NM_000249.4:c.1964T>C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM5

The NM_000249.4(MLH1):ā€‹c.1964T>Cā€‹(p.Ile655Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000552 in 1,613,532 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I655V) has been classified as Likely benign.

Frequency

Genomes: š‘“ 0.000092 ( 0 hom., cov: 31)
Exomes š‘“: 0.000051 ( 0 hom. )

Consequence

MLH1
NM_000249.4 missense

Scores

2
7
10

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:7B:10

Conservation

PhyloP100: 7.70
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM5
Other missense variant is known to change same aminoacid residue: Variant chr3-37048583-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MLH1NM_000249.4 linkc.1964T>C p.Ile655Thr missense_variant Exon 17 of 19 ENST00000231790.8 NP_000240.1 P40692-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MLH1ENST00000231790.8 linkc.1964T>C p.Ile655Thr missense_variant Exon 17 of 19 1 NM_000249.4 ENSP00000231790.3 P40692-1

Frequencies

GnomAD3 genomes
AF:
0.0000921
AC:
14
AN:
152048
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000944
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000756
AC:
19
AN:
251246
Hom.:
0
AF XY:
0.0000736
AC XY:
10
AN XY:
135778
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000185
Gnomad NFE exome
AF:
0.000132
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000513
AC:
75
AN:
1461484
Hom.:
0
Cov.:
31
AF XY:
0.0000523
AC XY:
38
AN XY:
727060
show subpopulations
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:
0.000169
Gnomad4 NFE exome
AF:
0.0000576
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.0000921
AC:
14
AN:
152048
Hom.:
0
Cov.:
31
AF XY:
0.0000539
AC XY:
4
AN XY:
74240
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000944
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000747
Hom.:
0
Bravo
AF:
0.0000642
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000233
AC:
2
ExAC
AF:
0.0000988
AC:
12
EpiCase
AF:
0.000109
EpiControl
AF:
0.00

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:7Benign:10
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:2Benign:3
Nov 03, 2021
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Sep 11, 2019
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 17510385, 22703879, 8938136, 17348456, 10970186, 18383312, 16341804, 11376800, 25637381, 27600092, 31159747, 31332305) -

Oct 10, 2024
Quest Diagnostics Nichols Institute San Juan Capistrano
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The MLH1 c.1964T>C (p.Ile655Thr) variant has been reported in the published literature in individuals with hereditary non-polyposis colon cancer (HNPCC), also known as Lynch syndrome (PMID: 11376800 (2001), 10970186 (2000), 8938136 (1996)), including one individual who also carried a pathogenic MSH2 variant (PMID: 17348456 (2007)). Additionally, this variant has been reported in individuals with a personal and/or family history of breast and/or ovarian cancer, and at least one reportedly healthy individual (PMIDs: 33471991 (2021), 31159747 (2019), see also LOVD (https://databases.lovd.nl/shared)). Functional studies demonstrated that this variant was not damaging to protein function (PMID: 17510385 (2007)). The frequency of this variant in the general population, 0.00016 (4/25086 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is deleterious or benign. Based on the available information, we are unable to determine the clinical significance of this variant. -

Jul 13, 2012
Biesecker Lab/Clinical Genomics Section, National Institutes of Health
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: research

- -

Nov 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

MLH1: BS3:Supporting -

not specified Uncertain:2Benign:1
Mar 04, 2025
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Dec 11, 2023
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

Variant summary: MLH1 c.1964T>C (p.Ile655Thr) results in a non-conservative amino acid change located in the DNA mismatch repair protein Mlh1, C-terminal domain (IPR032189) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 7.6e-05 in 251246 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in MLH1 causing Lynch Syndrome (7.6e-05 vs 0.00071), allowing no conclusion about variant significance. c.1964T>C has been reported in the literature in individuals with a personal or family history of colorectal or other MLH1-related cancers, and at-least one instance of co-occurrence in a patient with hMLH1 promoter hypermethylation suggestive of a sporadic etiology has been ascertained (e.g., Irmejs_2007, Keller_1996, Potocnik_2001, Ravnik-Glavac_2000, Schubert_2019, Svensson_2022, Tsoaousis_2019). These report(s) do not provide unequivocal conclusions about association of the variant with Lynch syndrome. A co-occurrence with another pathogenic variant has been reported (MSH2 c.1786_1788del, p.Asn596del; Irmejs_2007), providing supporting evidence for a benign role. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in 74% of normal activity in an in-vitro MMR assay and >75% relative MLH1 expression (Takahashi_2007). The following publications have been ascertained in the context of this evaluation (PMID: 31697235, 22290698, 25637381, 18383312, 11179758, 17348456, 22703879, 8938136, 27647783, 11376800, 10970186, 30426508, 35430768, 17510385, 31159747). Multiple submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments (likely benign, n = 6; VUS, n = 6). Based on the evidence outlined above, the variant was classified as likely benign. -

Aug 03, 2020
Genetic Services Laboratory, University of Chicago
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

DNA sequence analysis of the MLH1 gene demonstrated a sequence change, c.1964T>C, in exon 17 that results in an amino acid change, p.Ile655Thr. This sequence change has been described in the gnomAD database with a low frequency of 0.016% in the European sub-population (dbSNP rs63751225). The p.Ile655Thr change affects a poorly conserved amino acid residue located in a domain of the MLH1 protein that is not known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Ile655Thr substitution. The p.Ile655Thr change has previously been described in a family with gastric cancer (PMID: 8938136); however, functional studies have demonstrated mismatch repair activity similar to that of the wild type allele in the presence of this sequence change (PMID: 17510385). Due to these contrasting evidences, the clinical significance of the p.Ile655Thr change remains unknown at this time. -

Hereditary cancer-predisposing syndrome Uncertain:1Benign:2
Jul 20, 2015
Color Diagnostics, LLC DBA Color Health
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Aug 01, 2018
GeneKor MSA
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Oct 29, 2018
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Colorectal cancer, hereditary nonpolyposis, type 2 Uncertain:1Benign:1
Apr 18, 2017
Counsyl
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Nov 27, 2024
Myriad Genetics, Inc.
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 27363726]. -

Colorectal cancer, non-polyposis Uncertain:1
Jun 01, 2014
CSER _CC_NCGL, University of Washington
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: research

- -

Lynch syndrome Benign:1
Sep 17, 2024
All of Us Research Program, National Institutes of Health
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

MLH1-related disorder Benign:1
Mar 03, 2020
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Hereditary nonpolyposis colorectal neoplasms Benign:1
Jan 30, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Uncertain
0.12
D
BayesDel_noAF
Pathogenic
0.25
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.66
D;.;.;.;.;.
Eigen
Benign
-0.069
Eigen_PC
Benign
0.18
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.94
D;D;.;.;.;D
M_CAP
Benign
0.052
D
MetaRNN
Uncertain
0.44
T;T;T;T;T;T
MetaSVM
Uncertain
-0.25
T
MutationAssessor
Benign
0.41
N;.;.;.;.;.
PrimateAI
Benign
0.47
T
PROVEAN
Benign
-1.5
N;N;N;N;N;N
REVEL
Uncertain
0.59
Sift
Benign
0.15
T;T;T;T;T;T
Sift4G
Benign
0.43
T;T;T;T;T;T
Polyphen
0.0080
B;.;.;.;.;.
Vest4
0.57
MVP
0.97
MPC
0.084
ClinPred
0.15
T
GERP RS
5.8
Varity_R
0.29
gMVP
0.47

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs63751225; hg19: chr3-37090075; API