3-37017597-C-T

Position:

• chr3-37017597-C-T

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2 PP5_Very_Strong

The NM_000249.4(MLH1):​c.882C>T​(p.Leu294=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: MLH1 NM_000249.4 splice_region, synonymous
• Scores: Splicing: ADA: 0.5719
• Clinical Significance: Pathogenic reviewed by expert panel P:7
• Conservation: PhyloP100: 0.765

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 10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-37017597-C-T is Pathogenic according to our data. Variant chr3-37017597-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 90407.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37017597-C-T is described in Lovd as [Pathogenic]. Variant chr3-37017597-C-T is described in Lovd as [Benign]. Variant chr3-37017597-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4	c.882C>T	p.Leu294=	splice_region_variant, synonymous_variant	10/19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.882C>T	p.Leu294=	splice_region_variant, synonymous_variant	10/19	1	NM_000249.4	ENSP00000231790	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1460238 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 726496

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Aug 17, 2021	The c.882C>T pathogenic mutation (also known as p.L294L), located in coding exon 10, results from a C to T substitution at nucleotide position 882 of the MLH1 gene. This nucleotide substitution does not change the amino acid at codon 294. This alteration has been detected in an individual who met Amsterdam I criteria for Lynch syndrome and whose tumor demonstrated high microsatellite instability with loss of MLH1 protein expression by immunohistochemistry (Spaepen M et al. Fam. Cancer, 2006;5:179-89). This pathogenic mutation has also been reported in other Lynch syndrome families or those suspected of having Lynch syndrome (Bonadona V et al. JAMA, 2011 Jun;305:2304-10; Chubb D et al. Nat Commun, 2016 06;7:11883; Dedeurwaerdere F et al. Sci Rep, 2021 Jun;11:12880). In silico splice site analysis for this alteration is inconclusive. RT-PCR performed using patient samples and minigene analyses demonstrate that this alteration results in out-of-frame CDS 10 skipping (Ambry internal data; Soukarieh O et al. PLoS Genet., 2016 Jan;12:e1005756; Tournier I et al. Hum. Mutat., 2008 Dec;29:1412-24; Auclair J et al. Hum. Mutat., 2006 Feb;27:145-54; Spaepen M et al. Fam. Cancer, 2006;5:179-89; van der Klift HM et al. Mol Genet Genomic Med. 2015 Jul;3(4):327-45). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Nov 12, 2018	- -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Jul 18, 2023

This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad internal data]. -

Hereditary nonpolyposis colon cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Nov 10, 2023

Variant summary: MLH1 c.882C>T (p.Leu294Leu) alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Although 5/5 computational tools predict no significant impact on normal splicing, multiple functional studies report data showing that the variant is associated with exon 10 skipping (e.g., Soukarieh_2016), and may be due to disruption of an ESE site rather than the canonical splice signaling sequence (Auclair_2006). The variant was absent in 251622 control chromosomes. c.882C>T has been reported in the literature in multiple individuals affected with Lynch Syndrome/HNPCC, including cosegregation with disease in a family. These data indicate that the variant is likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 16395668, 26761715, 16736289, 18561205). Four submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Lynch syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

Variant allele results in splicing abberation leading to premature stop codon: full inactivation of variant allele -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

Dec 01, 2017

- -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 24, 2023

For these reasons, this variant has been classified as Pathogenic. Studies have shown that this variant alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 16395668, 16736289, 18561205, 26247049, 26761715). ClinVar contains an entry for this variant (Variation ID: 90407). This variant has been observed in individual(s) with Lynch syndrome (PMID: 16395668, 16736289, 18561205). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change affects codon 294 of the MLH1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the MLH1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	18
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.57
dbscSNV1_RF	Pathogenic	0.78
SpliceAI score (max)		0.28		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.28		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs63751707; hg19: chr3-37059088; COSMIC: COSV51615064; COSMIC: COSV51615064;