Submissions for variant NM_000249.4(MLH1):c.1808C>G (p.Pro603Arg)

gnomAD frequency: 0.00009  dbSNP: rs63750876

Total submissions: 16

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075369	SCV000106364	likely benign	Lynch syndrome	2013-09-05	reviewed by expert panel	research	Multifactorial likelihood analysis posterior probability 0.001-0.049
Ambry Genetics	RCV000130908	SCV000185817	likely benign	Hereditary cancer-predisposing syndrome	2018-12-19	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.
GeneDx	RCV000034541	SCV000211144	likely benign	not provided	2021-03-04	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 11726306, 17510385, 21404117, 23047549, 23741719, 19117025, 22736432, 24362816, 22949387, 22703879, 25871441, 18561205, 22290698, 31784484)
Invitae	RCV001082925	SCV000218694	benign	Hereditary nonpolyposis colorectal neoplasms	2024-01-31	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000130908	SCV000537430	likely benign	Hereditary cancer-predisposing syndrome	2015-03-07	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003891466	SCV000805956	likely benign	MLH1-related condition	2019-04-09	criteria provided, single submitter	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000034541	SCV000889389	benign	not provided	2022-07-10	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000417382	SCV000919654	benign	not specified	2021-10-03	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.1808C>G (p.Pro603Arg) results in a non-conservative amino acid change located in the DNA mismatch repair protein Mlh1, C-terminal domain (IPR032189) 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 0.00016 in 251344 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer (0.00016 vs 0.00071), allowing no conclusion about variant significance. However, it is predominantly observed in the Ashkenazi Jewish subpopulation at a frequency of 0.0028 (28/10076). This frequency is about 4 times the estimated maximal expected allele frequency of a pathogenic MLH1 variant (0.0007105), suggesting this is likely a benign polymorphism found primarily in the populations of Ashkenazi Jewish origin. c.1808C>G has been reported in the literature in individuals affected with a variety of cancers such as Hereditary Nonpolyposis Colorectal Cancer/Lynch syndrome, epithelial ovarian cancer (example, Hardt_2011, Tournier_2008, Pal_2012). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer/Lynch syndrome. At-least one co-occurrence with another pathogenic variant has been reported in the UMD database (MLH1 complete gene deletion), providing supporting evidence for a benign role. Several publications report experimental evidence evaluating an impact on protein function (example, Takahashi_2007, Drost_2018). The most pronounced variant effect results in 82.5% normal mismatch repair (MMR) activity (Takahashi_2007), while a subsequent study reports 97% of normal mismatch repair (MMR) activity (Drost_2018). Furthermore, binding partner interaction as determined by Y2H assays is +, Nuclear localization as determined by transfections of fluorescently tagged proteins combined with microscopy is + (Drost_2018). Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation with a predominant consensus as likely benign/benign (n=7) (VUS, n=2). Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as benign.
Mendelics	RCV000987184	SCV001136423	likely benign	Colorectal cancer, hereditary nonpolyposis, type 2	2019-05-28	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000987184	SCV001310414	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2017-04-28	criteria provided, single submitter	clinical testing	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Sema4, Sema4	RCV000130908	SCV002528678	benign	Hereditary cancer-predisposing syndrome	2020-07-15	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000417382	SCV002760293	likely benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV000987184	SCV004015884	likely benign	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-07	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000034541	SCV004033982	likely benign	not provided	2023-08-01	criteria provided, single submitter	clinical testing	MLH1: PP3, BS3
Biesecker Lab/Clinical Genomics Section, National Institutes of Health	RCV000034541	SCV000043326	variant of unknown significance	not provided	2012-07-13	no assertion criteria provided	research	Converted during submission to Uncertain significance.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001356052	SCV001551110	likely benign	Malignant tumor of breast		no assertion criteria provided	clinical testing	The MLH1 p.Pro603Arg variant was identified in 6 of 4996 proband chromosomes (frequency: 0.005) from individuals or families with lynch syndrome and ovarian cancer (Pal 2012, South 2009, Hardt 2011, Borras 2012, Tournier 2008). The variant was identified in dbSNP (rs63750876) as “with uncertain significance allele”, ClinVar (classified as likely benign by GeneDx, Ambry Genetics, Integrated Genetics, Color and 2 other submitters, uncertain significance by Prevention Genetics and NIH and benign by Invitae and Quest Diagnostics) and UMD-LSDB (observed 4x). The variant was identified in control databases in 44 of 282,716 chromosomes at a frequency of 0.0002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Ashkenazi Jewish in 29 of 10,366 chromosomes (freq: 0.003 increasing the likelihood this could be a low frequency benign variant), Other in 5 of 7218 chromosomes (freq: 0.0007), European in 8 of 129,068 chromosomes (freq: 0.00006), Latino in 2 of 35,438 chromosomes (freq: 0.00006), while the variant was not observed in the African, East Asian, Finnish, and South Asian populations. Expression of the variant in yeast and human cells had no demonstrated effect on MLH1 protein levels, MMR activity and splicing (Norras 2012, Hardt 2011, Tournier 2008, Takahashi 2007). The p.Pro603 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.