chr3-37048956-C-T

Position:

• chr3-37048956-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PP4_Strong PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The NM_000249.4: c.2042C>T variant in MLH1 is a missense variant predicted to cause substitution of Alanin by Valin at amino acid 681 (p.Ala681Val). This variant has been detected in at least three patient with colorectal or endometrial MSI-H / loss MLH1/PMS2 tumours (PP4_Strong). This variant is absent in gnomAD v2.1.1 using the non-cancer dataset and gnomAD v4.1 (PM2_Supporting). Due to insufficient evidence, this variant is classified as a variant of uncertain significance for Lynch-Syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/ Polyposis VCEP: PP4_STR, PM2_SUP (VCEP specifications version 1). LINK:https://erepo.genome.network/evrepo/ui/classification/CA008313/MONDO:0007356/115

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:3 U:1
• Conservation: PhyloP100: 5.71

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]

MLH1 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4	c.2042C>T	p.Ala681Val	missense_variant	18/19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.2042C>T	p.Ala681Val	missense_variant	18/19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:3 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Sep 27, 2023

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 21615986, 25111426, 23760103, 24710284, 12799449, 22753075, 20533529, 8993979, 31054147) -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 27, 2021

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Ala681 amino acid residue in MLH1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 18033691, 8880570, 10037723, 12810663). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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. This variant has been observed in individual(s) with suspected Lynch syndrome (PMID: 21615986, 24710284, Invitae). ClinVar contains an entry for this variant (Variation ID: 90011). This variant is not present in population databases (ExAC no frequency). This sequence change replaces alanine with valine at codon 681 of the MLH1 protein (p.Ala681Val). The alanine residue is weakly conserved and there is a small physicochemical difference between alanine and valine. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 12, 2024

The p.A681V variant (also known as c.2042C>T), located in coding exon 18 of the MLH1 gene, results from a C to T substitution at nucleotide position 2042. The alanine at codon 681 is replaced by valine, an amino acid with similar properties. This alteration has been reported in multiple families meeting Amsterdam or Bethesda criteria (Wei W et al. BMB Rep. 2011 May; 44(5):317-22; Tian W et al. Int J Cancer, 2019 09;145:1290-1298). This alteration has also been identified as either somatic or in the germline of individuals whose colorectal tumors demonstrated loss of both MLH1 and PMS2 on immunohistochemistry and/or high microsatellite instability (Herfarth KK et al. Genes Chromosomes Cancer. 1997 Jan;18:42-9; Geurts-Giele WR et al. J. Pathol. 2014 Dec;234:548-59); Liu Y et al. PLoS ONE. 2014 Apr;9:e94170; Ambry internal data). Further, a well-characterized mutation at the same codon, p.A681T (c.2041G>A), has been identified in multiple families either meeting Amsterdam II criteria or whose family history was suggestive of HNPCC/Lynch syndrome and has also been shown to co-segregate with disease (Froggatt et al. J Med Genet. 1996 Sep; 33(9): 762-30; Shimodaira et al. Nat Genet 1998 Aug; 19(4): 384-9; Kurzawski G et al. Clin. Genet. 2006 Jan; 69(1):40-7; Barnetson RA et al. Hum. Mutat. 2008 Mar; 29(3):367-74). Based on an internal structural assessment, the p.A681V alteration locally destabilizes the folding of the MLH1 C-terminal domain (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Muir-Torré syndrome;C1333991:Colorectal cancer, hereditary nonpolyposis, type 2;C5399763:Mismatch repair cancer syndrome 1 Uncertain:1

Uncertain significance, flagged submission

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.90
BayesDel_addAF	Pathogenic	0.48	D
BayesDel_noAF	Pathogenic	0.46
CADD	Pathogenic	27
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.92	D;.;.;.;.;.
Eigen	Pathogenic	0.83
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.95	D;D;.;.;.;D
M_CAP	Pathogenic	0.42	D
MetaRNN	Pathogenic	0.89	D;D;D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Uncertain	2.8	M;.;.;.;.;.
PrimateAI	Uncertain	0.52	T
PROVEAN	Uncertain	-3.4	D;D;D;D;D;D
REVEL	Pathogenic	0.79
Sift	Uncertain	0.023	D;D;D;D;D;D
Sift4G	Uncertain	0.0070	D;D;D;D;D;D
Polyphen		0.99	D;.;.;.;.;.
Vest4		0.92
MutPred		0.64		Loss of ubiquitination at K678 (P = 0.0907);.;.;.;.;.;
MVP		0.98
MPC		0.33
ClinPred		0.98	D
GERP RS		5.9
Varity_R		0.78
gMVP		0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs63750864; hg19: chr3-37090447; COSMIC: COSV51616385; COSMIC: COSV51616385;