2-47803546-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4 BP6

The NM_000179.3(MSH6):c.3299C>T(p.Thr1100Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000341 in 1,613,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. T1100R) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000031 (0 hom.)
• Consequence: MSH6 NM_000179.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:14 B:3
• Conservation: PhyloP100: 4.15

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 Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.34337825).
• BP6: Variant 2-47803546-C-T is Benign according to our data. Variant chr2-47803546-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 89369.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=13, Likely_benign=2, Benign=1}. Variant chr2-47803546-C-T is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSH6	NM_000179.3	c.3299C>T	p.Thr1100Met	missense_variant	5/10	ENST00000234420.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSH6	ENST00000234420.11	c.3299C>T	p.Thr1100Met	missense_variant	5/10	1	NM_000179.3	P4

Frequencies

GnomAD3 genomes AF: 0.0000657 AC: 10 AN: 152094 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.0000398 AC: 10 AN: 251432 Hom.: 0 AF XY: 0.0000368 AC XY: 5 AN XY: 135886

Gnomad AFR exome AF: 0.000123

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.0000653

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000264

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.0000308 AC: 45 AN: 1461886 Hom.: 0 Cov.: 33 AF XY: 0.0000316 AC XY: 23 AN XY: 727242

Gnomad4 AFR exome AF: 0.0000597

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000927

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000288

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000657 AC: 10 AN: 152094 Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3 AN XY: 74302

Gnomad4 AFR AF: 0.0000242

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000118

Gnomad4 OTH AF: 0.000478

Bravo AF: 0.0000529

TwinsUK AF: 0.000270 AC: 1

ALSPAC AF: 0.00 AC: 0

ExAC AF: 0.0000494 AC: 6

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.00

EpiControl AF: 0.000119

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:14 Benign:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not specified Uncertain:4

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	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 27, 2022	Variant summary: MSH6 c.3299C>T (p.Thr1100Met) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-05 in 251432 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in MSH6 causing Hereditary Nonpolyposis Colorectal Cancer (4e-05 vs 0.00014), allowing no conclusion about variant significance. c.3299C>T has been reported in the literature in individuals affected with or suspected to have Hereditary Nonpolyposis Colorectal Cancer, or colorectal cancer or breast cancer (Example: Ackay_2021, Schuber_2020, Berends_2002, deVoer_2016, Kwong_2020). The variant was also reported to cosegregate with heterozygous pathogenic MUTYH p.Tyr179Cys in multiple colorectal cancer-affected members of a suspected Lynch syndrome family (Schuber_2020). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. At least one publication reports experimental evidence evaluating an impact on protein function (Schuber_2020). These results showed no damaging effect of this variant. 12 clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Sep 23, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 25, 2017	The p.Thr1100Met variant in MSH6 has been reported in 2 individuals with suspect ed colorectal cancer or Lynch syndrome (Berends 2002, Yurgelun 2015). This varia nt has also been identified in 2/16512 of South Asian chromosomes by the Exome A ggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs63750442). Computational prediction tools and conservation analysis do not provide strong s upport for or against an impact to the protein. In addition, the p.Thr1100Met va riant has been classified as a variant of uncertain significance on Sept 5, 2013 by the ClinGen-approved InSiGHT expert panel (ClinVar SCV000108047.2). In summ ary, the clinical significance of the p.Thr1100Met variant is uncertain. -

Hereditary cancer-predisposing syndrome Uncertain:2 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Apr 05, 2023	This missense variant replaces threonine with methionine at codon 1100 of the MSH6 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). A functional study has reported that this variant does not impact in vitro DNA mismatch repair activity (PMID: 32615015). This variant has been reported in individuals affected with Lynch syndrome-associated cancer and/or polyps (PMID: 11709755, 25980754, 26901136, 30267214) and skin melanoma and thyroid cancer (PMID: 2968408). This variant also has been reported to cosegregate with heterozygous pathogenic MUTYH p.Tyr179Cys in three colorectal cancer-affected members of a suspected Lynch syndrome family (PMID: 32615015). This variant has been identified in 12/282832 chromosomes in the general population by the Genome Aggregation Database (gnomAD) and in healthy controls (PMID: 32980694). 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. -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 21, 2023	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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. -
Uncertain significance, criteria provided, single submitter	curation	Sema4, Sema4	Jun 04, 2021	- -

Lynch syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	research	CSER _CC_NCGL, University of Washington	Mar 11, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Dec 18, 2023	This missense variant replaces threonine with methionine at codon 1100 of the MSH6 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). A functional study has reported that this variant does not impact in vitro DNA mismatch repair activity (PMID: 32615015). This variant has been reported in individuals affected with Lynch syndrome-associated cancer and/or polyps (PMID: 11709755, 25980754, 26901136, 30267214) and skin melanoma and thyroid cancer (PMID: 2968408). This variant also has been reported to cosegregate with heterozygous pathogenic MUTYH p.Tyr179Cys in three colorectal cancer-affected members of a suspected Lynch syndrome family (PMID: 32615015). This variant has been identified in 12/282832 chromosomes in the general population by the Genome Aggregation Database (gnomAD) and in healthy controls (PMID: 32980694). 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. -

