2-47806231-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000179.3(MSH6):c.3674C>T(p.Thr1225Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000576 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1225K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00011 (0 hom., cov: 33)
  • Exomes 𝑓: 0.000052 (0 hom.)
• Consequence: MSH6 NM_000179.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:13 B:2
• Conservation: PhyloP100: 7.51

Genes affected

MSH6 (HGNC:7329): (mutS homolog 6) This gene encodes a member of the DNA mismatch repair MutS family. In E. coli, the MutS protein helps in the recognition of mismatched nucleotides prior to their repair. A highly conserved region of approximately 150 aa, called the Walker-A adenine nucleotide binding motif, exists in MutS homologs. The encoded protein heterodimerizes with MSH2 to form a mismatch recognition complex that functions as a bidirectional molecular switch that exchanges ADP and ATP as DNA mismatches are bound and dissociated. Mutations in this gene may be associated with hereditary nonpolyposis colon cancer, colorectal cancer, and endometrial cancer. Transcripts variants encoding different isoforms have been described. [provided by RefSeq, Jul 2013]

FBXO11 (HGNC:13590): (F-box protein 11) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbxs class. It can function as an arginine methyltransferase that symmetrically dimethylates arginine residues, and it acts as an adaptor protein to mediate the neddylation of p53, which leads to the suppression of p53 function. This gene is known to be down-regulated in melanocytes from patients with vitiligo, a skin disorder that results in depigmentation. Polymorphisms in this gene are associated with chronic otitis media with effusion and recurrent otitis media (COME/ROM), a hearing loss disorder, and the knockout of the homologous mouse gene results in the deaf mouse mutant Jeff (Jf), a single gene model of otitis media. Alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSH6	NM_000179.3	c.3674C>T	p.Thr1225Met	missense_variant	8/10	ENST00000234420.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSH6	ENST00000234420.11	c.3674C>T	p.Thr1225Met	missense_variant	8/10	1	NM_000179.3	P4

Frequencies

GnomAD3 genomes AF: 0.000112 AC: 17 AN: 152102 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.0000944

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000756 AC: 19 AN: 251248 Hom.: 0 AF XY: 0.0000884 AC XY: 12 AN XY: 135780

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.0000980

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.000123

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000520 AC: 76 AN: 1461712 Hom.: 0 Cov.: 33 AF XY: 0.0000578 AC XY: 42 AN XY: 727156

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000928

Gnomad4 FIN exome AF: 0.0000749

Gnomad4 NFE exome AF: 0.0000531

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.000112 AC: 17 AN: 152220 Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8 AN XY: 74408

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.0000944

Gnomad4 NFE AF: 0.000162

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000766 Hom.: 0

Bravo AF: 0.0000604

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.000115 AC: 14

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:13 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:4

Uncertain significance, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 17, 2020	- -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Mar 01, 2023	In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Identified in individuals with colorectal or endometrial cancer, including some with tumor studies demonstrating results inconsistent with pathogenic variants in this gene (Wijnen et al., 1999; Hampel et al., 2006; Lagerstedt Robinson et al., 2007; Nilbert et al., 2009; Drost et al., 2012; Houlleberghs et al., 2017); Published functional assays demonstrate mismatch repair activity comparable to wild type (Drost et al., 2012; Houlleberghs et al., 2017); This variant is associated with the following publications: (PMID: 27601186, 10508506, 22102614, 17312306, 18566915, 16885385, 23621914, 26333163, 33726816, 12019211, 17531815, 21120944, 28531214, 34598035, 30982232, 32091409, 26689913, 24448499, 32547938, 29945567) -

not specified Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Oct 10, 2023	Variant summary: MSH6 c.3674C>T (p.Thr1225Met) results in a non-conservative amino acid change located in the C-terminal region (IPR000432) and ATPase domain (Houlleberghs_MSH6_PLOS Genetics_2017) 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 7.6e-05 in 251248 control chromosomes, predominantly at a frequency of 0.00012 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is slightly less than the estimated maximal expected allele frequency for a pathogenic variant in MSH6 causing Lynch Syndrome phenotype (0.00014), suggesting that the variant might be a benign polymorphism found primarily in populations of Non-Finnish European origin. The variant, c.3674C>T, has been reported in the literature in individuals affected with Lynch Syndrome, colorectal cancer or other cancers, without strong evidence for causality (examples: Wijnen 1999, Hampel_2006, Nilbert_2009, Lagerstedt-Robinson_2007 and 2016, Bhai_2021, Djursby_2022, Fanale_2022, Okawa_2023). An endometrial tumor sample from one patient showed microsatellite instability but showed retention of MSH6 and MSH2 and loss of MLH1/PMS2 with MLH1 promoter hypermethylation (Hampel_2006). Thus these data do not allow any conclusion about variant significance. At least two publications reported experimental evidence evaluating an impact on protein function, and showed no damaging effect of this variant (Drost 2011, Houlleberghs 2017). The following publications have been ascertained in the context of this evaluation (PMID: 22102614, 16885385, 28531214, 27601186, 17312306, 18566915, 26333163, 30982232, 10508506, 29945567, 34326862, 35904628, 35223509, 36243179). Ten submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments. Based on the evidence outlined above, the variant was classified as VUS - possibly benign. -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	Feb 06, 2024	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Dec 07, 2017	- -

