Submissions for variant NM_000249.4(MLH1):c.1918C>T (p.Pro640Ser)

dbSNP: rs63749792

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075424	SCV000106419	likely pathogenic	Lynch syndrome	2018-10-18	reviewed by expert panel	curation	Abrogated function & >2 MSI-H tumours
Invitae	RCV000791363	SCV000254362	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2023-11-15	criteria provided, single submitter	clinical testing	This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 640 of the MLH1 protein (p.Pro640Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome (PMID: 15365995, 16276679, 22854115, 24278394, 24292105; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 89945). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt MLH1 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects MLH1 function (PMID: 21404117, 23403630). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics	RCV000569430	SCV000676063	pathogenic	Hereditary cancer-predisposing syndrome	2023-03-06	criteria provided, single submitter	clinical testing	The p.P640S variant (also known as c.1918C>T), located in coding exon 17 of the MLH1 gene, results from a C to T substitution at nucleotide position 1918. The proline at codon 640 is replaced by serine, an amino acid with similar properties. This alteration has been reported in multiple individuals with personal and/or family histories suggestive of, or consistent with, Lynch syndrome (Shin YK et al. Hum. Mutat. 2004 Oct;24:351; Giraldo A et al. Fam. Cancer. 2005;4:285-90; Hardt K et al. Fam. Cancer. 2011 Jun;10:273-84; Plummer JM et al. Can J Surg. 2012 Oct;55:294-300; De Lellis L et al. PLoS ONE. 2013 Nov;8:e81194). In our internal laboratory cohort, p.P640S was identified in a proband whose colorectal cancer exhibited microsatellite instability and absent MLH1 and PMS2 on IHC (Ambry internal data). In addition, this alteration has been seen in three unrelated probands meeting revised Bethesda criteria (Park K et al. Lab Med Online. 2018 Oct;8(4):156-166). Studies in yeast-based assays have shown this alteration results in reduced function and decreased relative MLH1 expression in a human cell line (Hardt K et al. Fam. Cancer. 2011 Jun;10:273-84). In an in vitro MMR complementation assay, this alteration had approximately 80% relative repair activity and also had reduced MLH1 expression (approximately 30% of wild type) in a human cell line (Hinrichsen I et al. Clin. Cancer Res. 2013 May;19:2432-41). Based on internal structure analysis, this variant is part of a structured region with known function and is more destabilizing than known likely pathogenic variants in the region (Ambry internal data). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. In addition, this alteration is predicted to be deleterious by MAPP-MMR in silico analysis (Chao EC et al. Hum. Mutat. 2008 Jun;29:852-60). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001193959	SCV001363155	likely pathogenic	Hereditary nonpolyposis colon cancer	2019-05-14	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.1918C>T (p.Pro640Ser) results in a non-conservative amino acid change located in the 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 was absent in 251338 control chromosomes (gnomAD). c.1918C>T has been reported in the literature in multiple individuals affected with Lynch Syndrome (e.g. Giraldo_2005, Kang_2015, Shin_2004, Woo_2014), where in one family co-segregation with the disease was observed (Giraldo_2005), and in several cases microsatellite instable tumor and the loss of MLH1 protein was indicated (Kang_2015, Plummer_2012, and in the UMD database). These data indicate that the variant is very likely to be associated with disease. Experimental evidence demonstrated the variant had no impact on splicing (Tournier_2008), however the variant protein had decreased stability, impaired interaction with PMS2 and exhibited about 30% repair activity compared to wild type (Hardt_2011, Hinrichsen_2013). Three submitters, have provided clinical-significance assessments for this variant in ClinVar after 2014 (without evidence for independent evaluation), and classified the variant as likely pathogenic (2x) and VUS (1x). Based on the evidence outlined above, the variant was classified as likely pathogenic.
AiLife Diagnostics, AiLife Diagnostics	RCV002223786	SCV002502695	likely pathogenic	not provided	2021-03-26	criteria provided, single submitter	clinical testing
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics	RCV002291271	SCV002583565	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2021-12-20	criteria provided, single submitter	research	A heterozygous missense variation in exon 17 of the MLH1gene that results in the amino acid substitution of Proline for serine at codon 640 was detected. The observed variant c.1918C>T (p.Pro640Ser) has not been reported in the 1000 genomes and gnomAD databases. but has been reported as pathogenic in ClinVar and InSiGHT database The reference codon is conserved across species.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001354000	SCV000592427	pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	The p.Pro640Ser variant was previously reported in 2/238 proband chromosomes (frequency of 0.006) in individuals with HNPCC or colorectal cancer (Giraldo_2005_16341804, Shin_2004_15365995), no controls were included in these studies. The p.Pro640 residue is conserved across mammals and lower species and computational analyses (Polyphen2, SIFT, AlignGVGD) suggest that the p.Pro640Ser variant may impact the protein with 3 out of 3 programs predicting pathogenicity. However, this information alone is not predictive enough to assume pathogenicity. An investigation of 23 MLH1 missense variants identified in families from the German HNPCC consortium by two functional in vivo assays in yeast concluded that p.Pro640Ser has a potential deleterious functional outcome (Hardt_2011_21404117). This variant occurs in the protein interaction domain and the p.Pro640Ser varaint also displayed a reduced capacity to interact with hMsh2 (Sun_2002_ 12414623). In addition, this variant was demonstrated to segregate in 3 affected Lynch syndrome family members (Giraldo_2005_16341804), suggesting this variant is pathogenic. In summary, based on the above information, this variant meets our laboratory's criteria to be classified as pathogenic.