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	May 03, 2023	In the published literature, the variant has been reported in individuals with colorectal cancer (PMIDs: 11709755 (2002), 26901136 (2016), 32658311 (2021), 30267214 (2018)), breast cancer (PMID: 32068069 (2020)) and suspected lynch syndrome (25980754 (2015)). In one family, this variant was found to co-occur with a pathogenic MUTYH variant in 3 individuals with colorectal cancer (PMID: 32615015 (2020)). One functional study demonstrated this variant has a mismatch repair efficiency similar to wildtype MSH6 in vitro (PMID: 32615015 (2020)). The frequency of this variant in the general population, 0.000031 (4/129154 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Sep 21, 2023	Observed in patients with melanoma, thyroid, colorectal, or other Lynch syndrome-associated cancers, co-segregating with CRC in one family together with a MUTYH pathogenic variant (Berends et al., 2002; Yurgelun et al., 2015; de Voer et al., 2016; Rosenthal et al., 2018; Yehia et al., 2018; Schubert et al., 2020); Published functional studies demonstrate no damaging effect: mismatch repair activity similar to wild-type (Schubert et al., 2020); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25801821, 32615015, 32980694, 25980754, 23621914, 24362816, 26269718, 26901136, 11709755, 35422474, 32658311, 33471991, 29684080, 17531815, 21120944, 30267214, 31422818, 32068069) -

MSH6-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 26, 2024

The MSH6 c.3299C>T variant is predicted to result in the amino acid substitution p.Thr1100Met. This variant has been reported in individuals with Lynch syndrome-associated cancers such as colorectal cancers and in controls (Examples: Table 1. Berends et al 2002. PubMed ID: 11709755; Supplemental Table 2. Yurgelun et al 2015. PubMed ID: 25980754; Supplemental Table 2. Rosenthal EA et al 2018. PubMed ID: 30267214; Table S2. Okawa et al 2022. PubMed ID: 36243179). This variant is reported in 0.0080% of alleles in individuals of African descent in gnomAD and is interpreted as uncertain in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/89369/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Endometrial carcinoma;C1833477:Lynch syndrome 5;C5399763:Mismatch repair cancer syndrome 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

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.Thr1100Met variant was identified in 3 of 3262 proband chromosomes (frequency: 0.001) from individuals or families with colorectal cancer (Berends 2002, de Voer 2016, Yurgelun 2015). The variant was also identified in dbSNP (ID: rs63750442) as With Uncertain significance allele, ClinVar (classified as uncertain significance by Invitae, Ambry Genetics, GeneDx, Color Genomics, and 5 clinical laboratories), Clinvitae, Cosmic, MutDB, UMD-LSDB (1X classified as uncertain significance), Mismatch Repair Genes Variant Database, and Insight Hereditary Tumors Database (as unclassified variant) databases. The variant was not identified in GeneInsight-COGR, or the Zhejiang Colon Cancer Database. The variant was identified in control databases in 11 of 277180 chromosomes at a frequency of 0.00004 (Genome Aggregation Database Feb 27, 2017). The variant was identified in the following populations: African in 2 of 24038 chromosomes (freq: 0.0001), “Other” in 1 of 6464 chromosomes (freq: 0.0002), European in 5 of 126684 chromosomes (freq: 0.00004), East Asian in 1 of 18868 chromosomes (freq: 0.0001), and South Asian in 2 of 30782 chromosomes (freq: 0.0001), while the variant was not observed in the Latino, Ashkenazi Jewish, or Finnish populations. The p.Thr1100 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 variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of 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. -

Endometrial carcinoma Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Baylor Genetics

Oct 26, 2023

- -

Lynch syndrome 5 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Jan 23, 2024

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: 27363726]. -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 28, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.00033	T
BayesDel_noAF	Uncertain	0.0
Cadd	Benign	19
Dann	Uncertain	0.99
Eigen	Benign	-0.25
Eigen_PC	Benign	-0.14
FATHMM_MKL	Uncertain	0.92	D
M_CAP	Benign	0.043	D
MetaRNN	Benign	0.34	T;T;T;T;T
MetaSVM	Uncertain	0.021	D
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.57	T
Sift4G	Uncertain	0.0090	D;D;T;D;D
Polyphen		0.12	.;.;.;B;.
Vest4		0.51
MutPred		0.53		.;.;.;Loss of methylation at K1101 (P = 0.0283);.;
MVP		0.94
ClinPred		0.10	T
GERP RS		4.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.16
gMVP		0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs63750442; hg19: chr2-48030685; COSMIC: COSV52274859; COSMIC: COSV52274859;