Submissions for variant NM_000249.4(MLH1):c.306G>A (p.Glu102=)

gnomAD frequency: 0.00001  dbSNP: rs63751665

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000622520	SCV000740677	uncertain significance	Lynch syndrome 1	2018-06-13	reviewed by expert panel	curation	Criteria changed for variants in last base of exon therefore downgrade classification
Ambry Genetics	RCV000215920	SCV000276776	pathogenic	Hereditary cancer-predisposing syndrome	2023-01-29	criteria provided, single submitter	clinical testing	The c.306G>A pathogenic mutation (also known as p.E102E), located in coding exon 3 of the MLH1 gene, results from a G to A substitution at nucleotide position 306. This nucleotide substitution does not change the codon at position 102. However, this change occurs in the last base pair of coding exon 3, which makes it likely to have some effect on normal mRNA splicing. This alteration has been observed in the homozygous state in a patient with clinical features of constitutional mismatch repair deficiency (CMMRD) and in a second patient without consistent clinical features of CMMRD (Ambry internal data, interlaboratory correspondence). This alteration has been observed in the heterozygous state in a proband whose Lynch-syndrome associated tumor demonstrated loss of both MLH1/PMS2 expression on immunohistochemistry (IHC) (Ambry internal data). In a cohort of hereditary breast and ovarian cancer patients (N=95), this alteration was identified once in an individual with invasive ductal carcinoma diagnosed at the age of 40 (da Costa E Silva Carvalho S et al. BMC Med Genomics, 2020 02;13:21). Another alteration at the same position, c.306G>T, has been reported to result in abnormal splicing and has been detected in multiple individuals with family histories meeting Amsterdam criteria and/or loss of PMS2 expression on IHC with high microsatellite instability in their Lynch syndrome-associated tumors (Ambry internal data). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Based on the total supporting evidence, this alteration is interpreted as a disease-causing mutation. However, in the homozygous state, this alteration may be associated with a variable phenotype with respect to CMMRD. Clinical correlation is advised.
GeneDx	RCV000519380	SCV000618506	likely pathogenic	not provided	2023-06-05	criteria provided, single submitter	clinical testing	Alters the last nucleotide of the exon and is predicted to destroy the splice donor site and result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown; Observed in individuals with colon cancer displaying loss of MLH1 on immunohistochemistry (IHC) studies at this laboratory and in an individual with breast cancer in published literature (da Costa e Silva Carvalho et al., 2020); Not observed at significant frequency in large population cohorts (gnomAD); Deletions involving coding exons of this gene are a known mechanism of disease (HGMD); This variant is associated with the following publications: (PMID: 32039725)
Invitae	RCV001241653	SCV001414684	likely pathogenic	Hereditary nonpolyposis colorectal neoplasms	2023-07-16	criteria provided, single submitter	clinical testing	This sequence change affects codon 102 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 likely results in a shortened protein product. This variant is present in population databases (rs63751665, gnomAD 0.01%). This variant has been observed in individual(s) with clinical features of Lynch syndrome (Invitae). ClinVar contains an entry for this variant (Variation ID: 232603). 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 3, but is expected to preserve the integrity of the reading-frame (Invitae). This variant disrupts the ATP binding and hydrolysis domain of the MLH1 protein, which is important for the mismatch repair activity (PMID: 22753075, 21404117). While functional studies have not been performed to directly test the effect of this variant on MLH1 protein function, this suggests that disruption of this region of the protein is causative of disease. This variant disrupts the c.306G nucleotide in the MLH1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 9536098, 17510385, 17576681, 21520333, 22736432, 23729658, 26659639, 26681312). 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001553750	SCV001774740	uncertain significance	not specified	2021-08-02	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.306G>A (p.Glu102Glu) 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 weakens a 5 prime donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 1.6e-05 in 251334 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.306G>A has been reported in the literature in one individual affected with Breast Cancer (Carvalho_2020). This report does not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (pathogenic/likely pathogenic n=2, VUS n=2). Another variant affecting same nucleotide, c. 306G>T, has been reported to associate with colorectal cancer (HGMD database). Based on the evidence outlined above, the variant was classified as uncertain significance.
All of Us Research Program, National Institutes of Health	RCV003997987	SCV004836938	pathogenic	Lynch syndrome	2023-10-02	criteria provided, single submitter	clinical testing	This synonymous variant does not change the encoded amino acid at codon 102 of the MLH1 protein, but it causes a G to A substitution at the last nucleotide of exon 3 of the MLH1 gene. Splice site prediction tools suggest that this variant may have a significant impact on RNA splicing by impairing the intron 3 splice donor site. RNA studies have shown that this variant results in exon 3 skipping resulting in an in-frame deletion within the ATPase domain, which is important for the mismatch repair activity (ClinVar: SCV001414684.3). Another variant at this position (c.306G>T) has also been observed to cause exon 3 skipping (PMID: 22736432). The MLH1 c.306G>A, p.Glu102= variant has been reported in individuals affected with Lynch syndrome tumors displaying loss of MLH1 on immunohistochemistry (ClinVar: SCV001414684.3, SCV000276776.7, SCV000618506.2), breast cancer (PMID: 32039725), and homozygous in a patient with constitutional mismatch repair deficiency syndrome (ClinVar: SCV000276776.7). Other variants at the same nucleotide position are classified as Pathogenic in ClinVar (Variation ID: 90150, 90151). This variant has been identified in 4/251334 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic.