Submissions for variant NM_000249.4(MLH1):c.1013A>G (p.Asn338Ser)

gnomAD frequency: 0.00006  dbSNP: rs63751467

Total submissions: 18

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000128912	SCV000172779	likely benign	Hereditary cancer-predisposing syndrome	2019-02-04	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: 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.
Invitae	RCV000524219	SCV000218987	benign	Hereditary nonpolyposis colorectal neoplasms	2024-02-01	criteria provided, single submitter	clinical testing
GeneDx	RCV000656860	SCV000279079	likely benign	not provided	2021-01-04	criteria provided, single submitter	clinical testing	Dominguez-Valentin M et al. (2013) Hereditary cancer in clinical practice 11 (1):18 (PMID: 24344984); Amendola LM et al. (2015) Genome Res 25 (3):305-15 (PMID: 25637381); Chao EC et al. (2008) Human mutation 29 (6):852-60 (PMID: 18383312); This variant is associated with the following publications: (PMID: 23741719, 23354017, 18561205, 24344984, 32659497, 21404117, 24096645, 22252508, 12095971, 23047549, 25637381, 18383312, 26898890, 28874130, 29520894, 28767289, 30998989, 31391288, 31784484, 31332305)
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000220791	SCV000539649	uncertain significance	not specified	2016-08-12	criteria provided, single submitter	clinical testing	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: ClinVar: VUS by expert panel in 2013, no new evidence suggesting pathogenicity since then
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000220791	SCV000601340	uncertain significance	not specified	2021-03-17	criteria provided, single submitter	clinical testing
Color Diagnostics, LLC DBA Color Health	RCV000128912	SCV000684708	uncertain significance	Hereditary cancer-predisposing syndrome	2023-02-08	criteria provided, single submitter	clinical testing	This missense variant replaces asparagine with serine at codon 338 of the MLH1 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have reported that this variant does not impact MLH1 function in a methylation tolerance assay (PMID: 30998989), or the MLH1 protein's stability, damage response signaling, and DNA repair function (doi: 10.1101/2021.12.14.472580). This variant has been detected in at least six individuals affected with Lynch syndrome or associated cancer (PMID: 12095971, 18561205, 21404117, 23047549, 23354017), multiple individuals affected with breast cancer (PMID: 26898890, 33471991), and an individual affected with pancreatic cancer (PMID: 28767289). This variant has also been detected in ten unaffected controls in a large breast cancer case-control study (PMID: 33471991). An analysis of tumor characteristic from a variant carrier reported a likelihood ratio for pathogenicity of 0.100 (PMID: 31391288). This variant has been identified in 24/282676 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may not be associated with disease, additional evidence is necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Mendelics	RCV000075074	SCV000838006	uncertain significance	Lynch syndrome	2018-07-02	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV000764485	SCV000895556	uncertain significance	Mismatch repair cancer syndrome 1; Muir-Torré syndrome; Colorectal cancer, hereditary nonpolyposis, type 2	2018-10-31	criteria provided, single submitter	clinical testing
Mendelics	RCV000987162	SCV001136393	uncertain significance	Colorectal cancer, hereditary nonpolyposis, type 2	2019-05-28	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000220791	SCV001339155	benign	not specified	2023-03-13	criteria provided, single submitter	clinical testing	Variant summary: MLH1 c.1013A>G (p.Asn338Ser) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 9.2e-05 in 251274 control chromosomes (gnomAD). This frequency is not higher than the estimated maximum expected for a pathogenic variant in MLH1 causing Hereditary Nonpolyposis Colorectal Cancer (0.00071), allowing no conclusion about variant significance. c.1013A>G has been reported in the literature in individuals affected with colorectal cancer and other tumor phenotypes (e.g. Hardt_2011, Pal_2012, Rodriguez-Soler_2013, Caminsky_2016, Rossi_2017, Shindo_2017, Koger_2018, Li_2020, Hu_2020, Mio_2021, Dorling_2021, Pearlman_2021, Brady_2022), but was also found in several cancer-free controls (Dorling_2021). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. Co-occurrences with other pathogenic variant(s) have been reported (MSH2 c.484G>A, p.Gly162Arg; in an internal LCA sample), providing supporting evidence for a benign role. In functional studies the variant was found to have no effect on RNA splicing (Tournier_2008, Morak_2019), protein expression, and protein stability, mismatch repair activity (Koger_2018, Bouvet_2019, Houlleberghs_2019, Rath_2022). 13 other submitters have provided clinical-significance assessments for this variant in ClinVar after 2014, mostly without evidence for independent evaluation, and classified the variant as VUS (n=9), likely benign (n=3) or benign (n=1). Based on the evidence outlined above, the variant was classified as benign.
