Submissions for variant NM_000249.4(MLH1):c.649C>T (p.Arg217Cys)

gnomAD frequency: 0.00007  dbSNP: rs4986984

Total submissions: 15

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000590255	SCV000149392	likely benign	not provided	2020-12-10	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 8581513, 11555625, 17594722, 21901500, 11920458, 27487738, 29752822, 32601921, 23760103, 11781295, 20176959, 17510385, 22949387, 12810663, 27553368, 18094436, 8797773, 9559627, 15613555, 16425354, 22136435, 17074586, 27173243, 28452373, 28389907, 29505604, 28767289, 31010795, 30740464, 30521064, 30850667, 31386297, 31784484)
Labcorp Genetics (formerly Invitae), Labcorp	RCV001079587	SCV000166256	benign	Hereditary nonpolyposis colorectal neoplasms	2024-01-31	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV000115483	SCV000184755	likely benign	Hereditary cancer-predisposing syndrome	2018-09-24	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
Color Diagnostics, LLC DBA Color Health	RCV000115483	SCV000689902	benign	Hereditary cancer-predisposing syndrome	2015-12-08	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000212524	SCV000696175	benign	not specified	2023-07-24	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.649C>T (p.Arg217Cys) results in a non-conservative amino acid change located in the 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. 4/4 computational tools predict no significant impact on normal splicing. The variant allele was found at a frequency of 0.00041 in 252977 control chromosomes, predominantly at a frequency of 0.0047 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 7 fold of the estimated maximal expected allele frequency for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer phenotype (0.00071), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.649C>T has also been reported in the literature in several individuals affected with Lynch Syndrome, who were predominantly of Asian descent and the majority of these publications only performed evaluation of MLH1 and could not rule out variants in other Lynch syndrome associated genes. These reports therefore do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. In addition, in one publication (Sapari 2014), the variant was found in co-occurrence with another pathogenic MLH1 variant, c.790+1G>A (although it was only identified through NGS and not confirmed by Sanger sequencing). One co-occurrence with another pathogenic variant has been reported internally (BRCA2 c.1648G>T , p.Glu550X), providing supporting evidence for a benign role. Several publications reported experimental evidence evaluating an impact on protein function (Ellison 2001, Trojan 2002, Kondo 2003, Takahashi 2007, Zhao 2008, Peng 2016), showing no or only a mild effect on function. A recent study suggested based on in vitro evidence that the variant might affect splicing by affecting splicesome assembly (Rhine 2018), however earlier reports that identified the variant in patients through RNA-based direct sequencing, did not indicate any specific splicing effect (Furukawa 2002, Wang 2005); therefore, the significance of this finding is uncertain. The following publications have been ascertained in the context of this evaluation (PMID: 12810663, 18373977, 11555625, 8797773, 18069769, 17510385, 9419403, 15342696, 8581513, 11781295, 15613555, 11920458, 24933000, 25882375, 21901500, 27553368, 22136435, 16425354, 27173243, 27093186, 25338684, 28767289, 29050249, 29505604, 30850667, 31666926). Nine submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified as benign/likely benign (n=7) and VUS (n=2). Based on the evidence outlined above, the variant was classified as benign.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000590255	SCV000889402	benign	not provided	2022-04-01	criteria provided, single submitter	clinical testing
Cancer Genomics Group, Japanese Foundation For Cancer Research	RCV001030563	SCV001193607	uncertain significance	Hereditary breast ovarian cancer syndrome	2019-05-01	criteria provided, single submitter	research
Illumina Laboratory Services, Illumina	RCV000987154	SCV001305703	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2017-05-04	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	RCV000115483	SCV002528765	benign	Hereditary cancer-predisposing syndrome	2020-12-09	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000212524	SCV002552435	likely benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
Ding PR Lab, Sun Yat-sen University Cancer Center	RCV001093666	SCV001250847	uncertain significance	Lynch syndrome 1		no assertion criteria provided	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001354844	SCV001549555	likely benign	Carcinoma of colon		no assertion criteria provided	clinical testing	The MLH1 p.Arg217Cys variant was identified in 12 of 656 proband chromosomes (frequency: 0.02) from individuals or families with Extramammary Paget disease or sporadic colorectal cancer and was present in 8 of 1260 control chromosomes (frequency: 0.006) from healthy individuals (Kang 2016, Peng 2015). The variant was also identified in dbSNP (ID: rs4986984) as "With other allele”, ClinVar (classified as benign by Color; as likely benign by Invitae, GeneDx, Ambry Genetics and one clinical laboratory; as uncertain significance by two clinical laboratories), Cosmic (4x in Skin or bone tissue), MutDB , UMD-LSDB (2x as neutral), Zhejiang University Database, Mismatch Repair Genes Variant Database, and in Insight Hereditary Tumors (42x as uncertain) databases. The variant was not identified in COGR database. The variant was identified in control databases in 91 of 276864 chromosomes at a frequency of 0.0003 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European in 2 of 126374 chromosomes (freq: 0.00002), East Asian in 83 of 18868 chromosomes (freq: 0.004), and South Asian in 6 of 30782 chromosomes (freq: 0.0002), while the variant was not observed in the African, Other, Latino, Ashkenazi Jewish, and Finnish, populations. The p.Arg217 residue is conserved in mammals but not in more distantly related organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the 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 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. Several functional studies identified the variant might affect the MMR process at different levels and might have functional relation to gastrointestinal cancer. The variant showed variable levels of MMR activity (50%, 64.8%, or 81.3%) compare to WT however overall the studies concluded that although efficiency of MMR is slightly reduced it is still proficient (Kang 2016, Lucci-Cordisco 2006, Fan 2007, Takahashi 2007, Trojan 2002). 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.
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000590255	SCV001808355	likely benign	not provided		no assertion criteria provided	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000590255	SCV001963472	likely benign	not provided		no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003944989	SCV004762801	likely benign	MLH1-related disorder	2024-02-15	no assertion criteria provided	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).