Hereditary cancer-predisposing syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 05, 2023	This missense variant replaces threonine with methionine at codon 1225 of the MSH6 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). Functional studies have shown that this variant does not affect MSH6 protein mismatch repair function or result in DNA damage resistance (PMID: 22102614, 28531214). This variant has been reported in individuals affected with Lynch syndrome (PMID: 10508506, 18566915, 27601186), endometrial cancer (PMID: 16885385), head and neck squamous cell carcinoma (PMID: 34598035) and breast cancer (PMID: 30982232, 32547938). This variant has also been observed in an individual affected with colorectal cancer, whose tumor showed microsatellite stability and normal MSH6 protein expression (PMID: 17312306). This variant has been identified in 22/282650 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 01, 2023	The p.T1225M variant (also known as c.3674C>T), located in coding exon 8 of the MSH6 gene, results from a C to T substitution at nucleotide position 3674. The threonine at codon 1225 is replaced by methionine, an amino acid with similar properties. This variant has been identified in multiple high-risk colorectal/endometrial cancer patients (Wijnen J et al. Nat. Genet., 1999 Oct;23:142-4; Hampel H et al. Cancer Res., 2006 Aug;66:7810-7; Lagerstedt Robinson K et al. J. Natl. Cancer Inst., 2007 Feb;99:291-9; Nilbert M et al. Fam Cancer, 2009 Jun;8:75-83). However, functional analyses have demonstrated near-wild-type mismatch repair activity for the p.T1225M allele (Drost M et al. Hum Mutat., 2012 Mar;33:488-94; Houlleberghs H et al. PLoS Genet, 2017 May;13:e1006765). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -

Lynch syndrome 5 Uncertain:1 Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 29, 2023	This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752]. -
Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Aug 19, 2016	- -

Ovarian cancer Pathogenic:1

Likely pathogenic, flagged submission

clinical testing

Laboratory of Molecular Epidemiology of Birth Defects, West China Second University Hospital, Sichuan University

Jan 01, 2022

- -

Lynch syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Dec 01, 2023

This missense variant replaces threonine with methionine at codon 1225 of the MSH6 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). Functional studies have shown that this variant does not affect MSH6 protein mismatch repair function or result in DNA damage resistance (PMID: 22102614, 28531214). This variant has been reported in individuals affected with Lynch syndrome (PMID: 10508506, 18566915, 27601186), endometrial cancer (PMID: 16885385), head and neck squamous cell carcinoma (PMID: 34598035) and breast cancer (PMID: 30982232, 32547938). This variant has also been observed in an individual affected with colorectal cancer, whose tumor showed microsatellite stability and normal MSH6 protein expression (PMID: 17312306). This variant has been identified in 22/282650 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. -

Malignant tumor of breast Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The MSH6 p.Thr1225Met variant was identified in 8 of 11332 proband chromosomes (frequency: 0.0007) from individuals or families with HNPCC, Lynch syndrome, endometrial cancer, or prostate adenocarcinoma (Hampel 2006, Lagerstedt-Robinson 2007, Lagerstedt-Robinson 2016, Lu 2015, Nilbert 2009). The variant was also identified in dbSNP (ID: rs63750370) as "With Uncertain significance allele", ClinVar (classified as uncertain significance by Invitae, GeneDx, Ambry Genetics and three other submitters), Mismatch Repair Genes Variant Database, and in Insight Hereditary Tumors Database (2x). The variant was not identified in the COGR, Cosmic, MutDB, UMD-LSDB, or the Zhejiang University database. The variant was identified in control databases in 24 of 276978 chromosomes at a frequency of 0.00009 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European in 19 of 126534 chromosomes (freq: 0.0002), East Asian in 1 of 18864 chromosomes (freq: 0.00005), Finnish in 1 of 25784 chromosomes (freq: 0.00004), and South Asian in 3 of 30782 chromosomes (freq: 0.0001); it was not observed in the African, Other, Latino, and Ashkenazi Jewish, populations. The p.Thr1225 residue is conserved across mammals and other organisms, and 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 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. 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. -

Endometrial carcinoma Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Baylor Genetics

Oct 03, 2023

- -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Pathogenic	0.36
Cadd	Uncertain	24
Dann	Pathogenic	1.0
Eigen	Uncertain	0.65
Eigen_PC	Pathogenic	0.70
FATHMM_MKL	Pathogenic	0.97	D
M_CAP	Uncertain	0.22	D
MetaRNN	Uncertain	0.74	D;D;D;D;D
MetaSVM	Uncertain	0.35	D
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.72	T
Sift4G	Pathogenic	0.0010	D;D;T;D;D
Polyphen		1.0	.;.;.;D;.
Vest4		0.83
MVP		0.91
ClinPred		0.91	D
GERP RS		5.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.83
gMVP		0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs63750370; hg19: chr2-48033370; COSMIC: COSV99316408; COSMIC: COSV99316408;