3-37048557-A-G

Position:

chr3-37048557-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.1937A>G(p.Tyr646Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,613,774 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 0.000053 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000060 ( 0 hom. )

Consequence

MLH1
NM_000249.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 8.94

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, 0.972

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4 linkuse as main transcript	c.1937A>G	p.Tyr646Cys	missense_variant	17/19	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.1937A>G	p.Tyr646Cys	missense_variant	17/19	1	NM_000249.4	ENSP00000231790	P1	P40692-1

Frequencies

GnomAD3 genomes

AF:

0.0000526

AC:

AN:

151998

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000242

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000656

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000946

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000735

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000438

AC:

AN:

251332

Hom.:

AF XY:

0.0000589

AC XY:

AN XY:

135824

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000289

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000792

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000602

AC:

AN:

1461776

Hom.:

Cov.:

AF XY:

0.0000605

AC XY:

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.0000597

Gnomad4 AMR exome

AF:

0.0000224

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000728

Gnomad4 OTH exome

AF:

0.0000331

GnomAD4 genome

AF:

0.0000526

AC:

AN:

151998

Hom.:

Cov.:

AF XY:

0.0000269

AC XY:

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.0000242

Gnomad4 AMR

AF:

0.0000656

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0000946

Gnomad4 NFE

AF:

0.0000735

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000574

Hom.:

Bravo

AF:

0.0000416

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000259

AC:

ExAC

AF:

0.0000330

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.000178

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1Uncertain:13

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Hereditary cancer-predisposing syndrome

Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 16, 2024	This missense variant replaces tyrosine with cysteine at codon 646 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 conflicting results with regard to the variant's impact on MLH1 protein interaction with PMS2 protein (PMID: 16083711, 16724012, 22753075). Multiple studies have shown that this variant does not affect mismatch repair activity (PMID: 16083711, 16724012, 20020535, 22753075). This variant has been reported in individuals affected with Lynch syndrome and Lynch syndrome-associated cancer (PMID: 11870161, 16083711, 16724012, 17250665, 21404117, 23047549, 25110875, 30521064). Tumor data from these individuals show conflicting evidence, with variability in microsatellite stability and protein expression via immunohistochemistry analysis (PMID: 11870161, 16083711, 16724012, 17250665, 21404117). This variant has also been observed in individuals affected with breast cancer or gastric cancer (PMID: 31650731, 36627197). This variant has also been identified in 12/282716 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, no assertion criteria provided	clinical testing	True Health Diagnostics	Oct 10, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Jan 12, 2024	The p.Y646C variant (also known as c.1937A>G), located in coding exon 17 of the MLH1 gene, results from an A to G substitution at nucleotide position 1937. The tyrosine at codon 646 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been reported in multiple individuals with clinical histories suspicious for Lynch syndrome, although tumor test results have been inconsistent (Scartozzi M et al. J. Clin. Oncol. 2002 Mar;20:1203-8; Hampel H et al. N. Engl. J. Med. 2005 May;352:1851-60; Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49; Belvederesi L et al. Eur. J. Hum. Genet. 2006 Jul;14:853-9; Hardt K et al. Fam. Cancer. 2011 Jun;10:273-84; Ambry internal data). Functional analyses of the p.Y646C variant have produced conflicting results. Two independent studies have shown this alteration to disrupt PMS2 interaction (Belvederesi L et al. Eur. J. Hum. Genet. 2006 Jul;14:853-9; Andersen SD et al. Hum. Mutat. 2012 Dec;33:1647-55), while another supported normal interaction (Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49). Multiple studies have demonstrated normal localization, normal mismatch repair activity, and expression similar to wild type (Andersen SD et al. Hum. Mutat. 2012 Dec;33:1647-55; Belvederesi L et al. Eur. J. Hum. Genet. 2006 Jul;14:853-9; Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49; Drost M et al. Hum. Mutat. 2010 Mar;31:247-53); however, one functional assay in yeast showed an intermediate activity level (Vogelsang M et al. BMC Cancer. 2009 Oct;9:382). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -
Uncertain significance, criteria provided, single submitter	curation	Sema4, Sema4	Jun 23, 2021	- -

