3-37040294-G-C

Variant names:

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong

The NM_000249.4(MLH1):c.1667G>C(p.Ser556Thr) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000311 in 1,608,450 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S556I) has been classified as Pathogenic.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

MLH1
NM_000249.4 missense, splice_region

Scores

Splicing: ADA: 1.000

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:8U:1

Conservation

PhyloP100: 9.74

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 Pathogenic. Variant got 18 ACMG points.

PM1

In a helix (size 14) in uniprot entity MLH1_HUMAN there are 9 pathogenic changes around while only 1 benign (90%) in NM_000249.4

PM2

Very rare variant in population databases, with high coverage;

PM5

Other missense variant is known to change same aminoacid residue: Variant chr3-37040294-G-T is described in Lovd as [Pathogenic].

PP3

Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.

PP5

Variant 3-37040294-G-C is Pathogenic according to our data. Variant chr3-37040294-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 185187.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-37040294-G-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4 link	c.1667G>C	p.Ser556Thr	missense_variant, splice_region_variant	Exon 14 of 19	ENST00000231790.8	NP_000240.1	P40692-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8 link	c.1667G>C	p.Ser556Thr	missense_variant, splice_region_variant	Exon 14 of 19	1	NM_000249.4	ENSP00000231790.3		P40692-1

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152106

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:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00000398

AC:

AN:

251200

Hom.:

AF XY:

0.00000737

AC XY:

AN XY:

135768

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:

0.00000880

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000275

AC:

AN:

1456344

Hom.:

Cov.:

AF XY:

0.00000552

AC XY:

AN XY:

724946

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000181

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152106

Hom.:

Cov.:

AF XY:

0.0000135

AC XY:

AN XY:

74284

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:

0.0000147

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000712

Hom.:

Bravo

AF:

0.00000756

ExAC

AF:

0.00000824

AC:

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:8Uncertain:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Pathogenic:2

Feb 13, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The frequency of this variant in the general population, 0.0000071 (2/282602 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals with Lynch syndrome (PMID: 21404117 (2011), or suspected of having hereditary breast cancer/Lynch syndrome (PMID: 28514183 (2017)). This variant is located at the last nucleotide of exon 14. In particular, the c.1667G>T (p.Ser556Ile) variant has been shown in experimental study to cause disruption of the adjacent splice site and incorporation of intronic sequences into the transcript, including a premature stop codon (PMID: 15300854 (2004)). Consistent with this finding, analysis of the c.1667G>C (p.Ser556Thr) variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper MLH1 mRNA splicing . Based on the available information, this variant is classified as likely pathogenic. -

Feb 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

MLH1: PM1, PM2, PM5, PS4:Moderate, PP3 -

Hereditary cancer-predisposing syndrome

Pathogenic:2

May 08, 2024

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1667G>C (p.S556T) alteration is located in exon 14 (coding exon 14) of the MLH1 gene. This alteration results from a G to C substitution at nucleotide position 1667, causing the serine (S) at amino acid position 556 to be replaced by a threonine (T). However, this change occurs in the last base pair of coding exon 14, which makes it likely to have some effect on normal mRNA splicing. Based on data from gnomAD, the C allele has an overall frequency of 0.001% (2/282602) total alleles studied. The highest observed frequency was 0.002% (2/129026) of European (non-Finnish) alleles. This alteration has been detected in multiple patients with personal and/or family histories of Lynch syndrome (LS)-associated cancers including a patient diagnosed with a MSI-H colorectal cancer whose tumor demonstrated loss of MLH1 and PMS2 on immunohistochemistry (Ambry internal data). This variant has also been reported in an individual affected with MSI-H colorectal cancer and had a family history that met Amsterdam II criteria (Yurgelun, 2017). Another alteration at the same last nucleotide position, p.S556I (c.1667G>T), has been reported in a family with colon and breast cancer meeting Amsterdam Criteria for HNPCC/LS. This nucleotide position is highly conserved in available vertebrate species. The p.S556I (c.1667G>T) alteration resulted in partial read through into intron 14 and the inclusion of an additional 88 bp of intronic sequence into the mRNA by RT-PCR analysis (Sharp, 2004). In silico splice site analysis predicts that this alteration will weaken the native splice donor site; however, direct evidence is insufficient at this time (Ambry internal data). In addition, as a missense substitution, this variant is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

