rs63750952

Positions:

chr3-36996693-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PP3_Strong

The NM_000249.4(MLH1):c.191A>G(p.Asn64Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,612,866 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).

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000026 ( 0 hom. )

Consequence

MLH1
NM_000249.4 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:13B:3

Conservation

PhyloP100: 8.87

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 4 ACMG points.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.975

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4 linkuse as main transcript	c.191A>G	p.Asn64Ser	missense_variant	2/19	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.191A>G	p.Asn64Ser	missense_variant	2/19	1	NM_000249.4	ENSP00000231790	P1	P40692-1

Frequencies

GnomAD3 genomes

AF:

0.0000263

AC:

AN:

152202

Hom.:

Cov.:

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:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000441

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.0000358

AC:

AN:

251442

Hom.:

AF XY:

0.0000294

AC XY:

AN XY:

135894

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:

0.00

Gnomad NFE exome

AF:

0.0000791

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000260

AC:

AN:

1460664

Hom.:

Cov.:

AF XY:

0.0000261

AC XY:

AN XY:

726742

show subpopulations

Gnomad4 AFR exome

AF:

0.0000299

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:

0.00

Gnomad4 NFE exome

AF:

0.0000333

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0000263

AC:

AN:

152202

Hom.:

Cov.:

AF XY:

0.0000403

AC XY:

AN XY:

74366

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:

0.00

Gnomad4 NFE

AF:

0.0000441

Gnomad4 OTH

AF:

0.000478

Alfa

AF:

0.0000718

Hom.:

Bravo

AF:

0.0000302

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.0000494

AC:

EpiCase

AF:

0.0000545

EpiControl

AF:

0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1Uncertain:13Benign:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Pathogenic:1Uncertain:2Benign:1

Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Feb 06, 2023	The frequency of this variant in the general population, 0.00007 (9/129152 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals/families with colorectal cancer (PMIDs: 21404117 (2011), 16736289 (2006), and 9311737 (1997)), endometrial cancer (PMID: 26552419 (2015)), breast cancer (PMID: 33471991 (2021); LOVD3 Shared (https://databases.lovd.nl/shared/)), and also in one case of pancreatic cancer (PMID: 28767289 (2017)). In addition, this variant has been reported in healthy control individuals (PMID: 33471991 (2021); LOVD3 Shared (https://databases.lovd.nl/shared/)). Functional studies have observed the variant having intermediate levels of MLH1 expression, mismatch repair activity, and PMS2 interaction (PMIDs: 30504929 (2018), 26552419 (2015), 22843852 (2012), 21404117 (2011), 17510385 (2007), 17210669 (2007), 17135187 (2006), and 15475387 (2004)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 21, 2020	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies are inconclusive: reduced MMR activity, no impact on nuclear localization, and conflicting results regarding mutator effect, PMS2 binding, MLH1 protein expression (Ellison 2004, Plotz 2006, Takahashi 2007, Wanat 2007, Hardt 2011, Bolz 2012, Drost 2018); Observed in individuals with MLH1-related cancers including segregation with disease in one family, as well as in individuals with melanoma (Wijnen 1997, Spaepen 2006, Hardt 2011, Shindo 2017, Yehia 2018); This variant is associated with the following publications: (PMID: 17135187, 21404117, 23741719, 29684080, 17510385, 17210669, 25525159, 9311737, 22843852, 15475387, 26552419, 16736289, 24362816, 28767289, 30504929, 31697235, 31332305, 32719484, 30755392) -

Colorectal cancer, hereditary nonpolyposis, type 2

Uncertain:2Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 15, 2023	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: 25085752]. -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 28, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	MGZ Medical Genetics Center	Aug 08, 2022	- -

