Submissions for variant NM_000249.4(MLH1):c.677G>A (p.Arg226Gln)

dbSNP: rs63751711

Total submissions: 20

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	RCV000075809	SCV000106823	pathogenic	Lynch syndrome	2013-09-05	reviewed by expert panel	research	Variant causes splicing aberration leading to truncated protein: full inactivation of variant allele
Ambry Genetics	RCV000132197	SCV000187278	pathogenic	Hereditary cancer-predisposing syndrome	2021-12-03	criteria provided, single submitter	clinical testing	The c.677G>A pathogenic mutation (also known as p.R226Q), located in coding exon 8 of the MLH1 gene, results from a G to A substitution at nucleotide position 677. The amino acid change results in arginine to glutamine at codon 226, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 8, which makes it likely to have some effect on normal mRNA splicing. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This alteration has been reported in numerous hereditary non-polyposis colorectal cancer (HNPCC)/Lynch syndrome families, including individuals whose early-onset tumors demonstrated microsatellite instability, absence of MLH1 and PMS2 on immunohistochemistry, and normal MLH1 methylation levels (Liu SR et al. World J. Gastroenterol. 2004 Sep;10(18):2647-2651; Pigatto F et al. Hered Cancer Clin Pract, 2004 Nov;2:175-84; Overbeek L et al. Br. J. Cancer. 2007 May;96(10):1605-1612; Mueller J et al. Cancer Res, 2009 Sep;69:7053-61; Zhang JX et al. World J Gastroenterol, 2015 Apr;21:4136-49; Goldberg Y et al. Clin Genet, 2015 Jun;87:549-53; Simbolo M et al. Hered Cancer Clin Pract, 2015 Aug;13:18; Carneiro da Silva F et al. PLoS One, 2015 Oct;10:e0139753; Guindalini RS et al. Gastroenterology, 2015 Nov;149:1446-53; Lee J et al. BMC Cancer, 2017 12;17:843; Rohlin A et al. Fam Cancer, 2017 04;16:195-203; Alqahtani M et al. Fam Cancer, 2018 04;17:197-203; Jiang W et al. Int J Cancer, 2019 05;144:2161-2168). In addition, multiple independent RT-PCR studies have demonstrated that this alteration is associated with exon 8 skipping, resulting in a deletion of 89 base pairs that is predicted to cause a translational frameshift (Sharp A et al. Hum. Mutat. 2004 Sep;24(3):272; Pagenstecher C et al. Hum. Genet. 2006 Mar;19(1-2):9-22; Tournier I et al. Hum. Mut. 2008 Dec;29(12):1412-24). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Invitae	RCV000524312	SCV000284072	pathogenic	Hereditary nonpolyposis colorectal neoplasms	2024-01-02	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 226 of the MLH1 protein (p.Arg226Gln). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Lynch syndrome (PMID: 8571956, 12362047, 12547705, 12624141, 15300854, 16341550, 17453009). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 90318). 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in skipping of exon 8 and introduces a premature termination codon (PMID: 15300854, 16341550, 18561205, 21034533; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
GeneDx	RCV000202049	SCV000321896	pathogenic	not provided	2021-12-22	criteria provided, single submitter	clinical testing	Alters the last nucleotide of the exon and in silico analysis supports a deleterious effect on splicing; Protein and RNA-based functional studies show that this variant disrupts the adjacent natural splice donor site and results in skipping of exon 8, resulting in a frameshift (Leung 1998, Sharp 2004, Pagenstecher 2006, Tournier 2008).; Observed in several individuals meeting Amsterdam criteria, segregating with disease in at least two kindreds, and with most studied tumors demonstrating microsatellite instability and/or loss of MLH1 expression (Winjen 1996, Gille 2002, Hendriks 2003, de Jong 2004, Sheng 2006, Overbeek 2007, van der Klift 2016, Lee 2017, Rohlin 2017).; Not observed at significant frequency in large population cohorts (Lek 2016); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 19690142, 27601186, 12624141, 27696107, 26078562, 19248199, 25980754, 25430799, 8571956, 15200905, 16736289, 16341550, 18561205, 9311737, 12373605, 23760103, 15300854, 12547705, 17453009, 15778432, 14871975, 10422993, 12067992, 17054581, 17569143, 18692554, 11524701, 21034533, 12740349, 24362816, 26248088, 25892863, 26300997, 27435373, 28643016, 28127413, 29237405, 28874130, 27978560, 22290698, 28596308, 12362047, 17192056, 29505604, 9777949, 30787465, 28932927, 29575718, 30521064, 29887214, 22753075)
Counsyl	RCV000410542	SCV000489235	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2016-09-09	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000202049	SCV000601408	pathogenic	not provided	2021-03-23	criteria provided, single submitter	clinical testing	This variant has been described as pathogenic and/or having a deleterious effect on MLH1 protein function in the published literature by compromising normal splicing and resulting in the skipping of exon 8 (PMID: 15300854 (2004), 16341550 (2006), and 18561205 (2008)). This variant has been identified in patients with a personal and/or family history consistent with Lynch syndrome (PMID: 17453009 (2007), 25980754 (2015), and 27601186 (2016)). Based on the available information, this variant is classified as pathogenic.
