chr3-37020463-G-A

Position:

• chr3-37020463-G-A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_000249.4(MLH1):​c.1038G>A​(p.Gln346Gln) variant causes a splice region, synonymous change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,754 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★★★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: MLH1 NM_000249.4 splice_region, synonymous
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:10
• Conservation: PhyloP100: 9.29

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 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Multiple lines of computational evidence support a deleterious effect 4: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai, phyloP100way_vertebrate [when BayesDel_noAF, Cadd was below the threshold]
• PP5: Variant 3-37020463-G-A is Pathogenic according to our data. Variant chr3-37020463-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 89616.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37020463-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4	c.1038G>A	p.Gln346Gln	splice_region_variant, synonymous_variant	11/19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.1038G>A	p.Gln346Gln	splice_region_variant, synonymous_variant	11/19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461754 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 727186

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: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Alfa AF: 0.0000611 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Nov 22, 2024	The MLH1 c.1038G>A (p.Gln346=) synonymous variant interferes with normal MLH1 mRNA splicing. Studies show this variant will result in premature termination of the protein (PMID: 12183410 (2002)). This variant has been reported in individuals meeting clinical criteria for Lynch syndrome/hereditary non-polyposis colorectal cancer (HNPCC) (PMID: 12183410 (2002), 15555211 (2004), 19731080 (2010)), one of whom had a microsatellite instability-high (MSI-H) colorectal cancer (PMID: 12183410 (2002)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Analysis of this 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 pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 15, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 08, 2023	Located at the last nucleotide of the exon and demonstrated to result in aberrant splicing producing an abnormal transcript that is subject to nonsense-mediated mRNA decay (Nakagawa et al., 2002); Reported in at least two individuals with colorectal cancer who met diagnostic criteria for Lynch syndrome (Nakagawa et al., 2002; Jasperson et al., 2010); Classified as pathogenic by a well-established clinical consortium and/or database (ClinVar); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 19731080, 16341550, 15555211, 30787465, 12183410) -

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Jul 19, 2023	This variant is considered pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 12183410]. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Aug 30, 2023	- -

Lynch syndrome Pathogenic:2

Pathogenic, reviewed by expert panel	research	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Sep 05, 2013	Variant causes splicing aberration predicted to produce truncated protein: full inactivation of variant allele -
Likely pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 09, 2018	Variant summary: MLH1 c.1038G>A (p.Gln346Gln) 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: Three predict the variant abolishes a 5' splicing donor site and two predict the variant weakens the same 5' donor site. These predictions are supported by at least one publication that reports experimental evidence that this variant affects mRNA splicing (Nakagawa_2002). The variant was absent in 245768 control chromosomes. c.1038G>A has been reported in the literature in individuals affected with Lynch Syndrome, indicating the variant may be associated with disease. Other nucleotide changes (c.1038G>C and c.1038G>T) at the same position are also reported in HNPCC patients (HGMD and literature). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and all classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Feb 18, 2022	The c.1038G>A pathogenic mutation (also known as p.Q346Q), located in coding exon 11 of the MLH1 gene, results from a G to A substitution at nucleotide position 1038. This nucleotide substitution does not change the glutamine at codon 346. However, this change occurs in the last base pair of coding exon 11, which makes it likely to have some effect on normal mRNA splicing. This mutation has been identified in individuals who fulfilled Amsterdam I/II criteria and had Lynch syndrome associated tumors that demonstrated microsatellite instability or loss of both MLH1/PMS2 staining on immunochemistry (IHC) (Nakagawa H et al. Cancer Res. 2002 Aug;62(16):4579-82; 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. RNA studies have demonstrated that this mutation results in the activation of a cryptic donor splice site and inclusion of 59 nucleotides from intron 11, which is predicted to result in a translational frameshift (Nakagawa H et al Cancer Res. 2002 Aug;62(16):4579-82; Ambry internal data). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Aug 01, 2022	This synonymous variant causes a G>A nucleotide change in exon 11 of the MLH1 gene. A functional RNA study has shown that this variant causes the activation of a cryptic donor site and the inclusion of 59 nucleotides in the transcript (PMID: 12183410). As a result, this variant creates a frameshift and premature translation stop signal and is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with Lynch syndrome (PMID: 12183410, 15555211), and in an individual with early onset colorectal cancer that exhibited microsatellite instability and loss of MLH1 protein by immunohistochemistry analysis (PMID: 19731080). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MLH1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 02, 2024

This sequence change affects codon 346 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. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 12183410, 19731080). ClinVar contains an entry for this variant (Variation ID: 89616). 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 aberrant splicing and introduces a premature termination codon (PMID: 12183410). The resulting mRNA is expected to undergo nonsense-mediated decay. This variant disrupts the c.1038 nucleotide in the MLH1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 16341550, 18561205, 19419416). 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	22
DANN	Uncertain	0.97

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.88		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.88		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: rs63751715; hg19: chr3-37061954;