rs63751608

Positions:

• chr3-37042321-T-C

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PP3_Strong PP5_Very_Strong

The NM_000249.4(MLH1):​c.1721T>C​(p.Leu574Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 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. L574V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:4
• Conservation: PhyloP100: 7.16

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.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 16 uncertain in NM_000249.4
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.975
• PP5: Variant 3-37042321-T-C is Pathogenic according to our data. Variant chr3-37042321-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 89846.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37042321-T-C is described in Lovd as [Likely_pathogenic]. Variant chr3-37042321-T-C is described in Lovd as [Benign]. Variant chr3-37042321-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4	c.1721T>C	p.Leu574Pro	missense_variant	15/19	ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8	c.1721T>C	p.Leu574Pro	missense_variant	15/19	1	NM_000249.4	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:4

Revision: reviewed by expert panel

Submissions by phenotype

Lynch syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	University of Washington Department of Laboratory Medicine, University of Washington	May 01, 2018	MLH1 NM_000249.3:c.1721T>C has a 95.4% probability of pathogenicity based on combining prior probability from public data with a likelihood ratio of 1.56 to 1, generated from evidence of seeing this as a somatic mutation in a tumor without loss of heterozygosity at the MLH1 locus. See Shirts et al 2018, PMID 29887214. -
Likely pathogenic, reviewed by expert panel	curation	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Jun 21, 2019	Abrogated function & co-segregation with disease -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 21, 2018

For these reasons, this variant has been classified as Pathogenic. This variant has been reported to affect MLH1 protein function (PMID: 21404117, 23403630, 9697702, 17510385, 10037723, 15864295, 12810663, 18094436, 11427529). This variant has been observed in several individuals affected with Lynch syndrome-related cancers (PMID: 7757073, 15365995), and was shown to segregate with colon cancer in a family (PMID: 7757073). ClinVar contains an entry for this variant (Variation ID: 89846). This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with proline at codon 574 of the MLH1 protein (p.Leu574Pro). The leucine residue is moderately conserved and there is a moderate physicochemical difference between leucine and proline. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 07, 2021

The p.L574P variant (also known as c.1721T>C), located in coding exon 15 of the MLH1 gene, results from a T to C substitution at nucleotide position 1721. The leucine at codon 574 is replaced by proline, an amino acid with similar properties. This alteration was identified as somatic in an individual with a second pathogenic somatic alteration and whose Lynch-related tumor demonstrated high microsatellite instability and loss of MLH1 and PMS2 expression on immunohistochemistry with negative MLH1 promoter hypermethylation (Ambry internal data). This alteration co-segregates with disease in a Korean family that meets Amsterdam criteria (Han HJ et al. Hum Mol Genet, 1995 Feb;4:237-42) and was also identified in a 32-year-old Korean male with colorectal cancer from a cohort of 141 HNPCC families (Shin YK et al. Hum Mutat, 2004 Oct;24:351). Functional studies demonstrate reduced MMR activity relative to wild-type MLH1, a dominant negative mutator effect in yeast, aberrant interaction with PMS2 that is similar to pathogenic controls, and reduced MLH1 protein stability/expression (Shimodaira H et al. Nat Genet, 1998 Aug;19:384-9; Guerrette S et al. J Biol Chem, 1999 Mar;274:6336-41; Kondo E et al. Cancer Res, 2003 Jun;63:3302-8; Takahashi M et al. Cancer Res, 2007 May;67:4595-604; Fan Y et al. Clin Cancer Res, 2007 Dec;13:7515-21; Hardt K et al. Fam Cancer, 2011 Jun;10:273-84; Hinrichsen I et al. Clin Cancer Res, 2013 May;19:2432-41). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.43
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.93	D;.;.;.;.;.
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.46
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.96	D;D;.;.;.;D
M_CAP	Uncertain	0.23	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D;D
MetaSVM	Benign	-0.48	T
MutationAssessor	Uncertain	2.1	M;.;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D
PrimateAI	Pathogenic	0.84	D
PROVEAN	Pathogenic	-5.1	D;D;D;D;D;D
REVEL	Pathogenic	0.85
Sift	Uncertain	0.0030	D;D;D;D;D;D
Sift4G	Uncertain	0.0040	D;D;D;D;D;D
Polyphen		0.61	P;.;.;.;.;.
Vest4		0.96
MutPred		0.93		Loss of sheet (P = 0.007);.;.;.;.;.;
MVP		0.99
MPC		0.49
ClinPred		0.99	D
GERP RS		5.4
Varity_R		0.94
gMVP		0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs63751608; hg19: chr3-37083812;