rs587779227

chr2-47800040-G-Achr2-47800040-G-Cchr2-47800040-G-T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1 PP3_Moderate PP5_Very_Strong

The NM_000179.3(MSH6):c.2057G>A(p.Gly686Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,614,032 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G686C) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: MSH6 NM_000179.3 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:14 U:1
• Conservation: PhyloP100: 4.50

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 Pathogenic. Variant got 12 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 17 uncertain in NM_000179.3
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.886
• PP5: Variant 2-47800040-G-A is Pathogenic according to our data. Variant chr2-47800040-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 89245.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47800040-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSH6	NM_000179.3	c.2057G>A	p.Gly686Asp	missense_variant	4/10	ENST00000234420.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSH6	ENST00000234420.11	c.2057G>A	p.Gly686Asp	missense_variant	4/10	1	NM_000179.3	P4

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152172 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

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: 0.0000294

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000342 AC: 5 AN: 1461860 Hom.: 0 Cov.: 34 AF XY: 0.00000413 AC XY: 3 AN XY: 727228

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000450

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152172 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74336

Gnomad4 AFR AF: 0.00

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: 0.0000294

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000113

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:14 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Lynch syndrome 5 Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Counsyl	May 11, 2017	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Mar 24, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 29, 2023	This variant is considered pathogenic. This variant is expected to disrupt protein structure [Myriad internal data]. Functional studies indicate this variant impacts protein function [PMID: 28531214]. This variant is strongly associated with more severe personal and family histories of cancer, typical for individuals with pathogenic variants in this gene [PMID: 25085752]. -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 27, 2023	Observed in patients with Lynch-related cancers, many with tumor studies consistent with pathogenic variants in this gene (Hampel et al., 2008; Goodfellow et al., 2015; Yurgelun et al., 2015; Chubb et al., 2016; Buchanan et al., 2017); Published functional studies demonstrate a damaging effect: defective mismatch binding and MMR activity (Houlleberghs et al., 2017; Drost et al., 2020); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 22949379, 25980754, 26552419, 18809606, 27329137, 17531815, 21120944, 24362816, 28531214, 27273229, 31965077, 25559809, 28514183, 28944238, 26681312, 30787465, 33087929, 28888541) -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 19, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Nov 04, 2022	The frequency of this variant in the general population, 0.000013 (2/152172 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals with In the published literature, the variant has been reported in individuals with Lynch Syndrome or a Lynch Syndrome associated phenotype (PMID: 28944238 (2017), PMID: 28514183 (2017), PMID: 26552419 (2015), PMID: 25980754 (2015), PMID: 25559809 (2015), PMID: 18809606 (2008)). Additionally, this variant was found to abrogate MMR activity in vitro (PMID: 28531214 (2017)). 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 damaging. Based on the available information, this variant is classified as pathogenic. -

Lynch syndrome Pathogenic:2

Likely pathogenic, reviewed by expert panel	curation	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Jun 21, 2019	Multifactorial likelihood analysis posterior probability 0.95-0.99 -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Oct 14, 2019	The p.Gly686Asp variant in MSH6 has been reported in at least 5 individuals with Lynch syndrome (Yurgelun 2015, Goodfellow 2015, Thompson 2013, Hampel 2008, DeRycke 2017) and in 1 individual with breast cancer, who also carried a likely pathogenic variant in CHEK2 (Susswein 2016). It was absent from large population studies. This variant was classified as likely pathogenic on September 5, 2013 by the ClinGen-approved InSiGHT expert panel (Variation ID 89245) and several clinical labs. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, and in vitro and in vivo (patient tumor) functional studies provide further evidence that this variant impacts protein function (Houlleberghs 2017, Goodfellow 2015, Thompson 2013). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PM2, PS4_Moderate, PS3_Moderate, PP3. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 05, 2023	The p.G686D pathogenic mutation (also known as c.2057G>A), located in coding exon 4 of the MSH6 gene, results from a G to A substitution at nucleotide position 2057. The glycine at codon 686 is replaced by aspartic acid, an amino acid with similar properties. This alteration has been identified in individuals who met Amsterdam II criteria for Lynch syndrome and one proband was reportedly diagnosed with rectal adenocarcinoma characterized by microsatellite instability as well as isolated loss of MSH6 protein expression on immunohistochemistry (IHC) (Ambry internal data; Buchanan DD et al. J. Gastroenterol. Hepatol., 2017 Feb;32:427-438). In addition, p.G686D has been identified in multiple individuals with Lynch syndrome-associated cancers undergoing multi-gene panel testing (Yurgelun MB et al. Gastroenterology. 2015 May. pii: S0016-5085(15)00678-2; DeRycke MS et al. Mol Genet Genomic Med, 2017 Sep;5:553-569; Roberts ME et al. Genet. Med., 2018 10;20:1167-1174). In a study that quantified tumor characteristics to assess pathogenicity for germline mismatch repair gene variants, this variant was reported in individuals with Lynch syndrome-associated tumors that demonstrated isolated loss of MSH6 protein expression on IHC (Ambry internal data; Li S et al. J. Med. Genet., 2020 Jan;57:62-69). Functional analyses of G686D suggest this alteration abrogates mismatch repair activity (Houlleberghs H et al. PLoS Genet., 2017 May;13:e1006765). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Oct 10, 2022	This missense variant replaces glycine with aspartic acid at codon 686 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). DNA mismatch repair and DNA damage tolerance assays have shown that this variant reduces protein function (PMID: 28531214, 31965077). This variant has been reported in individuals affected with Lynch syndrome or suspected of having Lynch syndrome (PMID: 25980754, 25559809, 26552419, 26552419, 27273229), colorectal cancer (PMID: 18809606, 22949379, 28944238), or breast cancer (PMID: 26681312). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -

