chr3-37020438-A-G

Position:

chr3-37020438-A-G

Variant summary

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

The NM_000249.4(MLH1):c.1013A>G(p.Asn338Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000126 in 1,614,198 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.000066 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00013 ( 0 hom. )

Consequence

MLH1
NM_000249.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:12B:7

Conservation

PhyloP100: 6.82

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4 linkuse as main transcript	c.1013A>G	p.Asn338Ser	missense_variant	11/19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8 linkuse as main transcript	c.1013A>G	p.Asn338Ser	missense_variant	11/19	1	NM_000249.4	ENSP00000231790	P1	P40692-1

Frequencies

GnomAD3 genomes

AF:

0.0000657

AC:

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000882

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000915

AC:

AN:

251274

Hom.:

AF XY:

0.000110

AC XY:

AN XY:

135832

show subpopulations

Gnomad AFR exome

AF:

0.0000615

Gnomad AMR exome

AF:

0.0000578

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0000653

Gnomad FIN exome

AF:

0.0000924

Gnomad NFE exome

AF:

0.000132

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000133

AC:

194

AN:

1461886

Hom.:

Cov.:

AF XY:

0.000129

AC XY:

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.000119

Gnomad4 AMR exome

AF:

0.0000894

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000927

Gnomad4 FIN exome

AF:

0.0000374

Gnomad4 NFE exome

AF:

0.000144

Gnomad4 OTH exome

AF:

0.000248

GnomAD4 genome

AF:

0.0000657

AC:

AN:

152312

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.000131

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000882

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000136

Hom.:

Bravo

AF:

0.0000907

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.0000576

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.000218

EpiControl

AF:

0.00

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:12Benign:7

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not specified

Uncertain:4Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Aug 15, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Aug 12, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ClinVar: VUS by expert panel in 2013, no new evidence suggesting pathogenicity since then -
Uncertain significance, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	Jul 12, 2022	DNA sequence analysis of the MLH1 gene demonstrated a sequence change, c.1013A>G, in exon 11 that results in an amino acid change, p.Asn338Ser. This sequence change has been previously described in individuals with colorectal cancer (PMIDs: 12095971, 23354017, 28874130, 29520894, 18561205) and other cancers including breast and pancreatic cancer (PMIDs: 26898890, 28767289). This sequence change has been described in the gnomAD database with a frequency of 0.012% in the European subpopulation (dbSNP rs63751467). The p.Asn338Ser change affects a moderately 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.Asn338Ser substitution. Experimental studies have shown that this variant does not have an impact on mRNA splicing (PMID: 18561205, 31332305) and on mismatch repair activity (PMID: 31784484). Another study reported that this variant does not impact MLH1 function in a methylation tolerance assay (PMID: 30998989) and other study reported that this variant has similar expression level as wildtype protein (PMID: 29520894). An analysis of tumor characteristic from a variant carrier reported a likelihood ratio for pathogenicity of 0.100 (PMID: 31391288). In another study, this variant was shown to have a deleterious effect with an in silico model (PMID: 18383312). While there is suspicion that this variant may not be associated with disease, additional studies are necessary to determine the role of this variant in disease conclusively. Due to contradictory evidence, the clinical significance of the p.Asn338Ser change therefore remains unknown at this time. -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Mar 17, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Mar 13, 2023	Variant summary: MLH1 c.1013A>G (p.Asn338Ser) results in a conservative amino acid change in 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 9.2e-05 in 251274 control chromosomes (gnomAD). This frequency is not higher than the estimated maximum expected for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer (0.00071), allowing no conclusion about variant significance. c.1013A>G has been reported in the literature in individuals affected with colorectal cancer and other tumor phenotypes (e.g. Hardt_2011, Pal_2012, Rodriguez-Soler_2013, Caminsky_2016, Rossi_2017, Shindo_2017, Koger_2018, Li_2020, Hu_2020, Mio_2021, Dorling_2021, Pearlman_2021, Brady_2022), but was also found in several cancer-free controls (Dorling_2021). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. Co-occurrences with other pathogenic variant(s) have been reported (MSH2 c.484G>A, p.Gly162Arg; in an internal LCA sample), providing supporting evidence for a benign role. In functional studies the variant was found to have no effect on RNA splicing (Tournier_2008, Morak_2019), protein expression, and protein stability, mismatch repair activity (Koger_2018, Bouvet_2019, Houlleberghs_2019, Rath_2022). 13 other submitters have provided clinical-significance assessments for this variant in ClinVar after 2014, mostly without evidence for independent evaluation, and classified the variant as VUS (n=9), likely benign (n=3) or benign (n=1). Based on the evidence outlined above, the variant was classified as benign. -