CeGaT Center for Human Genetics Tuebingen	RCV000656860	SCV001500304	likely benign	not provided	2020-08-01	criteria provided, single submitter	clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	RCV000656860	SCV002009382	uncertain significance	not provided	2021-11-03	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000128912	SCV002536424	uncertain significance	Hereditary cancer-predisposing syndrome	2021-11-07	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000220791	SCV002552450	uncertain significance	not specified	2023-08-15	criteria provided, single submitter	clinical testing
German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne	RCV003483462	SCV004228280	uncertain significance	Hereditary breast ovarian cancer syndrome	2023-07-14	criteria provided, single submitter	curation	33/60466 cases; 10/53461 controls, Prediction uneinheitlich. According to the ACMG standard criteria we chose this criterium: BS3 (strong benign): In functional studies the variant was found to have no effect on RNA splicing (Tournier_2008, Morak_2019), protein expression, and protein stability, mismatch repair activity (Koger_2018, Bouvet_2019, Houlleberghs_2019, Rath_2022).
CSER _CC_NCGL, University of Washington	RCV000148621	SCV000190336	uncertain significance	Colorectal cancer, non-polyposis	2014-06-01	no assertion criteria provided	research
Department of Pathology and Laboratory Medicine, Sinai Health System	RCV001356843	SCV001552114	uncertain significance	Malignant tumor of breast		no assertion criteria provided	clinical testing	The MLH1 p.Asn338Ser variant was identified in 5 of 7614 proband chromosomes (frequency: 0.001) from individuals or families with colon, and ovarian cancer (Chao 2008, Hardt 2011, Pal 2012, Rodriguez-Soler 2013). The variant was also identified in the following databases: dbSNP (ID: rs63751467) as “With Uncertain significance allele”, in ClinVar (classified as likely benign by Ambry Genetics; classified as uncertain significance by Invitae, GeneDx, Color Genomics and 4 clinical laboratories), Clinvitae, UMD-LSDB (5X as unclassified variant), Mismatch Repair Genes Variant Database, and the Insight Hereditary Tumors Database (15X Class3). The variant was not identified in COGR, Cosmic, MutDB, or the Zhejiang Colon Cancer Database. The variant was identified in control databases in 23 of 277060 chromosomes at a frequency of 0.0001 (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: African in 1 of 24032 chromosomes (freq: 0.00004), Latino in 2 of 34418 chromosomes (freq: 0.0001), European in 16 of 126584 chromosomes (freq: 0.0001), Finnish in 2 of 25792 chromosomes (freq: 0.0001), and South Asian in 2 of 30780 chromosomes (freq: 0.0001); it was not observed in the “Other”, Ashkenazi Jewish, or East Asian populations. Several publications provide inconsistent predictions regarding the effect of the variant on protein and splicing. The variant was shown to have a deleterious effect with an in silico model (Chao 2008), while the variant has no effect on splicing in the pCAS ExVivo Splicing Assay (Tournier 2008). The p.Asn338 residue is conserved in mammals but not in more distantly related organisms, and four out of five 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 4 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. However, this information is not predictive enough to assume pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.
Genetic Services Laboratory, University of Chicago	RCV000220791	SCV003839720	uncertain significance	not specified	2022-07-12	no assertion criteria provided	clinical testing	DNA sequence analysis of the MLH1 gene demonstrated a sequence change, c.1013A>G, in exon 11 that results in an amino acid change, p.Asn338Ser. This sequence change has been previously described in individuals with colorectal cancer (PMIDs: 12095971, 23354017, 28874130, 29520894, 18561205) and other cancers including breast and pancreatic cancer (PMIDs: 26898890, 28767289). This sequence change has been described in the gnomAD database with a frequency of 0.012% in the European subpopulation (dbSNP rs63751467). The p.Asn338Ser change affects a moderately conserved amino acid residue located in a domain of the MLH1 protein that is not known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Asn338Ser substitution. Experimental studies have shown that this variant does not have an impact on mRNA splicing (PMID: 18561205, 31332305) and on mismatch repair activity (PMID: 31784484). Another study reported that this variant does not impact MLH1 function in a methylation tolerance assay (PMID: 30998989) and other study reported that this variant has similar expression level as wildtype protein (PMID: 29520894). An analysis of tumor characteristic from a variant carrier reported a likelihood ratio for pathogenicity of 0.100 (PMID: 31391288). In another study, this variant was shown to have a deleterious effect with an in silico model (PMID: 18383312). While there is suspicion that this variant may not be associated with disease, additional studies are necessary to determine the role of this variant in disease conclusively. Due to contradictory evidence, the clinical significance of the p.Asn338Ser change therefore remains unknown at this time.