3-37049017-G-C

Variant names:

• chr3-37049017-G-C
• rs63750603
• NM_000249.4:c.2103G>C

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000249.4(MLH1):​c.2103G>C​(p.Gln701His) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q701K) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:8
• Conservation: PhyloP100: 8.05

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]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-37049015-C-A is described in Lovd as [Likely_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 3-37049017-G-C is Pathogenic according to our data. Variant chr3-37049017-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 90049.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37049017-G-C is described in Lovd as [Pathogenic]. Variant chr3-37049017-G-C is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLH1	NM_000249.4	c.2103G>C	p.Gln701His	missense_variant, splice_region_variant	Exon 18 of 19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.2103G>C	p.Gln701His	missense_variant, splice_region_variant	Exon 18 of 19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:8

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:2

May 16, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The MLH1 c.2103G>C (p.Gln701His) variant (also known as Q701H) has been reported in the published literature in individuals and families affected with colorectal cancer (PMIDs: 16216036 (2005), 16341550 (2006), 21404117 (2011), 30521064 (2019), 31491536 (2020)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Studies of RNA splicing and immunohistochemistry in tumors have shown that this variant causes complete exon skipping and loss of MLH1 expression (PMIDs: 15849733 (2005), 16216036 (2005), 16341550 (2006), 36593122 (2023)). Based on the available information, this variant is classified as pathogenic. -

Mar 04, 2025

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Jan 14, 2022

MGZ Medical Genetics Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary nonpolyposis colon cancer Pathogenic:1

Jul 07, 2021

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: MLH1 c.2103G>C (p.Gln701His) 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. Four of five in-silico tools predict a damaging effect of the variant on protein function. This nucleotide is located at the exon/intron junction at the end of exon 18. Several computational tools predict a significant impact on normal splicing: Four predict that the variant abolishes a 5-prime splicing donor site. This finding has been corroborated by at least one publication reporting experimental evidence that this variant affects mRNA splicing, resulting in the skipping of exon 18 (e.g. Pagenstecher_2006). The variant was absent in 250694 control chromosomes. c.2103G>C has been reported in the literature in multiple individuals affected with Hereditary Nonpolyposis Colorectal Cancer (e.g. Hardt_2011, Yanus_2020). These data indicate that the variant is very likely to be associated with disease. Two other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Both laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Lynch syndrome 1 Pathogenic:1

-

Ding PR Lab, Sun Yat-sen University Cancer Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Lynch syndrome Pathogenic:1

Sep 05, 2013

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: research

Variant causing splicing aberration predicted to interrupt known functional domains: full inactivation of variant allele -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Dec 18, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces glutamine, which is neutral and polar, with histidine, which is basic and polar, at codon 701 of the MLH1 protein (p.Gln701His). RNA analysis indicates that this missense change induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of Lynch syndrome (PMID: 15849733, 16341550, 21404117, 30521064, 31491536; internal data). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 90049). 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 results in skipping of exon 18, but is expected to preserve the integrity of the reading-frame (PMID: 15849733, 16341550). For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Nov 14, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2103G>C pathogenic mutation (also known as p.Q701H) located in coding exon 18 of the MLH1 gene. This pathogenic mutation results from a G to C substitution at nucleotide position 2103. The glutamine at codon 701 is replaced by histidine, an amino acid with highly similar properties. This change occurs in the last base pair of exon 18 which makes it likely to have some effect on normal mRNA splicing. In two studies, RNA analyses showed that this mutation lead to the complete loss of coding exon 18 (Mangold E et al. Int J Cancer. 2005 Sep 20;116(5):692-702; Pagenstecher C. Hum Genet. 2006 Mar;119(1-2):9-22). This mutation has been reported in numerous Lynch syndrome families that met either Amsterdam or Bethesda criteria, and whose tumor analyses showed high microsatellite instability and absent MLH1 expression on IHC (Mangold E et al. Int J Cancer. 2005 Sep 20;116(5):692-702; Pagenstecher C. Hum Genet. 2006 Mar;119(1-2):9-22; Lucci-Cordisco E et al. Cancer Biomark. 2006;2(1-2):11-27; Hardt K et al. Fam Cancer. 2011 Jun;10(2):273-84). In addition, this alteration has been classified as pathogenic using the following lines of evidence: in silico prediction models, segregation with disease, clinical phenotype including tumor characteristics, mutation co-occurrence, and functional studies (Thompson BA et al. Hum. Mutat. 2013 Jan;34:200-9; Thompson BA et al. Nat. Genet. 2014 Feb;46:107-15; available at [www.insight-group.org/variants/classifications/]). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Pathogenic	0.51	D
BayesDel_noAF	Pathogenic	0.50
CADD	Pathogenic	32
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.67	D;.;.;.;.;.
Eigen	Uncertain	0.59
Eigen_PC	Uncertain	0.61
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.77	T;T;.;.;.;T
M_CAP	Benign	0.064	D
MetaRNN	Benign	0.41	T;T;T;T;T;T
MetaSVM	Pathogenic	0.81	D
MutationAssessor	Benign	1.9	L;.;.;.;.;.
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-1.0	N;N;N;N;N;N
REVEL	Uncertain	0.49
Sift	Benign	0.11	T;D;T;T;T;T
Sift4G	Benign	0.13	T;T;T;T;T;T
Polyphen		0.90	P;.;.;.;.;.
Vest4		0.59
MutPred		0.096		Loss of glycosylation at S702 (P = 0.1765);.;.;.;.;.;
MVP		0.98
MPC		0.074
ClinPred		0.79	D
GERP RS		4.9
Varity_R		0.11
gMVP		0.66

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.91		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.91		Position offset: 0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs63750603; hg19: chr3-37090508;