3-37025751-C-T

Variant names:

• chr3-37025751-C-T
• rs63750760
• NM_000249.4:c.1153C>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 6P and 5B. PM1 PP3_Strong BP6 BS1

The NM_000249.4(MLH1):​c.1153C>T​(p.Arg385Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000483 in 1,613,496 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R385H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000046 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000049 (0 hom.)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:9 B:7
• Conservation: PhyloP100: 4.28
• Publications: 44 publications found

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 Gene-Disease associations (from GenCC):

• Lynch syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, ClinGen, Orphanet
• Lynch syndrome 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp
• Muir-Torre syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Ambry Genetics, G2P, Orphanet
• mismatch repair cancer syndrome 1

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
• Lynch syndrome 1

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• ovarian cancer

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• malignant pancreatic neoplasm

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• rhabdomyosarcoma

  Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
• prostate cancer

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• breast cancer

  Inheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics
• hereditary breast carcinoma

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 5 benign, 43 uncertain in NM_000249.4
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.943
• BP6: Variant 3-37025751-C-T is Benign according to our data. Variant chr3-37025751-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 89653.
• BS1: Variant frequency is greater than expected in population eas. GnomAdExome4 allele frequency = 0.0000486 (71/1461874) while in subpopulation EAS AF = 0.000856 (34/39700). AF 95% confidence interval is 0.00063. There are 0 homozygotes in GnomAdExome4. There are 29 alleles in the male GnomAdExome4 subpopulation. Median coverage is 34. This position passed quality control check.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.1153C>T	p.Arg385Cys	missense_variant	Exon 12 of 19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.1153C>T	p.Arg385Cys	missense_variant	Exon 12 of 19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes AF: 0.0000462 AC: 7 AN: 151622 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000243

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000589

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000597 AC: 15 AN: 251422 AF XY: 0.0000442

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000435

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000264

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000486 AC: 71 AN: 1461874 Hom.: 0 Cov.: 34 AF XY: 0.0000399 AC XY: 29 AN XY: 727246

African (AFR) AF: 0.0000896 AC: 3 AN: 33478

American (AMR) AF: 0.0000447 AC: 2 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26136

East Asian (EAS) AF: 0.000856 AC: 34 AN: 39700

South Asian (SAS) AF: 0.0000232 AC: 2 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53420

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.0000243 AC: 27 AN: 1112000

Other (OTH) AF: 0.0000497 AC: 3 AN: 60392

GnomAD4 genome AF: 0.0000462 AC: 7 AN: 151622 Hom.: 0 Cov.: 31 AF XY: 0.0000405 AC XY: 3 AN XY: 74008

African (AFR) AF: 0.0000243 AC: 1 AN: 41220

American (AMR) AF: 0.00 AC: 0 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5168

South Asian (SAS) AF: 0.00 AC: 0 AN: 4806

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10502

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000589 AC: 4 AN: 67966

Other (OTH) AF: 0.00 AC: 0 AN: 2076

Alfa AF: 0.0000540 Hom.: 0

Bravo AF: 0.0000529

ExAC AF: 0.0000330 AC: 4

EpiCase AF: 0.00

EpiControl AF: 0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:9 Benign:7

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not specified Uncertain:2 Benign:1

-

Mayo Clinic Laboratories, Mayo Clinic

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

- -

Mar 21, 2025

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

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: MLH1 c.1153C>T (p.Arg385Cys) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 6.2e-05 in 1739538 control chromosomes, predominantly at a frequency of 0.0008 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 1.13 fold of the estimated maximal expected allele frequency for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer phenotype (0.00071). Additionally, at least 1 individual was homozygous for this variant but unaffected with the recessive phenotype associated with MLH1 (constitutional mismatch repair deficiency; Labcorp Genetics (formerly Invitae) internal data). Further, at least 1 publication has reported a very high prevalence in healthy controls (example, Chang_2017 listing 1.3% among 150 healthy Taiwanese individuals), suggesting this variant is likely to be a benign polymorphism prevalent among East Asian subpopulations. c.1153C>T has been reported in the presumed heterozygous state in the literature in numerous individuals affected with different types of cancer including Lynch/colorectal cancer, breast cancer, pancreatic cancer, and FAP (e.g. Cravo_2002, Lage_2004, Castera_2014, Shirts_2016, Sun_2017, Shang_2018, Wardell_2018, Kiyozumi_2019, Wang_2019, Chen_2020, Horiuchi_2020, Dorling_2021, Kim_2022, Chang_2017, Fujitani_2023, Ma_2020, Takai_2016), without strong evidence for causality. One of these studies reports the variant segregated with colorectal cancer phenotype in some instances in a family, except from two family members (aged 62 and 30 years) who had the variant and were healthy (Cravo_2002). These report(s) do not provide unequivocal conclusions about association of the variant with MLH1-related conditions. At least one publication reports experimental evidence evaluating an impact on protein function in vitro. These results showed no damaging effect of this variant (example, Gong_2019, Houlleberghs_2020). The following publications have been ascertained in the context of this evaluation (PMID: 24549055, 31127692, 29069792, 31867841, 11839723, 33471991, 36896836, 31118792, 32710294, 31784484, 35884469, 31386297, 15222003, 31958074, 28822769, 29419868, 26845104, 25115387, 28724667, 27732944, 24362816, 30982232, 29360550). ClinVar contains an entry for this variant (Variation ID: 89653). Based on the evidence outlined above, the variant was classified as benign. -

