proficient MMR activity and intermediate expression (Takahashi M et al. Cancer Res, 2007 May;67:4595-604; Hinrichsen I et al. Clin Cancer Res, 2013 May;19:2432-41); however, in another functional study, this alteration demonstrated reduced MMR activity and expression compared to wild-type MLH1 (González-Acosta M et al. J Mol Diagn, 2020 03;22:376-385). 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 supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Oct 18, 2022	This missense variant replaces leucine with histidine at codon 622 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have demonstrated that this variant results in reduced expression and stability of the MLH1 protein, but the mutant protein had sufficient mismatch repair activity compared to wild type (PMID: 17510385, 23403630). This variant has been reported in over 20 affected individuals from more than 10 different families with Lynch syndrome (PMID: 20858721, 21778331). This variant has been described as a Spanish founder mutation (PMID: 20858721), and it has been shown that this variant segregates with disease in multiple families (PMID: 20858721). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Oct 01, 2010

- -

Lynch syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

Multifactorial likelihood analysis posterior probability >0.99 -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jul 22, 2021

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Leu622 amino acid residue in MLH1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 1749856, 21404117; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this variant affects MLH1 protein function (PMID: 17210669, 17510385, 20533529, 20858721, 23403630, 30998989). 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: 29657). This variant has been observed in individual(s) with Lynch syndrome (PMID: 11748856, 20858721, 23523604). 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 leucine with histidine at codon 622 of the MLH1 protein (p.Leu622His). The leucine residue is highly conserved and there is a moderate physicochemical difference between leucine and histidine. -

Lynch syndrome 1 Other:1

not provided, no classification provided

literature only

GeneReviews

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.54
Cadd	Pathogenic	27
Dann	Uncertain	0.99
DEOGEN2	Pathogenic	0.95	D;.;.;.;.;.
Eigen	Uncertain	0.60
Eigen_PC	Uncertain	0.62
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Uncertain	0.86	D;D;.;.;.;D
M_CAP	Pathogenic	0.60	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D;D
MetaSVM	Pathogenic	0.97	D
MutationAssessor	Pathogenic	3.6	H;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D
PrimateAI	Pathogenic	0.81	D
PROVEAN	Pathogenic	-6.4	D;D;D;D;D;D
REVEL	Pathogenic	0.97
Sift	Pathogenic	0.0	D;D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D
Polyphen		1.0	D;.;.;.;.;.
Vest4		0.82
MutPred		0.91		Gain of disorder (P = 0.0461);.;.;.;.;.;
MVP		0.98
MPC		0.45
ClinPred		1.0	D
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.99
gMVP		0.94

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

Publications

LitVar

Other links and lift over

dbSNP: rs63750693; hg19: chr3-37089143;