3-37048952-T-C

Variant names:

• chr3-37048952-T-C
• rs63750809
• NM_000249.4:c.2038T>C

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_000249.4(MLH1):​c.2038T>C​(p.Cys680Arg) variant causes a missense change involving the alteration of a non-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. C680G) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:7
• Conservation: PhyloP100: 3.08

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 14 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-37048952-T-G is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.939
• PP5: Variant 3-37048952-T-C is Pathogenic according to our data. Variant chr3-37048952-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 90006.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37048952-T-C is described in Lovd as [Likely_pathogenic]. Variant chr3-37048952-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.2038T>C	p.Cys680Arg	missense_variant	Exon 18 of 19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.2038T>C	p.Cys680Arg	missense_variant	Exon 18 of 19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:7

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:2

Apr 12, 2022

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 25, 2023

Myriad Genetics, Inc.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 25077178]. This variant is expected to disrupt protein structure [Myriad internal data]. -

Lynch syndrome Pathogenic:2

Jun 21, 2019

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Likely pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

Multifactorial likelihood analysis posterior probability 0.95-0.99 -

Jan 08, 2016

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: The c.2038T>C variant affects a conserved nucleotide, resulting in amino acid change from Cys to Arg. Protein studies confirmed that p.Cys680 resides in a tight hydrophobic cavity and that the p.Cys680Arg mutation disrupts the folding of the C-terminal domain of MLH1 (Bell_2013_abstract). Thus, this missense change may not be tolerated. 3/4 in-silico tools used predict this variant to be damaging. This variant is found exclusively in South Asian population (12/16476 control chromosomes) at a frequency of 0.000728, which is in the similar range with that of the maximal expected frequency of a pathogenic allele (0.0007105) in this gene based on the estimated population prevalence of LS (1/440). The prevalence of LS in South Asian population is not known. From peer-reviewed publications, this variant has been reported in two LS families from different ethnic populations (Sheng_2008, Dominguez-Valentin_2014). Additonally, one conference abstract reported that this variant cosegregated in 12 patients from 2 LS families (Bell_2013). One functional study (Dominguez-Valentin_2014) used yeast two-hybrid and cell-free mismatch repair assays to show that p.Cys680Arg not only affects the formation of MutLalfa complex but also the MMR activity -- a strong data for a pathogenic outcome. With patient and functional data in favor of pathogenicity, the frequency data of this variant in South Asian population alone is not sufficient to rule out pathogenicity in the same or other populations. In addition, multiple reputable databases have classified this variant as likely pathogenic/pathogenic. Taken together, this variant has currently been classified as Likely Pathogenic. -

Carcinoma of colon Pathogenic:1

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The p.Cys680Arg variant has been previously reported in the literature in one of 76 probands with HNPCC and this individual was MSI high. This report also suggests an affected brother was a carrier and that the variant was not identified in 200 control chromosomes (Sheng_2008_18931482). In addition, this variant has been previously identified by our lab. In two families this variant segregated with disease in a total of 12 individuals and 3 had an MLH1 deficient tumour. In addition, another variant at the same position, p.Cys680Gly, has been observed in one family from India with MSI-High status and multiple Lynch related cancers, suggesting this residue is important for normal protein function (Rajkumar, 2004). In summary, based on the above information, this variant is classified as pathogenic. Well conserved in mammals but not lower organisms and in-silico studies disagree on the classification of this variant. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Dec 24, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces cysteine, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 680 of the MLH1 protein (p.Cys680Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Lynch syndrome (PMID: 18931482, 23729658, 25077178, 27601186). ClinVar contains an entry for this variant (Variation ID: 90006). Invitae Evidence Modeling incorporating data from in vitro experimental studies (internal data) indicates that this missense variant is expected to disrupt MLH1 function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects MLH1 function (PMID: 25077178). For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Oct 25, 2019

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.C680R pathogenic mutation (also known as c.2038T>C), located in coding exon 18 of the MLH1 gene, results from a T to C substitution at nucleotide position 2038. The cysteine at codon 680 is replaced by arginine, an amino acid with highly dissimilar properties. This alteration has been identified in a cohort of Swedish Lynch syndrome families (Lagerstedt-Robinson K et al. Oncol. Rep. 2016 Nov;36:2823-2835), and in one Chinese family diagnosed with Lynch syndrome (Sheng JQ et al. Cytogenet. Genome Res. 2008;122(1):22-7). Another study identified this alteration in an individual with four Lynch syndrome-associated tumors; all of which showed microsatellite instability and loss of MLH1 and PMS2 on IHC. The effect of this alteration on MMR function was also assessed by looking at its ability to repair a GT mismatched substrate in a cell-free mismatch repair assay. Authors found the efficiency of this alteration to be comparable to that of another well-described pathogenic MLH1 mutation. Further, a yeast-based assay showed that this alteration does not interact with PMS2 suggesting that the MMR-deficiency is caused by failure to form the essential MutLa complex (Dominguez-Valentin M et al. Mol Genet Genomic Med. 2014 Jul; 2(4):352-5). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, p.C680R is classified as a pathogenic mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
BayesDel_addAF	Pathogenic	0.41	D
BayesDel_noAF	Pathogenic	0.35
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.86	D;.;.;.;.;.
Eigen	Uncertain	0.54
Eigen_PC	Uncertain	0.52
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Uncertain	0.88	D;D;.;.;.;D
M_CAP	Pathogenic	0.46	D
MetaRNN	Pathogenic	0.94	D;D;D;D;D;D
MetaSVM	Uncertain	0.75	D
MutationAssessor	Uncertain	2.5	M;.;.;.;.;.
PrimateAI	Uncertain	0.72	T
PROVEAN	Pathogenic	-5.3	D;D;D;D;D;D
REVEL	Pathogenic	0.88
Sift	Uncertain	0.0090	D;D;D;D;D;D
Sift4G	Uncertain	0.039	D;D;D;D;D;D
Polyphen		0.97	D;.;.;.;.;.
Vest4		0.93
MutPred		0.78		Gain of disorder (P = 0.0144);.;.;.;.;.;
MVP		0.96
MPC		0.39
ClinPred		0.98	D
GERP RS		4.8
Varity_R		0.98
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: rs63750809; hg19: chr3-37090443;