3-37025751-C-T

Position:

chr3-37025751-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 6P and 4B. PM5PP3_StrongBS1

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 Likely benign.

Frequency

Genomes: 𝑓 0.000046 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000049 ( 0 hom. )

Consequence

MLH1
NM_000249.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:11B:3

Conservation

PhyloP100: 4.28

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]

MLH1 links:

MLH1 (HGNC:):

MLH1 links:

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 chr3-37025752-G-C is described in Lovd as [Pathogenic].

PP3

MetaRNN computational evidence supports a deleterious effect, 0.943

BS1

Variant frequency is greater than expected in population eas. gnomad4_exome 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 gnomad4_exome. There are 29 alleles in male gnomad4_exome subpopulation. Median coverage is 34. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4 linkuse as main transcript	c.1153C>T	p.Arg385Cys	missense_variant	12/19	ENST00000231790.8	NP_000240.1	P40692-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8 linkuse as main transcript	c.1153C>T	p.Arg385Cys	missense_variant	12/19	1	NM_000249.4	ENSP00000231790.3		P40692-1

Frequencies

GnomAD3 genomes

AF:

0.0000462

AC:

AN:

151622

Hom.:

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.0000597

AC:

AN:

251422

Hom.:

AF XY:

0.0000442

AC XY:

AN XY:

135878

show subpopulations

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 SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000264

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000486

AC:

AN:

1461874

Hom.:

Cov.:

AF XY:

0.0000399

AC XY:

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.0000896

Gnomad4 AMR exome

AF:

0.0000447

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000856

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000243

Gnomad4 OTH exome

AF:

0.0000497

GnomAD4 genome

AF:

0.0000462

AC:

AN:

151622

Hom.:

Cov.:

AF XY:

0.0000405

AC XY:

AN XY:

74008

show subpopulations

Gnomad4 AFR

AF:

0.0000243

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000387

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000589

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000415

Hom.:

Bravo

AF:

0.0000529

ExAC

AF:

0.0000330

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:11Benign:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not specified

Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 13, 2021	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 0.00012 in 377464 control chromosomes, predominantly at a frequency of 0.00078 within the East Asian subpopulation in the gnomAD database and Japanese control databases (HGVD and jMorp). The observed variant frequency within East Asian control individuals is approximately equal to the estimated maximal expected allele frequency for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer phenotype (0.00071), suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.1153C>T has been reported in the literature in individuals affected with different types of cancer including Lynch/colorectal cancer, breast 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) but it was also reported in unaffected controls (Dorling_2021). One of these studies reports the variant segregated with colorectal cancer phenotype in most instances in a family, except from two family members (aged 62 and 30 years) who had the variant and were healthy (Cravo_2002). Other studies report co-occurrences with pathogenic variants, providing supporting evidence for a benign role. Particularly the variant was reported to co-occur with APC c.637C>T (p.R213X) in one individual affected with FAP (Shang_2018) and with TP53 c.1010G>A (p.Arg337His) in one individual affected with breast cancer (Wang_2019). Experimental evidence evaluating an impact on protein function demonstrated no damaging effect of this variant (Gong_2019, Houlleberghs_2020). Nine ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly benign. -
Uncertain significance, no assertion criteria provided	research	Mayo Clinic Laboratories, Mayo Clinic	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 16, 2016	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. -

not provided

Uncertain:1Benign:1

Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	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 Polymorphismsâ€šÃ„Ã¬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. -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 20, 2021	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) -

Hereditary cancer-predisposing syndrome

Uncertain:1Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 02, 2022	This missense variant replaces arginine with cysteine at codon 385 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown that this variant leads to a MLH1 protein level and mismatch repair activity that are comparable to the wild-type control in a cell-based assay (PMID: 31784484). This variant has been reported in individuals affected with gastric cancer (PMID: 10348818), colon cancer (PMID: 11839723, 15222003, 25110875), and pancreatic cancer (PMID: 27732944) and in individuals having a personal and/or family history of breast and/or ovarian cancer (PMID: 24549055, 24918944, 26010451, 26845104). This variant has also been identified in 15/251422 chromosomes in the general population by the Genome Aggregation Database (gnomAD) and in the Chinese general population (PMID: 34172528). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 09, 2021	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:1

Uncertain significance, criteria provided, single submitter

reference population

Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center

Mar 18, 2016

- -

Breast and/or ovarian cancer

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

May 02, 2022

- -

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

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

Lynch syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

University of Washington Department of Laboratory Medicine, University of Washington

Jul 11, 2017

- -

Hereditary nonpolyposis colorectal neoplasms

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 26, 2024

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 385 of the MLH1 protein (p.Arg385Cys). This variant is present in population databases (rs63750760, gnomAD 0.05%). This missense change has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 10348818, 15222003, 27732944, 30309722, 31118792, 31386297, 32710294, 35449176, 36243179). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 89653). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MLH1 protein function. Experimental studies have shown that this missense change does not substantially affect MLH1 function (PMID: 31118792, 31784484). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Hereditary breast ovarian cancer syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

research

Cancer Genomics Group, Japanese Foundation For Cancer Research

May 01, 2019

- -

Hereditary cancer

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Mendelics

Jan 23, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.95

BayesDel_addAF

Pathogenic

0.22

BayesDel_noAF

Pathogenic

0.41

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Pathogenic

0.88

D;.;.;.;.;.

Eigen

Pathogenic

0.87

Eigen_PC

Pathogenic

0.81

FATHMM_MKL

Uncertain

0.94

LIST_S2

Pathogenic

0.99

D;D;.;.;.;D

M_CAP

Pathogenic

0.36

MetaRNN

Pathogenic

0.94

D;D;D;D;D;D

MetaSVM

Pathogenic

0.94

MutationAssessor

Pathogenic

3.0

M;.;.;.;.;.

PrimateAI

Uncertain

0.66

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

GERP RS

5.7

Varity_R

0.80

gMVP

0.73

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over