Submissions for variant NM_000249.4(MLH1):c.883A>G (p.Ser295Gly)

dbSNP: rs63751598

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075902	SCV000106918	pathogenic	Lynch syndrome	2013-09-05	reviewed by expert panel	research	Variant causes aberrant splicing leading to protein conformational change and inactive protein: full inactivation of variant allele.
Ambry Genetics	RCV000561374	SCV000676030	pathogenic	Hereditary cancer-predisposing syndrome	2020-03-20	criteria provided, single submitter	clinical testing	The c.883A>G pathogenic mutation (also known as p.S295G), located in coding exon 10 of the MLH1 gene, results from an A to G substitution at nucleotide position 883, adjacent to the splice junction site. The serine at codon 295 is replaced by glycine, an amino acid with similar properties. This mutation has been reported in several families with Lynch syndrome to date (Wijnen J, et al. Am. J. Hum. Genet. 1997 Aug;61(2):329-35; Goldschmidt et al. Int. J. Cancer. 2005 116 (5): 808-12; Yurgelun et al. Gastroenterology. 2015; 149 (3): 604-13e20). In one such family, the alteration segregated with disease (Goldschmidt et al. Int. J. Cancer. 2005 116 (5): 808-12). Immunohistochemistry testing on the tumor of an individual with this alteration who meets Amsterdam I criteria showed absence of the MLH1 protein (Casey G et al. JAMA. 2005 Feb 16;293(7):799-809). Splicing analyses via mini-gene reporter assay and RT-PCR of patient lymphoblastoid cell lines indicated that this alteration results in aberrant splicing and exon skipping (van der Kilft et al. Mol. Genet. Genomic Med. 2015 3(4): 327-45; Casey G et al. JAMA. 2005 Feb 16;293(7):799-809). Further, functional studies suggest that this alteration results in moderately reduced mismatch repair activity and MLH1 expression levels (Takahashi M et al. Cancer Res. 2007 May; 67(10):4595-604). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Myriad Genetics, Inc.	RCV003452782	SCV004190046	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-07-18	criteria provided, single submitter	clinical testing	This variant is considered pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 15849752, 15713769].
Baylor Genetics	RCV003452782	SCV004190612	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-09-06	criteria provided, single submitter	clinical testing
Invitae	RCV003593892	SCV004293459	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2023-03-23	criteria provided, single submitter	clinical testing	For these reasons, this variant has been classified as Pathogenic. Studies have shown that this missense change alters mRNA splicing and is expected to lead to the loss of protein expression (PMID: 15713769, 15849752, 26247049, 26761715). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on MLH1 function (PMID: 17510385, 31697235). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 90409). This missense change has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 9311737, 15713769, 15849752, 17510385, 25980754). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 295 of the MLH1 protein (p.Ser295Gly). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product.
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001353633	SCV000592384	pathogenic	Carcinoma of colon		no assertion criteria provided	clinical testing	The MLH1 p.Ser295Gly variant has been previously reported in the literature. It was identified in 4 of 215 probands with colorectal cancer or who met Amsterdam criteria for HNPCC (Casey 2005, Wijnen 1997; Goldshmidt 2005). In one individual, absence of MLH1 expression was demonstrated by immunohistochemistry, strongly suggesting that this variant is pathogenic (Casey 2005). Another study demonstrated absence of the mutant product by RT-PCR and ~50% reduction of the transcript as the result of an unstable mRNA product. Furthermore, the variant was demonstrated to segregate with disease in 2 other family members (Goldshmidt 2005). One functional study showed this variant had reduced in-vitro mismatch repair activity and a dominant mutator phenotype (Takahashi 2007). In addition, the p.Ser295Gly variant occurs in the second last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position may affect splicing. In summary, based on the above information, this variant is classified as pathogenic.