rs587778964

Positions:

• chr3-37048604-A-C
• chr3-37048604-A-G
• chr3-37048604-A-T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2 PP3_Moderate PP5_Very_Strong

The NM_000249.4(MLH1):​c.1984A>C​(p.Thr662Pro) 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 (★★★). Synonymous variant affecting the same amino acid position (i.e. TE662?) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 31)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:5 U:1
• Conservation: PhyloP100: 8.88

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 12 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.877
• PP5: Variant 3-37048604-A-C is Pathogenic according to our data. Variant chr3-37048604-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 89968.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37048604-A-C is described in Lovd as [Likely_pathogenic]. Variant chr3-37048604-A-C is described in Lovd as [Pathogenic]. Variant chr3-37048604-A-C is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4	c.1984A>C	p.Thr662Pro	missense_variant	17/19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.1984A>C	p.Thr662Pro	missense_variant	17/19	1	NM_000249.4	ENSP00000231790	P1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 31

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:5 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 24, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Jul 25, 2023	This variant is considered likely pathogenic. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 27363726]. -

Lynch syndrome Pathogenic:1

Likely pathogenic, reviewed by expert panel

curation

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Jun 21, 2019

Abrogated function (2 independent assays with reduced expression) & 6 MSI-H tumours -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 16, 2023

This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 662 of the MLH1 protein (p.Thr662Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Lynch syndrome (PMID: 11726306, 11754112, 16341550, 19621678, 21404117). ClinVar contains an entry for this variant (Variation ID: 89968). 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 not expected to disrupt MLH1 protein function with a negative predictive value of 95%. Experimental studies have shown that this missense change affects MLH1 function (PMID: 17510385, 20533529, 23403630, 31332305). 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. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 01, 2020

The p.T662P variant (also known as c.1984A>C), located in coding exon 17 of the MLH1 gene, results from an A to C substitution at nucleotide position 1984. The threonine at codon 662 is replaced by proline, an amino acid with highly similar properties. This variant was reported in four individuals from four different families who met Bethesda guidelines. Furthermore, tumor analysis revealed MSI-H in all four individuals and IHC revealed three individuals had loss of MLH1 as well as PMS2 and one individual had loss of MLH1 (Hardt K et al., Fam. Cancer 2011 Jun; 10(2):273-84). This variant has also been reported in families meeting Amsterdam criteria (Müller-Koch Y et al. Eur. J. Med. Res., 2001 Nov;6:473-82; Krüger S et al. Hum. Mutat., 2002 Jan;19:82). Additional studies combining family history, segregation with disease, functional analyses, and/or in silico predictions have also demonstrated that this alteration is likely pathogenic (Thompson BA et al., Nat. Genet. 2014 Feb; 46(2):107-15). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Dec 11, 2018

Variant summary: The variant, MLH1 c.1984A>C (p.Thr662Pro) results in a non-conservative amino acid change located in the DNA mismatch repair protein Mlh1, C-terminal domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. In vitro/vivo studies have shown that this variant results in a partial deletion of exon 17, reduces interaction with PMS2, and significantly reduces protein expression (Pagenstecher_2006, Kosinski_2010, Hinrichsen_2013). The variant, when expressed from cDNA, has been shown not to have a significant reduction in MMR activity by multiple studies, however, the MMR proficiency of the partial deletion of exon 17 caused by the variant was not addressed (Takahashi_2007, Hinrichsen_2013). The variant was absent in 276836 control chromosomes (gnomAD and publications) and has been reported in the literature in individuals affected with Lynch Syndrome (Hardt_2011, Pagenstecher_2006, Kruger_2001, Takahashi_2007). These data indicate that the variant is likely to be associated with disease. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified this variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as VUS possibly pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.86
BayesDel_addAF	Pathogenic	0.48	D
BayesDel_noAF	Pathogenic	0.45
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.72	D;.;.;.;.;.
Eigen	Uncertain	0.48
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.94	D;D;.;.;.;D
M_CAP	Uncertain	0.27	D
MetaRNN	Pathogenic	0.88	D;D;D;D;D;D
MetaSVM	Pathogenic	0.80	D
MutationAssessor	Benign	1.4	L;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D
PrimateAI	Uncertain	0.68	T
PROVEAN	Uncertain	-2.8	D;D;D;D;D;D
REVEL	Pathogenic	0.91
Sift	Uncertain	0.019	D;D;D;D;D;D
Sift4G	Uncertain	0.050	T;D;D;D;D;D
Polyphen		0.070	B;.;.;.;.;.
Vest4		0.87
MutPred		0.78		Loss of sheet (P = 0.0011);.;.;.;.;.;
MVP		0.99
MPC		0.16
ClinPred		0.94	D
GERP RS		5.5
Varity_R		0.90
gMVP		0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs587778964; hg19: chr3-37090095;