2-47799737-T-C

Position:

• chr2-47799737-T-C

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PS1 PM2 PP3_Strong PP5_Very_Strong

The ENST00000234420.11(MSH6):​c.1754T>C​(p.Leu585Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L585Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MSH6 ENST00000234420.11 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:10 U:1
• Conservation: PhyloP100: 7.96

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 18 ACMG points.

• PS1: Transcript ENST00000234420.11 (MSH6) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar as 1779438
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.966
• PP5: Variant 2-47799737-T-C is Pathogenic according to our data. Variant chr2-47799737-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 89220.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSH6	NM_000179.3	c.1754T>C	p.Leu585Pro	missense_variant	4/10	ENST00000234420.11	NP_000170.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSH6	ENST00000234420.11	c.1754T>C	p.Leu585Pro	missense_variant	4/10	1	NM_000179.3	ENSP00000234420	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:10 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Lynch syndrome 5 Pathogenic:2

Likely pathogenic, no assertion criteria provided	research	deCODE genetics, Amgen	Jul 21, 2023	The variant NM_000179.3:c.1754T>C (chr2:47799737) in MSH6 was detected in 34 heterozygotes out of 58K WGS Icelanders (MAF= 0,029%). Following imputation in a set of 166K Icelanders (102 imputed heterozygotes) we observed an association with colorectal cancer using 4991 cases and 314812 controls (OR= 9.62, P= 9.55e-12). This variant has been reported in ClinVar previously as pathogenic, likely pathogenic and as a variant of uncertain significance. Based on ACMG criteria (PS4, PM2, PP3, PP5) this variant classifies as likely pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Aug 15, 2023	This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 22581703]. This variant is expected to disrupt protein structure [Myriad internal data]. -

not provided Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 01, 2024	Observed in patients with Lynch syndrome-related cancers and tumor studies consistent with pathogenic variants in this gene (PMID: 22581703, 25617771, 28466842, 35430768, 30877237, 37153042); Common founder variant in the Icelandic population (PMID: 28466842); Published functional studies demonstrate a damaging effect: deficient in mismatch repair activity and reduction of MSH6 protein (PMID: 22581703); Not observed at significant frequency in large population cohorts (gnomAD); 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: 22949387, 25617771, 29887214, 30322717, 29485237, 32719484, 17531815, 21120944, 34445333, 35430768, 37937776, 33471991, 23773459, 30877237, 28466842, 22581703, 37153042) -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jan 16, 2023	The MSH6 c.1754T>C (p.Leu585Pro) variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). In the published literature, the variant has been reported in individuals with colorectal cancer (PMID: 30877237 (2019), 22581703 (2012)) and ovarian/endometrial cancer (PMIDs: 30322717 (2018), 25617771 (2015)). It has also been described as a founder mutation associated with colorectal and endometrial cancer risk in Iceland (PMID: 28466842 (2017)). In addition, functional studies indicate this variant had deleterious effects on MSH6 protein stability and DNA mismatch repair activity (PMID: 22581703 (2012)). Based on the available information, this variant is classified as pathogenic. -

Endometrial carcinoma Pathogenic:2

Likely pathogenic, no assertion criteria provided	clinical testing	CZECANCA consortium	Feb 21, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 24, 2023	- -

Hereditary nonpolyposis colon cancer Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

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

Jan 16, 2024

Variant summary: MSH6 c.1754T>C (p.Leu585Pro) 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 250308 control chromosomes (gnomAD). c.1754T>C has been reported in the literature in individuals affected or suspected to be affected with Hereditary Nonpolyposis Colorectal Cancer (Lynch Sydrome; e.g., Kantelinin_2012, Cushman-Vokoun_2013, Haraldsdottir_2017, Pearlman_2019, Svensson_2022). However, no conclusive evidence for causality, such as cosegregation with disease in family studies, has been reported in these publications; therefore this evidence does not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. The variant has also been reported in an individual with endometrial cancer who had a family history of Lynch Syndrome-associated cancers and whose tumor tested MSH6-negative by IHC staining (e.g. Frolova_2015), a second individual with endometrial cancer (e.g., Kral_2023), and an individual with ovarian cancer (e.g. Carter_2018). At least one publication reports experimental evidence evaluating an impact on protein function, indicating that the variant impairs mismatch repair activity and results in unstable MSH6 protein when studied in vitro (e.g. Kantelinin_2012). The following publications have been ascertained in the context of this evaluation (PMID: 30322717, 23773459, 25617771, 28466842, 22581703, 37153042, 30877237, 29887214, 35430768). ClinVar contains an entry for this variant (Variation ID: 89220). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

