Submissions for variant NM_000249.4(MLH1):c.27G>A (p.Arg9=)

dbSNP: rs759680369

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000166655	SCV000217460	likely pathogenic	Hereditary cancer-predisposing syndrome	2024-01-31	criteria provided, single submitter	clinical testing	The c.27G>A variant (also known as p.R9R), located in coding exon 1 of the MLH1 gene, results from a G to A substitution at nucleotide position 27. This nucleotide substitution does not change the arginine at codon 9. This alteration was detected along with low-level constitutional MLH1 promoter methylation in a Caucasian male with 3 colorectal cancers, one of which demonstrated high microsatellite instability (MSI-H) with loss of MLH1 protein expression on immunohistochemistry (IHC). The father and mother of this proband were both diagnosed with colorectal cancer as well as a son, who died at age 22 from colorectal cancer. The son also carried the c.27G>A variant allele along with low-level constitutional MLH1 promoter methylation; however, two affected maternal family members did not carry this alteration and were negative for constitutional MLH1 promoter methylation indicating the variant allele may have been paternally inherited (Ward RL et al. Genet. Med. 2013 Jan;15:25-35). This alteration was also reported in a French family that fulfilled Amsterdam I criteria and exhibited low-level constitutional MLH1 promoter methylation. Four family members, two diagnosed with colorectal cancer and two with colorectal adenomas, carried the c.27G>A allele along with low-level constitutional MLH1 promoter methylation. This alteration was identified in another unrelated individual in this study who was diagnosed with colorectal cancer as well as endometrial cancer and had constitutional MLH1 promoter methylation (Leclerc J et al. Genet. Med. 2018 12;20:1589-1599). In our clinical cohort, this alteration also segregated with low-level constitutional MLH1 promoter methylation and disease in families meeting clinical diagnostic criteria for Lynch syndrome (Ambry internal data). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. RNA studies have demonstrated this alteration does not result in abnormal splicing in the set of samples tested (Ambry internal data). Based on the majority of available evidence to date, this variant is likely to be pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000471119	SCV000555984	likely pathogenic	Hereditary nonpolyposis colorectal neoplasms	2024-12-20	criteria provided, single submitter	clinical testing	This sequence change affects codon 9 of the MLH1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the MLH1 protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with Lynch syndrome-associated tumors and Lynch syndrome (PMID: 22878509, 29790873; internal data). It has also been observed to segregate with disease in related individuals. Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this MLH1 variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 1,370,736 individuals referred to our laboratory for MLH1 testing. ClinVar contains an entry for this variant (Variation ID: 186982). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. 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.
Baylor Genetics	RCV003468790	SCV004190605	likely pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2024-01-05	criteria provided, single submitter	clinical testing
Clinical Genetics Laboratory, Skane University Hospital Lund	RCV004696863	SCV005199133	likely pathogenic	not provided	2024-03-25	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV004700511	SCV005203190	likely pathogenic	Hereditary nonpolyposis colon cancer	2024-07-08	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.27G>A alters a non-conserved nucleotide resulting in a synonymous change. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 251448 control chromosomes. c.27G>A has been reported in the literature in multiple individuals from a family affected with colorectal cancer (Leclerc_2018, Ward_2013). This variant also co-occurred with two pathogenic variants in CHEK2 and HOXB13 in a patient with multiple cancers including colon cancer, ovarium cancer, endometrium cancer and and CLL (Wallander_2021). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 29790873, 34711244, 22878509). ClinVar contains an entry for this variant (Variation ID: 186982). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV004696863	SCV005623578	uncertain significance	not provided	2024-06-07	criteria provided, single submitter	clinical testing	The MLH1 c.27G>A (p.Arg9=) synonymous variant has been reported in the published literature along with low-level constitutional MLH1 promoter methylation in families with colorectal cancer (PMID: 29790873 (2018), 22878509 (2013)). This variant along with MLH1 promoter methylation has also been reported in an individual with colorectal cancer and endometrial cancer that showed microsatellite instability and loss of MLH1 and PMS2 protein expression (PMID: 29790873 (2018)). In addition, this variant has been reported in individuals with early onset colon cancer, breast cancer, and with a family history of Lynch syndrome associated cancers (personal communication with Ambry Genetics and Invitae related to ClinVar ID: 186982). 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 does not affect MLH1 mRNA splicing. Based on the available information, we are unable to determine the clinical significance of this variant.