Lynch syndrome

Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	Jul 02, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Nov 30, 2023	This missense variant replaces asparagine with serine at codon 64 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). Functional studies have shown that this variant results in a partial loss of mismatch repair function and moderately reduced protein stability and binding ability to PMS2 protein (PMID: 17135187, 17510385, 21404117, 30504929, 36054288). This variant has been reported in individuals from Lynch syndrome families (PMID: 9311737, 16736289, 21404117). In one of these families, two affected siblings were carriers of this variant but their affected sister with microsatellite instability-high tumor did not carry this variant (PMID: 16736289). Three unaffected siblings from this family did not carry this variant. In another family, this variant co-occurred in trans with a different pathogenic variant in the MLH1 gene (PMID: 21404117, 31332305). This variant has also been reported in individuals affected with endometrial cancer (PMID: 26552419) or pancreatic cancer (PMID: 28767289). In a large breast cancer case-control study, this variant was observed in 6/60466 cases and 5/53461 unaffected controls (PMID: 33471991) This variant has been identified in 10/282844 chromosomes in the general population by the Genome Aggregation Database (gnomAD). 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. -

Hereditary cancer-predisposing syndrome

Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 17, 2024	This missense variant replaces asparagine with serine at codon 64 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). Functional studies have inconclusive results, with several showing this variant results in partial loss of mismatch repair function and moderately reduced protein stability and binding ability to PMS2 protein (PMID: 17135187, 17510385, 21404117, 30504929, 36054288). Another cell-based functional assay also demonstrated the variant resulted in partial protein stability, however, the variant also displayed positive damage response signaling and DNA repair function (PMID: 36054288). This variant has been reported in individuals from Lynch syndrome families (PMID: 9311737, 16736289, 21404117). In one of these families, two affected siblings were carriers of this variant but their affected sister with microsatellite instability-high tumor did not carry this variant (PMID: 16736289). Three unaffected siblings from this family did not carry this variant. In another family, this variant co-occurred in trans with a different pathogenic variant in the MLH1 gene (PMID: 21404117, 31332305). This variant has also been reported in individuals affected with endometrial cancer (PMID: 26552419) or pancreatic cancer (PMID: 28767289). In a large breast cancer case-control study, this variant was observed in 6/60466 cases and 5/53461 unaffected controls (PMID: 33471991) This variant has been identified in 10/282844 chromosomes in the general population by the Genome Aggregation Database (gnomAD). 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	May 27, 2024	The p.N64S variant (also known as c.191A>G), located in coding exon 2 of the MLH1 gene, results from an A to G substitution at nucleotide position 191. The asparagine at codon 64 is replaced by serine, an amino acid with highly similar properties. This alteration has been identified in several colorectal cancer cohorts that are suspicious for Lynch syndrome and, in at least one case, the tumor retained expression of MLH1 and MSH2 on immunohistochemical staining (Wijnen J et al. Am. J. Hum. Genet. 1997 Aug;61:329-35; Spaepen M et al. Fam. Cancer 2006;5:179-89; Hardt K et al. Fam. Cancer 2011 Jun;10:273-84; Stojcev Z et al. Acta Biochim Pol, 2013 Jun;60:195-8). One report shows that this alteration segregates with 5 of 6 siblings affected with colorectal cancer (Spaepen M et al. Fam. Cancer 2006;5:179-89). In another report, this alteration was found to co-occur with MLH1 c.986A>C, a functionally validated splicing mutation, in a patient with three gastrointestinal primary tumors diagnosed at 47. The MLH1 p.N64S alteration was inherited from the proband's mother who was unaffected at age 71, and while the paternal family history met Amsterdam criteria, suggesting the father likely carried the MLH1 c.986A>C pathogenic mutation, the inheritance of this alteration was not confirmed (Hardt K et al. Fam. Cancer 2011 Jun;10:273-84). Numerous functional studies show reduced but not abolished function including yeast mutator assays, expression assays, in vitro mismatch repair assays and heterodimerization assays (Ellison AR et al. Nucleic Acids Res. 2004 Oct;32:5321-38; Plotz G et al. Nucleic Acids Res. 2006 Nov;34:6574-86; Takahashi M et al. Cancer Res. 2007 May;67:4595-604; Wanat JJ et al. Hum. Mol. Genet. 2007 Feb;16:445-52; Hardt K et al. Fam. Cancer 2011 Jun;10:273-84). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Lynch syndrome 1