Endometrial carcinoma Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jul 12, 2023	- -
Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The p.Gly686Asp variant was identified in 1 of 226 proband chromosomes (frequency: 0.004) from individuals or families with colorectal cancers (Hampel 2008). The variant was not identified in dbSNP, NHLBI Exome Sequencing Project (Exome Variant Server), Exome Aggregation Consortium (ExAC) databases. The variant was identified in Insight Colon Cancer Database (1x classified as likely pathogenic) and in Clinvitae (2x as likely pathogenic). In the ClinVar database, the variant was reported as likely pathogenic by Insight, Ambry Genetics, and GeneDX; Invitae classified the variant as of uncertain significance. The p.Gly686 residue is conserved across mammals but not in all other organisms, and four out of five computational analyses (PolyPhen-2, SIFT, BLOSUM, MutationTaster) suggest that the Aspartic Acid variant may impact the protein. In silico splicing analysis suggests that this variant leads to creation of a cryptic 5’ donor splice site in 4 out 5 programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, Human Splicing Finder). However, this information is not predictive enough to assume pathogenicity. In addition, a multifactorial analysis study (Thompson 2013) concluded that the variant was likely pathogenic (posterior probability 0.95-0.99). This variant has been previously seen by our laboratory in one family with Lynch syndrome. In this family the variant was identified in four affected members, there are two affected obligate carries, across 2 generations, for a total of 6 dominant segregations. The four variant positive family members had MSH6 deficient tumors, although one of these tumors was deficient for MLH1, MSH2 and PMS2 as well. The cancers in the family include ureter, endometrial and skin cancer however one obligate carrier was reported to have skin cancer which has not been confirmed with medical documentation. We cannot rule out the possibility that the cancer in this family is due to a separate pathogenic variant that is also tracking with the disease. However, at least one family member with this variant had complete sequencing (by Sanger) and deletion duplication analysis (by MLPA) for the MLH1, MSH2 (EPCAM del/dup) and MSH6 genes which did not identify other causal variants. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Hereditary nonpolyposis colon cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Jun 03, 2021

Variant summary: MSH6 c.2057G>A (p.Gly686Asp) results in a non-conservative amino acid change located in the connector domain (IPR007860) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251270 control chromosomes (gnomAD). c.2057G>A has been reported in the literature in multiple individuals affected with colorectal cancer (Hampel _2008, Thompson_ 2013, Chubb_2015, DeRycke_2017, Buchanan_2016), in patients with a history of LS-associated cancer and/or colorectal polyps (Yurgelun_2015, Li_2020) endometrial (Goodfellow_2015) and breast cancer (Susswein 2016). Tumor samples showed microsatellite instability in several cases (Chubb_2015, Buchanan_2016, Goodfellow_2015). These data indicate that the variant may be associated with disease. In addition, a multifactorial likelihood analysis classified this MSH6 variant as likely pathogenic (Thompson_2014). A recent functional study demonstrated reduced MMR activity for the variant compared to wild type (Drost_2020). Six other ClinVar submitters (evaluation after 2014) cite the variant as likely pathogenic (n=4) and pathogenic (n=2). Based on the evidence outlined above, the variant was classified as pathogenic. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 28, 2024

This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 686 of the MSH6 protein (p.Gly686Asp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of Lynch syndrome and/or constitutional mismatch repair deficiency syndrome (PMID: 18809606, 22949379, 25559809, 26552419, 26681312, 27273229, 28514183, 28944238; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 89245). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MSH6 protein function with a negative predictive value of 95%. Experimental studies have shown that this missense change affects MSH6 function (PMID: 28531214, 31965077). For these reasons, this variant has been classified as Pathogenic. -

not specified Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Mayo Clinic Laboratories, Mayo Clinic

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.43	D
BayesDel_noAF	Pathogenic	0.38
Cadd	Uncertain	24
Dann	Uncertain	1.0
Eigen	Pathogenic	0.74
Eigen_PC	Pathogenic	0.69
FATHMM_MKL	Pathogenic	0.97	D
M_CAP	Pathogenic	0.38	D
MetaRNN	Pathogenic	0.89	D;D;D;D;D
MetaSVM	Uncertain	0.74	D
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.80	T
Sift4G	Uncertain	0.030	D;D;D;D;D
Polyphen		0.98	.;.;D;.;.
Vest4		0.69
MVP		0.94
ClinPred		0.99	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.96
gMVP		0.90

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: rs587779227; hg19: chr2-48027179;