rs63750641

chr3-37000997-A-Gchr3-37000997-A-T

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.250A>G(p.Lys84Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,670 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. K84N) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:7
• Conservation: PhyloP100: 8.79

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 4 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 chr3-37000999-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2034168.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.988
• PP5: Variant 3-37000997-A-G is Pathogenic according to our data. Variant chr3-37000997-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 90120.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37000997-A-G is described in Lovd as [Likely_pathogenic]. Variant chr3-37000997-A-G is described in Lovd as [Pathogenic]. Variant chr3-37000997-A-G is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.250A>G	p.Lys84Glu	missense_variant	3/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.250A>G	p.Lys84Glu	missense_variant	3/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1459670 Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1 AN XY: 726324

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:7

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Feb 14, 2017	- -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Jul 12, 2023

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 16083711]. -

Carcinoma of colon Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The p.Lys84Glu variant has been reported in the literature in 5 out of 2140 proband chromosomes (frequency of 0.002) from patients with HNPCC; the variant was not reported in any of at least 600 control chromosomes, increasing the likelihood this variant may be a low frequency variant with clinical significance (Ellison 2004, Raevaara 2005, Takahashi 2007, Wanat 2007, Lamberti 1999, Ou 2007, Quaresima 2003, Martinez 2010, Tang 2009, Overbeek 2007). The p.Lys84 residue is conserved across mammals and lower species and computational analyses (PolyPhen2, SIFT, AlignGVGD) suggest that the p.Lys84Glu variant may impact the protein. However, this information is not predictive enough to assume pathogenicity. It is listed in the dbSNP database as coming from a "clinical source" (ID#: rs63750641) but no frequency information was provided so this was not informative for assessing the population frequency. Functional assays using site-directed mutagenesis and in vitro mismatch repair (MMR) assays found the p.Lys84Glu variant to be deficient in MMR function, increasing the likelihood that an alteration to this residue might have clinical significance (Ellison 2004, Raevaara 2005, Takahashi 2007, Wanat 2007, Quaresima 2003). In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time, although we would lean towards a more pathogenic role for this variant. This variant is classified as Predicted Pathogenic. -

Lynch syndrome Pathogenic:1

Likely pathogenic, reviewed by expert panel

curation

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Jun 21, 2019

Abrogated function & >2 MSI-H tumours -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jun 26, 2022

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. This variant is not present in population databases (gnomAD no frequency). Experimental studies have shown that this missense change affects MLH1 function (PMID: 12513688, 15475387, 16083711, 17510385, 21404117, 23403630, 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) performed at Invitae indicates that this missense variant is expected to disrupt MLH1 protein function. ClinVar contains an entry for this variant (Variation ID: 90120). This missense change has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 10323887, 17453009, 19419416, 21404117, 26053027). This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 84 of the MLH1 protein (p.Lys84Glu). -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 05, 2022

The p.K84E variant (also known as c.250A>G), located in coding exon 3 of the MLH1 gene, results from an A to G substitution at nucleotide position 250. The lysine at codon 84 is replaced by glutamic acid, an amino acid with similar properties. This alteration was detected in 1 of 93 unrelated families from Taiwan who met Amsterdam Criteria II for a clinical diagnosis of Lynch syndrome (Tang R et al. Clin Genet. 2009 Apr;75(4):334-45). This variant was also detected in an individual whose tumor exhibited high microsatellite instability (Lamberti et al. Gut. 1999 Jun; 44(6): 839-43). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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	0.53	D
BayesDel_noAF	Pathogenic	0.52
Cadd	Pathogenic	30
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.96	D
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	1.0	D
M_CAP	Pathogenic	0.33	D
MetaRNN	Pathogenic	0.99	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	5.0	H
MutationTaster	Benign	1.0	D;D;D;D;D;D
PrimateAI	Uncertain	0.73	T
PROVEAN	Uncertain	-3.7	D
REVEL	Pathogenic	0.95
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		1.0	D
Vest4		0.95
MutPred		0.92		Loss of ubiquitination at K84 (P = 0.0161);
MVP		0.99
MPC		0.47
ClinPred		1.0	D
GERP RS		5.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.96
gMVP		0.95

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: rs63750641; hg19: chr3-37042488;