Submissions for variant NM_000249.4(MLH1):c.803A>G (p.Glu268Gly)

gnomAD frequency: 0.00014  dbSNP: rs63750650

Total submissions: 15

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075874	SCV000106889	no known pathogenicity	Lynch syndrome	2013-09-05	reviewed by expert panel	research	Multifactorial likelihood analysis posterior probability <0.001
Ambry Genetics	RCV000130956	SCV000185871	likely benign	Hereditary cancer-predisposing syndrome	2018-12-27	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Invitae	RCV000524319	SCV000253146	benign	Hereditary nonpolyposis colorectal neoplasms	2024-01-24	criteria provided, single submitter	clinical testing
Counsyl	RCV000410902	SCV000488222	benign	Colorectal cancer, hereditary nonpolyposis, type 2	2016-02-02	criteria provided, single submitter	clinical testing
GeneDx	RCV001703977	SCV000513617	likely benign	not provided	2019-06-05	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 25637381, 26761715, 21404117, 18383312, 17510385, 9611074, 11304573, 25871441, 17192056, 23741719, 22290698)
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000434087	SCV000539639	uncertain significance	not specified	2016-03-28	criteria provided, single submitter	clinical testing	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Insufficient evidence for pathogenicity, ExAC: 0.1% (6/6614) Finnish chromosomes
Color Diagnostics, LLC DBA Color Health	RCV000130956	SCV000684872	likely benign	Hereditary cancer-predisposing syndrome	2015-12-02	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000434087	SCV000919658	likely benign	not specified	2020-10-05	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.803A>G (p.Glu268Gly) results in a non-conservative amino acid change located in the DNA mismatch repair protein family, N-terminal domain (IPR002099) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00025 in 251626 control chromosomes, predominantly at a frequency of 0.00015 within the Non-Finnish European subpopulation in the gnomAD database. This frequency is not significantly higher than expected for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer (0.00025 vs 0.00071), allowing no conclusion about variant significance. c.803A>G has been reported in the literature in individuals affected with Hereditary Nonpolyposis Colorectal Cancer and also in breast and ovarian cancer (example: Jarhelle_2019, Liu_1998). These reports however, do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. Co-occurrence with other pathogenic variant have been reported (MSH2 c.1552_1553delCA, p.Gln518fs), providing supporting evidence for a benign role (Liu_1998). In in vitro functional MMR activity assays, the variant was found to have >50%-90% of normal activity. Seven other ClinVar submitters (evaluation after 2014) cite the variant as benign/likely benign (n=6) or uncertain significance (n=1). Based on the evidence outlined above, the variant was classified as likely benign.
Mendelics	RCV000410902	SCV001136386	benign	Colorectal cancer, hereditary nonpolyposis, type 2	2019-05-28	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000434087	SCV002773901	benign	not specified	2021-07-30	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV000410902	SCV004018131	likely benign	Colorectal cancer, hereditary nonpolyposis, type 2	2023-03-14	criteria provided, single submitter	clinical testing	This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752].
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000434087	SCV004024900	benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne	RCV003483464	SCV004228269	likely benign	Hereditary breast ovarian cancer syndrome	2023-12-12	criteria provided, single submitter	curation	BS1, BS3_sup, BP5. According to the ACMG standard criteria we chose these criteria: BP5 (supporting benign): 3 MSS tumours (1 Chao et al., 2008; 1 Hardt et al., 2011; 1 CRC LOVD:French), BS1 (strong benign): gnomad 0.0002404, BS3 (strong benign): Y2H, 25-75% Expression , 75 % MMR activity
CSER _CC_NCGL, University of Washington	RCV000148616	SCV000190331	likely benign	Colorectal cancer, non-polyposis	2014-06-01	no assertion criteria provided	research
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001357445	SCV001552919	likely benign	Carcinoma of colon		no assertion criteria provided	clinical testing	The MLH1 p.Glu268Gly variant was identified in 1 of 284 proband chromosomes (frequency: 0.004) from Swedish individuals or families with CRC, cooccurring with MSH2 c.1552_1553del, p.Gln518ValfsX10 (alias del CA at 518), and the proband’s tumour characterized as MSI positive, MLH1 IHC intact but MSH2 IHC deficient (Wahlberg 1999, Liu 1998, Salahshor 2001). Functional assays using minigene assays showed the variant yielded >70% transcripts with exon 10 inclusion; and ESR-dedicated bioinformatics tools showed there was no effect on splicing (Soukarieh 2016). Additional functional analyses using yeast assays/other demonstrated a dominant mutator effect, 79% in vitro MMR activity and 25-75% MLH1 expression (Takahashi 2007). A further bioinformatics algorithm using multivariate analysis assessed the variant to be deleterious with a MAPP-MMR score of 5.2, the optimal MAPP-MMR threshold segregating deleterious and neutral variants being 4.55 (Chao 2008). The variant was also identified in dbSNP (ID: rs63750650) as “other”, ClinVar (classified as benign, reviewed by an expert panel (2013); submitters: benign by InSIGHT, Counsyl; likely benign by Ambry Genetics, Invitae, GeneDx, CSER-CC-NCGL: University of Washington Medical Center; uncertain significance by Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine)), Clinvitae (5X), Insight Colon Cancer Gene Variant Database (21X as Class 1), and Mismatch Repair Genes Variant Database, but was not identified in Genesight-COGR, Cosmic, MutDB, UMD-LSDB, Zhejiang Colon Cancer Database, and Insight Hereditary Tumors Database. The variant was identified in control databases in 65 of 277192 chromosomes at a frequency of 0.0002 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The p.Glu268 residue is conserved in mammals but not in more distantly related organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the Gly variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and 4 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; however, this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.