Variant chr3-37011867-G-A details in Genebe, Genetics Data Aggregator

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:

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 11 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

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 3-37011867-G-A is Pathogenic according to our data. Variant chr3-37011867-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 90285.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37011867-G-A is described in Lovd as [Likely_pathogenic]. Variant chr3-37011867-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLH1	NM_000249.4 linkuse as main transcript	c.588+5G>A		splice_donor_5th_base_variant, intron_variant		ENST00000231790.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLH1	ENST00000231790.8 linkuse as main transcript	c.588+5G>A		splice_donor_5th_base_variant, intron_variant		1	NM_000249.4	P1	P40692-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10

Revision: reviewed by expert panel

LINK: link

Submissions by phenotype

Lynch syndrome

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	Mar 18, 2014	- -
Pathogenic, reviewed by expert panel	research	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Sep 05, 2013	Variant causes splicing aberrations: full inactivation of variant allele -

not provided

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Oct 20, 2021	This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in HNPCC families (PMIDs: 18389388 (2008), 16206289 (2006), 15926618 (2005)). The variant has demonstrated to affect normal MLH1 mRNA splicing, causing a skip of exon 7 (PMIDs: 24090359 (2013), 18561205 (2008), 16341550 (2006)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 01, 2023	Intronic +5 splice variant in a gene for which loss-of-function is a known mechanism of disease, and skipping of exon 7 has been observed (Pagenstecher et al., 2006; Peterson et al., 2013; Pinero et al., 2020); Observed in multiple individuals with suspected Lynch syndrome, including those with Lynch related tumors found to be MSI-H and/or show loss of MLH1 via immunohistochemistry (Casey et al., 2005; Wolf et al., 2005; Pagenstecher et al., 2006; Batte et al., 2014; Sunga et al., 2017); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 16341550, 15713769, 15926618, 24933100, 28449805, 18561205, 24090359, 29887214, 30787465, 32363481) -

Hereditary cancer-predisposing syndrome

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	May 06, 2022	The c.588+5G>A intronic pathogenic mutation results from a G to A substitution 5 nucleotides after coding exon 7 in the MLH1 gene. This intronic mutation has been detected in multiple families meeting Amsterdam and/or Bethesda criteria for HNPCC/Lynch syndrome, with tumor results revealing absence of MLH1 protein expression on immunohistochemistry (Ambry internal data, Casey et al. JAMA. 2005. 293(7): 799–809; Wolf et al. Int J Cancer. 2006. 118(6):1465-70; Pagenstecher et al. Hum Genet. 2006. 119: 9–22; Sunga AY et al. Cancer Genet 2017 04;212-213:1-7). Functional studies have demonstrated aberrant splicing, leading to skipping of exon 7 and a truncated protein product (Pagenstecher et al. Hum Genet. 2006. 119: 9–22; Petersen SM et al. BMC Medical Genetics 2013,14:103; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	May 04, 2019	- -

Colorectal cancer, hereditary nonpolyposis, type 2

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Jul 17, 2023

This variant is considered pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 18561205]. -

Hereditary nonpolyposis colon cancer

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Aug 21, 2020

Variant summary: MLH1 c.588+5G>A alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant weakens a 5' splicing donor site and two predict it abolishes it. Experimental evidence from multiple studies supports these predictions demonstrating the variant affects mRNA splicing leading to exon skipping (Casey_2005, Pagenstecher_2006, Tournier_2008, Petersen_2013). The variant was absent in 251328 control chromosomes (gnomAD). c.588+5G>A has been reported in the literature in individuals affected with Hereditary Nonpolyposis Colorectal Cancer (e.g. Casey_2005, Pagenstecher_2006, Wolf_2006, Tournier_2008, Petersen_2013). These data indicate that the variant is likely to be associated with disease. Six ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Muir-Torré syndrome;C1333991:Colorectal cancer, hereditary nonpolyposis, type 2;C5399763:Mismatch repair cancer syndrome 1

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Dec 14, 2021

- -

Hereditary nonpolyposis colorectal neoplasms

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 12, 2023

This sequence change falls in intron 7 of the MLH1 gene. It does not directly 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. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with Lynch syndrome (PMID: 15713769, 16341550, 18561205, 24090359, 26437257; Invitae). It has also been observed to segregate with disease in related individuals. This variant is also known as IVS07+5G>A. ClinVar contains an entry for this variant (Variation ID: 90285). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 7 and introduces a premature termination codon (PMID: 15713769, 16341550, 18561205). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.18

CADD

Uncertain

DANN

Benign

0.94

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.98

SpliceAI score (max)

0.73

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.73

Position offset: -5

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.

chr3-37011867-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

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