Color Diagnostics, LLC DBA Color Health	RCV000132197	SCV000684857	pathogenic	Hereditary cancer-predisposing syndrome	2022-01-03	criteria provided, single submitter	clinical testing	This variant changes the last nucleotide c.G of exon 8 of the MLH1 gene and is predicted to impair RNA splicing at the intron 8 splice donor site. RNA studies with carrier individuals have shown that this variant cause an out-of-frame skipping of exon 8 (PMID:18561205) and exons 8-10 (PMID: 21034533). This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with Lynch syndrome (PMID: 12362047, 12547705, 12624141, 15300854, 16341550, 17453009, 18561205, 21034533). Loss of MLH1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.
Mendelics	RCV000075809	SCV000838003	pathogenic	Lynch syndrome	2018-07-02	criteria provided, single submitter	clinical testing
A.C.Camargo Cancer Center / LGBM, A.C.Camargo Cancer Center	RCV000075809	SCV000914317	pathogenic	Lynch syndrome	2019-01-30	criteria provided, single submitter	research
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000075809	SCV000917644	pathogenic	Lynch syndrome	2017-10-20	criteria provided, single submitter	clinical testing	Variant summary: The MLH1 c.677G>A (p.Arg226Gln) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). 4/5 splice prediction tools predict a significant impact on normal splicing. These predictions were also confirmed by functional studies, showing that the variant which is located at the last nucleotide of exon 8, disrupts the splice donor site and leads to skipping of exon 8, resulting in a frameshift with a consequential stop codon (Sharp 2004, Pagenstecher 2006, Tournier2008). Although the variant can be found in the literature under the name of p.Arg226Gln, the consequence of the variant nucleotide change at the amino acid level is more properly described as p.Gln197ArgfsX8, as cited in the literature (Moussa 2011, Lagerstedt-Robinson 2016). The variant has been reported in several individuals with Lynch syndrome tumors, with cases of confirmed co-segregation data (Wijnen 1996, de Jong 2004, Sharp 2004, Pagenstecher 2006, Moussa 2011, Lagerstedt-Robinson 2016). This variant is absent in 245866 control chromosomes. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.
Sema4, Sema4	RCV000132197	SCV002528768	pathogenic	Hereditary cancer-predisposing syndrome	2022-01-15	criteria provided, single submitter	curation
Revvity Omics, Revvity	RCV000202049	SCV003821617	pathogenic	not provided	2022-08-10	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV000410542	SCV004018169	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2023-03-15	criteria provided, single submitter	clinical testing	This variant is considered pathogenic. Functional studies indicate this variant impacts protein function [PMID:16341550]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 8571956,16341550].
Baylor Genetics	RCV000410542	SCV004193046	pathogenic	Colorectal cancer, hereditary nonpolyposis, type 2	2022-06-22	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000202049	SCV000257113	pathogenic	not provided		no assertion criteria provided	research
Ding PR Lab, Sun Yat-sen University Cancer Center	RCV001093688	SCV001250872	pathogenic	Lynch syndrome 1		no assertion criteria provided	clinical testing
Constitutional Genetics Lab, Leon Berard Cancer Center	RCV001250009	SCV001423910	pathogenic	Lynch-like syndrome	2019-07-01	no assertion criteria provided	clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV000202049	SCV001549017	pathogenic	not provided		no assertion criteria provided	clinical testing	 The MLH1 p.Arg226Gln variant was identified in 15 of 4876 proband chromosomes (frequency: 0.003) from individuals or families with Lynch Syndrome or  HNPCC  (Papp 2007, Spaepen 2006, Pagenstecher 2006, Dominguez-Valentin 2016, Gille 2002, Lagerstedt-Robinson 2016, Mensenkamp 2014, Overbeek 2007, Sheng 2006, Shirts 2018, Simbolo 2015, Spaepen 2006). The variant was also identified in dbSNP (ID: rs63751711) as "With Likely pathogenic, Pathogenic allele", ClinVar (classified as pathogenic by Invitae, GeneDx, Ambry Genetics and six other submitters), Cosmic (3x in skin or Large intestine tissue), UMD-LSDB (15x as causal), Zhejiang University Database (3x), Mismatch Repair Genes Variant Database, and in Insight Hereditary Tumors Database (64x as class 5). The variant was not identified in COGR, or MutDB, databases. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Arg226 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 p.Arg226Gln variant occurs in the last three bases of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In addition, 3 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. The variant is detected in Exon 8 at donor site of the intron, localized in the splice junction and is predicted to cause abnormal splicing. RNA analysis with a primer localized in exon 8, have shown that this substitution results in a complete loss of exon 8 (Pagenstecher 2006, Sharp 2004, Tournier 2008).  In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic.
Laboratory for Genotyping Development, RIKEN	RCV003162489	SCV002758042	pathogenic	Gastric cancer	2021-07-01	no assertion criteria provided	research
CZECANCA consortium	RCV003128139	SCV003804347	pathogenic	Endometrial carcinoma	2023-02-21	no assertion criteria provided	clinical testing