Hereditary cancer-predisposing syndrome

Uncertain:2Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Feb 04, 2019	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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 08, 2023	This missense variant replaces asparagine with serine at codon 338 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have reported that this variant does not impact MLH1 function in a methylation tolerance assay (PMID: 30998989), or the MLH1 protein's stability, damage response signaling, and DNA repair function (doi: 10.1101/2021.12.14.472580). This variant has been detected in at least six individuals affected with Lynch syndrome or associated cancer (PMID: 12095971, 18561205, 21404117, 23047549, 23354017), multiple individuals affected with breast cancer (PMID: 26898890, 33471991), and an individual affected with pancreatic cancer (PMID: 28767289). This variant has also been detected in ten unaffected controls in a large breast cancer case-control study (PMID: 33471991). An analysis of tumor characteristic from a variant carrier reported a likelihood ratio for pathogenicity of 0.100 (PMID: 31391288). This variant has been identified in 24/282676 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may not be associated with disease, additional evidence is necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	curation	Sema4, Sema4	Nov 07, 2021	- -

not provided

Uncertain:1Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jan 04, 2021	Dominguez-Valentin M et al. (2013) Hereditary cancer in clinical practice 11 (1):18 (PMID: 24344984); Amendola LM et al. (2015) Genome Res 25 (3):305-15 (PMID: 25637381); Chao EC et al. (2008) Human mutation 29 (6):852-60 (PMID: 18383312); This variant is associated with the following publications: (PMID: 23741719, 23354017, 18561205, 24344984, 32659497, 21404117, 24096645, 22252508, 12095971, 23047549, 25637381, 18383312, 26898890, 28874130, 29520894, 28767289, 30998989, 31391288, 31784484, 31332305) -

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

- -

Colorectal cancer, non-polyposis

Uncertain:1

Uncertain significance, no assertion criteria provided

research

CSER _CC_NCGL, University of Washington

Jun 01, 2014

- -

Lynch syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Feb 05, 2024

This missense variant replaces asparagine with serine at codon 338 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have reported that this variant does not impact MLH1 function in a methylation tolerance assay (PMID: 30998989), or the MLH1 protein's stability, damage response signaling, and DNA repair function (doi: 10.1101/2021.12.14.472580). This variant has been detected in at least six individuals affected with Lynch syndrome or associated cancer (PMID: 12095971, 18561205, 21404117, 23047549, 23354017), multiple individuals affected with breast cancer (PMID: 26898890, 33471991), and an individual affected with pancreatic cancer (PMID: 28767289). This variant has also been detected in ten unaffected controls in a large breast cancer case-control study (PMID: 33471991). An analysis of tumor characteristic from a variant carrier reported a likelihood ratio for pathogenicity of 0.100 (PMID: 31391288). This variant has been identified in 24/282676 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may not be associated with disease, additional evidence is necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

MLH1-related disorder

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 28, 2024

The MLH1 c.1013A>G variant is predicted to result in the amino acid substitution p.Asn338Ser. This variant has been reported in individuals with Lynch syndrome, colorectal, breast, pancreatic, or ovarian cancers (Rossi et al. 2002. PubMed ID: 12095971; Rodríguez-Soler et al. 2013. PubMed ID: 23354017; Pal et al. 2012. PubMed ID: 23047549; Hardt et al. 2011. PubMed ID: 21404117; Shindo et al. 2017. PubMed ID: 28767289). This variant is reported in 0.012% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/89605/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Malignant tumor of breast

