ClinVar Miner

Submissions for variant NM_000249.3(MLH1):c.52C>T (p.Arg18Cys) (rs367654552)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000130101 SCV000184931 likely benign Hereditary cancer-predisposing syndrome 2019-01-04 criteria provided, single submitter clinical testing Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;Other data supporting benign classification
Invitae RCV000199110 SCV000254370 uncertain significance Hereditary nonpolyposis colorectal neoplasms 2020-10-21 criteria provided, single submitter clinical testing This sequence change replaces arginine with cysteine at codon 18 of the MLH1 protein (p.Arg18Cys). The arginine residue is highly conserved and there is a large physicochemical difference between arginine and cysteine. This variant is present in population databases (rs367654552, ExAC 0.003%). This variant has been observed in individuals with colorectal cancer, suspected Lynch syndrome, and acute lymphocytic leukemia (PMID: 14635101, 21404117, 25980754, 26580448), and is recorded in the Universal Mutation Database (PMID: 22144684). However, in two individuals it co-occurs with a pathogenic MSH2 variant, suggesting that this c.52C>T substitution in MLH1 was not the primary cause of disease in these individuals. ClinVar contains an entry for this variant (Variation ID: 134656). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Counsyl RCV000410307 SCV000489172 uncertain significance Lynch syndrome II 2016-09-09 criteria provided, single submitter clinical testing
Color Health, Inc RCV000130101 SCV000537559 uncertain significance Hereditary cancer-predisposing syndrome 2020-12-23 criteria provided, single submitter clinical testing This missense variant replaces arginine with cysteine at codon 18 of the MLH1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in individuals affected Lynch syndrome-associated cancer and/or colorectal polyps (PMID: 14635101, 21404117, 25559809, 25980754) and breast cancer (PMID: 32601921) and in a healthy control (PMID: 24728327). This variant has been identified in 8/251420 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
GeneDx RCV000656856 SCV000565138 uncertain significance not provided 2020-09-21 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in individuals suspected of having Lynch syndrome, including at least one individual whose tumor showed microsatellite instability (Hardt 2011, Taylor 2013, Chubb 2015, Yurgelun 2015); This variant is associated with the following publications: (PMID: 24728327, 14635101, 22949387, 21404117, 25980754, 25559809, 26296696, 32008151, 29625052)
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000121355 SCV000592327 uncertain significance not specified 2016-02-10 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000656856 SCV000888190 uncertain significance not provided 2017-10-13 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000121355 SCV001360806 uncertain significance not specified 2020-07-10 criteria provided, single submitter clinical testing Variant summary: MLH1 c.52C>T (p.Arg18Cys) 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. The variant allele was found at a frequency of 3.2e-05 in 251420 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.52C>T has been reported in the literature in individuals affected with Hereditary Nonpolyposis Colorectal Cancer/Lynch Syndrome/Pediatric cancer cohort (example, Taylor_2003, Hardt_2011, Yurgelun_2015, Chubb_2015, Zhang_2015). These report(s) do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer/Lynch syndrome. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (VUS, n=6, likely benign, n=1). Based on the evidence outlined above, the variant was classified as uncertain significance.
Baylor Genetics RCV000410307 SCV001482846 uncertain significance Lynch syndrome II 2020-12-04 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
ITMI RCV000121355 SCV000085534 not provided not specified 2013-09-19 no assertion provided reference population

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