Feb 24, 2025

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces serine with threonine at codon 556 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function. This variant (c.1667G>C) alters the conserved G nucleotide at the last nucleotide position of exon 14 of the MLH1 gene, and is predicted to disrupt RNA splicing. To our knowledge, RNA studies have not been reported for this variant. This variant has been reported in individuals affected with or suspected of having Lynch syndrome (PMID: 21404117, 28514183). This variant has been identified in 1/245968 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different variants affecting the same nucleotide position c.1667G>T and c.1667G>A have been shown to impact RNA splicing and are associated with disease (Clinvar variation ID: 89825, 449776). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Hereditary nonpolyposis colon cancer

Pathogenic:1

Dec 31, 2024

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: MLH1 c.1667G>C (p.Ser556Thr) results in a conservative amino acid change located in the DNA mismatch repair protein Mlh1, C-terminal domain (IPR032189) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Two predict the variant weakens a 5' donor site. One predicts the variant abolishes a 5' splicing donor site. One predicts the variant no significant impact on splicing. Internal RNA splicing data showed this variant results in an out of frame insertion of part of intron 14 (r.1667_1668ins1667+1_1667+88) presumed to result in nonsense mediated decay due to the introduction of a novel stop codon (Labcorp, formerly Invitae), however the level of missplicing did not reach a clear threshold of biological significance. The variant allele was found at a frequency of 4e-06 in 251200 control chromosomes. c.1667G>C has been reported in the heterozygous state in the literature in individuals affected with features of Lynch syndrome whose tumors were MSI-high and showed positive staining for MLH1 by IHC (example, Alter_2018, Hardt_2011). Co-occurrences with other pathogenic variant(s) have been reported (MSH2, exon 9 deletion), providing some supporting evidence for a benign role. Additionally, a different variant at the same nucleotide position c.1667G>T (the last nucleotide "G" of the exon) has been shown in patient RNA splicing assays to result in a similar 88 bp intron inclusion event as was observed for c.1667G>C (PMID: 15300854), and a 2nd different variant at this nucleotide position has been classified as Pathogenic by expert panel review based on clinical evidence (c.1667G>A, ClinVar). The following publications have been ascertained in the context of this evaluation (PMID: 28514183, 21404117, 28152038, 15300854). ClinVar contains an entry for this variant (Variation ID: 185187). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Lynch syndrome

Pathogenic:1

Mar 25, 2024

All of Us Research Program, National Institutes of Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense variant replaces serine with threonine at codon 556 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). This variant (c.1667G>C) alters the conserved G nucleotide at the last nucleotide position of exon 14 of the MLH1 gene, and is predicted to disrupt RNA splicing. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected with or suspected of having Lynch syndrome (PMID: 21404117, 28514183). This variant has been identified in 1/245968 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Different variants affecting the same nucleotide position c.1667G>T and c.1667G>A have been shown to impact RNA splicing and are associated with disease (Clinvar variation ID: 89825, 449776). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Hereditary nonpolyposis colorectal neoplasms

Pathogenic:1

Jan 08, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 556 of the MLH1 protein (p.Ser556Thr). This variant also falls at the last nucleotide of exon 14, which is part of the consensus splice site for this exon. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 21404117, 28514183). ClinVar contains an entry for this variant (Variation ID: 185187). Invitae Evidence 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 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change is associated with inconclusive levels of altered splicing (internal data). This variant disrupts the c.1667G nucleotide in the MLH1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 27064304, 28135145; external communication, internal data). This suggests that this nucleotide is clinically significant, and that variants that disrupt this position are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Familial cancer of breast

Pathogenic:1

Feb 02, 2022

Human Genetics Bochum, Ruhr University Bochum

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG criteria used to clasify this variant: PVS1, PM2, PM5, PM1, PP3 -

Muir-Torré syndrome

Uncertain:1

Oct 12, 2022

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Pathogenic

0.27

BayesDel_noAF

Pathogenic

0.16

CADD

Pathogenic

DANN

Benign

0.93

DEOGEN2

Benign

0.37

Eigen

Uncertain

0.44

Eigen_PC

Uncertain

0.36

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.29

M_CAP

Pathogenic

0.30

MetaRNN

Uncertain

0.51

MetaSVM

Benign

-0.36

PROVEAN

Benign

1.5

REVEL

Uncertain

0.44

Sift

Benign

0.11

Sift4G

Pathogenic

0.0

MutPred

0.42

Loss of helix (P = 0.0123);

MVP

0.94

ClinPred

0.63

GERP RS

4.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.99

SpliceAI score (max)

0.92

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.92

Position offset: 0

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