Jun 16, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant classified as Uncertain Significance - Favor Pathogenic. The p.Arg385Cys variant in MLH1 has been reported in at least 2 individuals with MLH1-associate d cancers and segregated with disease in multiple relatives from 1 family (Cravo 2002, Lage 2004, Chao 2008, Shirts 2016). This variant has also been identified in 3/8648 of East Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs63750760). This frequency is low enough to be consistent with the frequency of Lynch syndrome in the general population. Computational prediction tools and conservation analysis suggest that the p.Arg 385Cys variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, while there is some suspicion fo r a pathogenic role, the clinical significance of the p.Arg385Cys variant is unc ertain. -

Colorectal cancer, hereditary nonpolyposis, type 2 Uncertain:1 Benign:1

Jan 17, 2025

Myriad Genetics, Inc.

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered 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]. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance. -

Mar 18, 2016

Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: reference population

- -

not provided Uncertain:1 Benign:1

Sep 20, 2021

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect This variant is associated with the following publications: (PMID: 31386297, 31118792, 30309722, 27732944, 26845104, 10348818, 28706299, 29419868, 28822769, 29192238, 29258903, 28724667, 27071721, 26010451, 27683556, 25148578, 27311873, 24918944, 27831900, 24549055, 14514376, 24362816, 18383312, 25115387, 15222003, 11839723, 31127692) -

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Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

The MLH1 p.Arg385Cys variant was identified in 9 of 8796 proband chromosomes (frequency: 0.001) from individuals or families with colon, breast, ovarian, pancreatic or gastric cancer, and was not identified in 100 control chromosomes from healthy individuals (Castera 2014, Cravo 2002, Lage 2004, Natarajan 2016, Shirts 2015, Stenzinger 2014, Takai 2016, Wong 2016, Yamamoto 1999). The variant was also identified in dbSNP (ID: rs63750760) as "With Likely pathogenic allele", ClinVar (classified as uncertain significance by InSight, Invitae, Ambry Genetics, GeneDx, Color Genomics, and three clinical laboratories; as likely pathogenic by University of Washington Department of Laboratory Medicine), in Cosmic (6x in Haematopoietic and lymphoid tissue, skin, Large intestine or NS), MutDB, UMD-LSDB (2x as unclassified variant), Mismatch Repair Genes Variant Database, and Insight Hereditary Tumors databases. The variant was not identified in COGR, or Zhejiang University databases. The variant was identified in control databases in 13 of 246188 chromosomes at a frequency of 0.000053 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 15300 chromosomes (freq: 0.00006), Latino in 1 of 33578 chromosomes (freq: 0.00003), European in 2 of 111650 chromosomes (freq: 0.00002), East Asian in 8 of 17248 chromosomes (freq: 0.0005), and South Asian in 1 of 30782 chromosomes (freq: 0.00003), while the variant was not observed in the Other, Ashkenazi Jewish, and Finnish populations. By a multivariate Analysis of Protein Polymorphisms–Mismatch Repair system, the variant was classified as uncertain significance (Chao 2008). The p.Arg385 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

Hereditary cancer-predisposing syndrome Benign:2

Feb 15, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 09, 2021

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. -

Breast and/or ovarian cancer Uncertain:1

May 02, 2022

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Childhood neoplasm Uncertain:1

May 26, 2020

Cambridge Genomics Laboratory, East Genomic Laboratory Hub, NHS Genomic Medicine Service

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

Oct 31, 2018

Fulgent Genetics, Fulgent Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Lynch syndrome Uncertain:1

Jul 11, 2017

University of Washington Department of Laboratory Medicine, University of Washington

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary breast ovarian cancer syndrome Uncertain:1

May 01, 2019

Cancer Genomics Group, Japanese Foundation For Cancer Research

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: research

- -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Jan 12, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer Benign:1

Jan 23, 2024

Mendelics

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	Pathogenic	0.95
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Pathogenic	0.41
CADD	Pathogenic	31
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.88	D;.;.;.;.;.
Eigen	Pathogenic	0.87
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Pathogenic	0.99	D;D;.;.;.;D
M_CAP	Pathogenic	0.36	D
MetaRNN	Pathogenic	0.94	D;D;D;D;D;D
MetaSVM	Pathogenic	0.94	D
MutationAssessor	Pathogenic	3.0	M;.;.;.;.;.
PhyloP100		4.3
PrimateAI	Uncertain	0.66	T
PROVEAN	Pathogenic	-7.1	D;D;D;D;D;D
REVEL	Pathogenic	0.84
Sift	Pathogenic	0.0	D;D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D
Polyphen		1.0	D;.;.;.;.;.
Vest4		0.79
MVP		0.98
MPC		0.47
ClinPred		0.81	D
GERP RS		5.7
PromoterAI		-0.030	Neutral
Varity_R		0.80
gMVP		0.73
Mutation Taster		=3/97	disease causing

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

Other links and lift over

dbSNP: rs63750760; hg19: chr3-37067242; COSMIC: COSV51614892; COSMIC: COSV51614892;