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Counsyl

Jun 29, 2017

- -

Muir-Torré syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University of Leipzig Medical Center

Jan 01, 2019

- -

MLH1-related disorder

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 08, 2024

The MLH1 c.191A>G variant is predicted to result in the amino acid substitution p.Asn64Ser. This variant has been reported in individuals with hereditary nonpolyposis colorectal cancer (Wijnen et al. 1997. PubMed ID: 9311737; Hardt et al. 2011. PubMed ID: 21404117) and ovarian cancer (Table S7 in Lilyquist et al. 2017. PubMed ID: 28888541) and pancreatic cancer (Shindo et al. 2017. PubMed ID: 28767289). Functional studies have indicated the p.Asn65Ser variant results in reduced mismatch repair activity and reduced MLH1 expression (Ellison et al. 2004. PubMed ID: 15475387; Wanat et al. 2007. PubMed ID: 17210669; Takahashi et al. 2007. PubMed ID: 17510385). This variant is reported in 0.0070% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant has conflicting interpretations in ClinVar with the majority being uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/89947). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Choreoathetosis;C0266476:Aqueductal stenosis;C0557874:Global developmental delay

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Center for Personalized Medicine, Children's Hospital Los Angeles

Mar 15, 2016

- -

Hereditary nonpolyposis colorectal neoplasms

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 64 of the MLH1 protein (p.Asn64Ser). This variant is present in population databases (rs63750952, gnomAD 0.006%). This missense change has been observed in individual(s) with colorectal, endometrial, pancreatic, ovarian cancer and/or Lynch syndrome (PMID: 9311737, 16736289, 21404117, 26552419, 28514183, 28767289, 28888541, 31332305). ClinVar contains an entry for this variant (Variation ID: 89947). 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 with a positive predictive value of 80%. Experimental studies have shown that this missense change affects MLH1 function (PMID: 17135187, 17510385, 21404117, 30504929). 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

Benign:1

Benign, criteria provided, single submitter

curation

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

Oct 11, 2024

According to the ClinGen InSiGHT ACMG MLH1 v1.0.0 criteria we chose these criteria: PP3 (supporting pathogenic): Applied prior : 0.72 (thus >0.68 & ≤0.81), BS2 (strong benign): Hardt 2011 (PMID: 21404117): reported to co-occur in trans with a known pathogenic MLH1 variant (H329P, ClinVar ID: 17085) in a patient who did not demonstrate a Constitutive MMR-Deficiency Disease phenotype, BS3 (strong benign): Rath 2022 (PMID: 36054288): OddsPath_Non-functional = 5.00E-2 (thus > 0.48) + Morak 2019 (PMID: 31332305): No effect on splicing. Drost 2019 (PMID: 30504929): study was supportive of neither a pathogenic or benign classification Invitae (Accession: SCV000218899.13): Advanced modeling of protein sequence and biophysical properties [...] performed at Invitae indicates that this missense variant is expected to disrupt MLH1 protein function with a positive predictive value of 80%. Various old functional studies showing conflicting results regarding effect of variant on protein function. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Uncertain

0.11

BayesDel_noAF

Uncertain

0.10

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Pathogenic

0.95

Eigen

Pathogenic

1.1

Eigen_PC

Pathogenic

0.97

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.93

M_CAP

Pathogenic

0.39

MetaRNN

Pathogenic

0.97

MetaSVM

Pathogenic

1.1

MutationAssessor

Pathogenic

4.0

MutationTaster

Benign

1.0

D;D;D;D;D;D

PrimateAI

Uncertain

0.68

PROVEAN

Pathogenic

-4.4

REVEL

Pathogenic

0.93

Sift

Uncertain

0.0030

Sift4G

Uncertain

0.0060

Polyphen

1.0

Vest4

0.93

MVP

0.96

MPC

0.37

ClinPred

0.99

GERP RS

5.8

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.6

Varity_R

0.83

gMVP

0.84

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