chr2-47799737-T-C
Position:
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PS1PM2PP3_StrongPP5_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
ENST00000234420.11 missense
Scores
14
4
1
Clinical Significance
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]
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ACMG classification
Classification made for transcript
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
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:10Uncertain:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Pathogenic
.;.;D;D;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
.;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
.;.;H;.;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
.;D;D;.;D
REVEL
Pathogenic
Sift
Uncertain
.;D;D;.;D
Sift4G
Uncertain
D;D;D;D;D
Polyphen
1.0
.;.;D;.;.
Vest4
MutPred
0.78
.;.;Loss of stability (P = 0.0291);.;.;
MVP
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at