not provided

Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jun 05, 2024	Observed in individuals with Lynch-syndrome associated cancers and/or polyps, with most tumors demonstrating absence of MLH1 protein expression and/or microsatellite instability; however, one tumor also demonstrated MLH1 promoter hypermethylation (PMID: 11870161, 17250665, 21404117, 25110875, 25980754, 32661327, 15256438, 15872200); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31650731, 19389263, 32547938, 22949387, 19863800, 22753075, 16083711, 15256438, 20020535, 23047549, 21120944, 17594722, 25980754, 25372392, 22426235, 17192056, 25186627, 18383312, 18951440, 29368341, 24073290, 15872200, 11870161, 17250665, 21404117, 25110875, 16724012, 30521064, 32068069, 32661327, 34039291, 35467778, 35449176, 34326862, 32756484, 12799449, 20533529, 31830689, 36627197) -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The MLH1 p.Tyr646Cys variant was identified in 3 of 6722 proband chromosomes (frequency: 0.0004) from individuals or families with Lynch syndrome, ovarian cancer, and colorectal cancer and was not identified in 870 chromosomes from healthy individuals (Yurgelun 2015, Pal 2012, Hampel 2005). The variant was also identified in the following databases: dbSNP (ID: rs35045067) â€šÃ„ÃºWith Uncertain significance alleleâ€šÃ„Ã¹, ClinVar (classified uncertain significance, reviewed by an expert panel in 2013; submitters: InSIGHT, Ambry Genetics, GeneDx, Invitae, and Laboratory Corporation of America), UMD-LSDB (1x, unclassified variant), and Mismatch Repair Genes Variant Database. The c.1937A>G variant was not identified in COGR, Cosmic, MutDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, or the Insight Hereditary Tumors Database. The variant was identified in control databases in 12 of 277044 chromosomes at a frequency of 0.00004 (Genome Aggregation Database Feb 27, 2017). The variant was identified in the following populations: European in 9 of 126552 chromosomes (freq: 0.00007), African in 1 of 24036 chromosomes (freq: 0.00004), Latino in 1 of 34418 chromosomes (freq: 0.00003), and East Asian in 1 of 18862 chromosomes (freq: 0.00005); it was not observed in the Other, Ashkenazi Jewish, Finnish, or South Asian populations. Functional assays on this variant report conflicting assessments of pathogenicity (Andersen 2012, Belvederesi 2006, Drost 2010, Nakagawa 2004, Raevaara 2005, Vogelsang 2009). The p.Tyr646 residue is conserved across mammals and other organisms and 5 of 5 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 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Sep 05, 2023	In the published literature, it has been reported in individuals affected with colon cancer (PMID: 15872200 (2005), 16724012 (2006), 21404117 (2011), 25110875 (2015), 25980754 (2015), 30521064 (2019)), breast cancer (PMID: 11870161 (2002), 25186627 (2015), 31650731 (2020), 32547938 (2020)), ovarian cancer (PMID: 23047549 (2012)), and prostate cancer (PMID: 29368341 (2018)). Functional studies were conflicting particularly when evaluating binding to PMS2 (PMID: 16083711 (2005), 16724012 (2006), 22753075 (2012)). A study in yeast observing mutation rates (PMID: 19863800 (2009)) also suggests pathogenicity. However, mismatch repair activity has been reported to be proficient (PMID: 16083711 (2005), 20020535 (2010)). The frequency of this variant in the general population, 0.00007 (9/129044 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 predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -

not specified

Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 15, 2024	Variant summary: MLH1 c.1937A>G (p.Tyr646Cys) 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. 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 4.4e-05 in 251732 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer (4.4e-05 vs 0.00071), allowing no conclusion about variant significance. c.1937A>G has been reported in the literature in individuals affected with prostate cancer, breast cancer and/or ovarian cancer, gastric cancer, HNPCC or HNPCC-related cancers, all without strong evidence for causality (Scartozzi_2002, Nakagawa_2004, Belvederesi_2006, Hardt_2011, Yurgelun_2015, IsaacssonVelho_2018, Jiang_2019, Kwong_2020, Yoo_2020, Nikitin_2020, Xiao_2020, Talbot_2021, Hu_2022, Brady_2022, Zhang_2023). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. A co-occurrence with another pathogenic variant has been reported (BRCA1 c.5266dupC, p.Q1756fs), providing supporting evidence for a benign role (Nikitin_2020). In vitro functional studies provided conflicting results in relation to binding of this MLH1 Y646C mutant with PMS2 (Raevaara_2005, Belvederesi_2006, Drost_2011, Andersen_2012). Localization and expression of this variant and MMR activity of this mutant were found to be normal (Raevaara_2005, Belvederesi_2006, Vogelsang_2009, Drost_2011, Andersen_2012). However, in vitro measurement of mutation rate of this mutant was highly impaired (Vogelsang_2009) and it was also defective in binding with Exo1 protein (Andersen_2012). Thus, based on the functional assays, it is uncertain whether this variant leads to functional impairment. The following publications have been ascertained in the context of this evaluation (PMID: 19389263, 18383312, 15256438, 21120944, 16724012, 17250665, 20020535, 17192056, 16083711, 11870161). ClinVar contains an entry for this variant (Variation ID: 36545). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Jul 31, 2024	- -

Colorectal cancer, hereditary nonpolyposis, type 2

Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 09, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Jul 25, 2017	- -

Hereditary nonpolyposis colorectal neoplasms

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 18, 2024

This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 646 of the MLH1 protein (p.Tyr646Cys). This variant is present in population databases (rs35045067, gnomAD 0.007%). This missense change has been observed in individuals with clinical features of Lynch syndrome (PMID: 11870161, 30521064; Invitae). ClinVar contains an entry for this variant (Variation ID: 36545). 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 95%. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on MLH1 function (PMID: 16083711, 16724012, 19863800, 20020535, 22753075). For these reasons, this variant has been classified as Pathogenic. -

Lynch syndrome 1

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Ding PR Lab, Sun Yat-sen University Cancer Center

- -

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 tyrosine with cysteine at codon 646 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 conflicting results with regard to the variant's impact on MLH1 protein interaction with PMS2 protein (PMID: 16083711, 16724012, 22753075). Multiple studies have shown that this variant does not affect mismatch repair activity (PMID: 16083711, 16724012, 20020535, 22753075). This variant has been reported in individuals affected with Lynch syndrome and Lynch syndrome-associated cancer (PMID: 11870161, 16083711, 16724012, 17250665, 21404117, 23047549, 25110875, 30521064). Tumor data from these individuals show conflicting evidence, with variability in microsatellite stability and protein expression via immunohistochemistry analysis (PMID: 11870161, 16083711, 16724012, 17250665, 21404117). This variant has also been observed in individuals affected with breast cancer or gastric cancer (PMID: 31650731, 36627197). This variant has also been identified in 12/282716 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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.25

BayesDel_addAF

Pathogenic

0.36

BayesDel_noAF

Pathogenic

0.47

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Pathogenic

0.90

D;.;.;.;.;.

Eigen

Pathogenic

0.94

Eigen_PC

Pathogenic

0.90

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.93

D;D;.;.;.;D

M_CAP

Pathogenic

0.59

MetaRNN

Pathogenic

0.97

D;D;D;D;D;D

MetaSVM

Pathogenic

0.95

MutationAssessor

Pathogenic

3.7

H;.;.;.;.;.

MutationTaster

Benign

1.0

D;D;D;D;D;D

PrimateAI

Uncertain

0.71

PROVEAN

Pathogenic

-8.3

D;D;D;D;D;D

REVEL

Pathogenic

0.96

Sift

Uncertain

0.0020

D;D;D;D;D;D

Sift4G

Uncertain

0.0030

D;D;D;D;D;D

Polyphen

1.0

D;.;.;.;.;.

Vest4

0.88

MVP

0.95

MPC

0.45

ClinPred

0.99

GERP RS

5.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.96

gMVP

0.91

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