MSH6-related disorder Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 13, 2023

The MSH6 c.1754T>C variant is predicted to result in the amino acid substitution p.Leu585Pro. This variant was reported in an individual with hereditary nonpolyposis colorectal cancer (Kantelinen J et al 2012. PubMed ID: 22581703). In a large study from Iceland, the c.1754T>C variant was detected as a germline variant in 9 patients with mismatch repair deficiency colorectal cancer (Table 1 in Haraldsdottir et al 2017. PubMed ID: 28466842). This variant was also reported in an individual with ovarian cancer (Carter NJ et al 2018. PubMed ID: 30322717) and a patient with endometrial cancer with a family history of Lynch Syndrome-associated cancers (Frolova AI et al 2015. PubMed ID: 25617771). In vitro mismatch repair assays indicate this variant impacts protein function (Kantelinen J et al 2012. PubMed ID: 22581703). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org) and is reported by most labs in ClinVar as likely pathogenic or pathogenic (https://www.ncbi.nlm.nih.gov/clinvar/variation/89220/). This variant is interpreted as likely pathogenic. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 02, 2024

This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 585 of the MSH6 protein (p.Leu585Pro). 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 (PMID: 22581703, 23773459, 25617771, 30877237). ClinVar contains an entry for this variant (Variation ID: 89220). 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 expected to disrupt MSH6 protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects MSH6 function (PMID: 22581703). For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 30, 2024

The p.L585P variant (also known as c.1754T>C), located in coding exon 4 of the MSH6 gene, results from a T to C substitution at nucleotide position 1754. The leucine at codon 585 is replaced by proline, an amino acid with similar properties. This alteration has been reported in conjunction with another MSH6 alteration (p.S677T) in an individual diagnosed with colon cancer at age 38 whose tumor showed high microsatellite instability and intact MLH1, MSH2, and PMS2 staining on immunohistochemistry (IHC), but inconclusive MSH6 staining. Furthermore, in vitro MMR assays showed that the p.L585P alteration displayed deficient MMR activity, while the second variant, p.S677T, displayed proficient MMR activity (Kantelinen J et al. Hum Mutat. 2012 Aug;33(8):1294-301). In addition, this alteration has been detected in several individuals diagnosed with colorectal and/or endometrial cancer whose tumor results revealed loss of MSH6 on IHC (Ambry internal data; Frolova AI et al. Gynecol. Oncol. 2015 Apr;137:7-13; Haraldsdottir S et al. Nat Commun. 2017 May;8:14755; Kral J et al. Oncol Lett, 2023 Jun;25:216). This alteration has also been identified in a cohort of 4,439 women with ovarian cancer (Carter NJ et al. Gynecol. Oncol., 2018 12;151:481-488). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. In addition, based on internal structural analysis, p.L585P is predicted to strongly perturb the structure of the ATPase domain; however, the local sensitivity of the region has not been well characterized (Warren JJ et al. Mol. Cell. 2007 May; 26(4):579-92). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the majority of available evidence to date, this alteration is likely to be pathogenic. -

Lynch syndrome Uncertain:1

Uncertain significance, flagged submission

clinical testing

University of Washington Department of Laboratory Medicine, University of Washington

May 01, 2018

MSH6 NM_000179.2:c.1754T>C has a 96.7% probability of pathogenicity based on combining prior probability from public data with a likelihood ratio of 1.56 to 1, generated from evidence of seeing this as a somatic mutation in a tumor without loss of heterozygosity at the MSH6 locus. See Shirts et al 2018, PMID 29887214. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.48	D
BayesDel_noAF	Pathogenic	0.45
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.96	.;.;D;D;.
Eigen	Pathogenic	0.87
Eigen_PC	Pathogenic	0.80
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.98	.;D;D;D;D
M_CAP	Pathogenic	0.46	D
MetaRNN	Pathogenic	0.97	D;D;D;D;D
MetaSVM	Pathogenic	0.94	D
MutationAssessor	Pathogenic	4.3	.;.;H;.;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.74	T
PROVEAN	Pathogenic	-6.1	.;D;D;.;D
REVEL	Pathogenic	0.94
Sift	Uncertain	0.0010	.;D;D;.;D
Sift4G	Uncertain	0.0020	D;D;D;D;D
Polyphen		1.0	.;.;D;.;.
Vest4		0.95
MutPred		0.78		.;.;Loss of stability (P = 0.0291);.;.;
MVP		0.99
ClinPred		1.0	D
GERP RS		5.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.99
gMVP		0.93

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: rs587779220; hg19: chr2-48026876;