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

The MLH1 p.Asn338Ser variant was identified in 5 of 7614 proband chromosomes (frequency: 0.001) from individuals or families with colon, and ovarian cancer (Chao 2008, Hardt 2011, Pal 2012, Rodriguez-Soler 2013). The variant was also identified in the following databases: dbSNP (ID: rs63751467) as â€šÃ„ÃºWith Uncertain significance alleleâ€šÃ„Ã¹, in ClinVar (classified as likely benign by Ambry Genetics; classified as uncertain significance by Invitae, GeneDx, Color Genomics and 4 clinical laboratories), Clinvitae, UMD-LSDB (5X as unclassified variant), Mismatch Repair Genes Variant Database, and the Insight Hereditary Tumors Database (15X Class3). The variant was not identified in COGR, Cosmic, MutDB, or the Zhejiang Colon Cancer Database. The variant was identified in control databases in 23 of 277060 chromosomes at a frequency of 0.0001 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 1 of 24032 chromosomes (freq: 0.00004), Latino in 2 of 34418 chromosomes (freq: 0.0001), European in 16 of 126584 chromosomes (freq: 0.0001), Finnish in 2 of 25792 chromosomes (freq: 0.0001), and South Asian in 2 of 30780 chromosomes (freq: 0.0001); it was not observed in the â€šÃ„ÃºOtherâ€šÃ„Ã¹, Ashkenazi Jewish, or East Asian populations. Several publications provide inconsistent predictions regarding the effect of the variant on protein and splicing. The variant was shown to have a deleterious effect with an in silico model (Chao 2008), while the variant has no effect on splicing in the pCAS ExVivo Splicing Assay (Tournier 2008). The p.Asn338 residue is conserved in mammals but not in more distantly related organisms, and four out of five 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 4 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. 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 nonpolyposis colorectal neoplasms

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Hereditary cancer

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Mendelics

Sep 11, 2024

This variant is considered likely benign or benign based on one or more of the following: it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease, and/or has normal protein function, and/or has lack of segregation with disease, and/or has been detected in co-occurrence with known pathogenic variant, and/or has lack of disease association in case-control studies, and/or is located in a region inconsistent with a known cause of pathogenicity. -

Hereditary breast ovarian cancer syndrome

Benign:1

Likely benign, criteria provided, single submitter

curation

German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne

Sep 09, 2024

According to the ClinGen InSiGHT ACMG MLH1 v1.0.0 criteria we chose these criteria: BP4 (supporting benign): HCI-prior probability of pathogenicity <0.11, BS1 (strong benign): gnomADv4 Grpmax FAF von >0.01% in NFE, BS3 (supporting benign): Functional Assay show no impact on protein function -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.010

BayesDel_noAF

Uncertain

-0.020

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.67

D;.;.;.;.;.;.

Eigen

Uncertain

0.33

Eigen_PC

Uncertain

0.37

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.96

D;D;.;.;.;D;D

M_CAP

Uncertain

0.15

MetaRNN

Uncertain

0.58

D;D;D;D;D;D;D

MetaSVM

Uncertain

0.68

MutationAssessor

Uncertain

2.5

M;.;.;.;.;.;.

MutationTaster

Benign

1.0

D;D;D;D;D;D

PrimateAI

Benign

0.43

PROVEAN

Uncertain

-2.6

D;D;D;D;D;D;D

REVEL

Pathogenic

0.67

Sift

Benign

0.17

T;T;T;T;T;T;T

Sift4G

Benign

0.28

T;T;T;T;T;T;T

Polyphen

0.51

P;.;.;.;.;.;.

Vest4

0.82

MVP

0.93

MPC

0.092

ClinPred

0.50

GERP RS

4.1

Varity_R

0.12

gMVP

0.25

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.

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