rs267608098

Positions:

• chr2-47804908-A-G
• chr2-47804908-A-T

Variant summary

Our verdict is Pathogenic. Variant got 22 ACMG points: 22P and 0B. PVS1 PM2 PP3_Strong PP5_Very_Strong

The NM_000179.3(MSH6):​c.3439-2A>G variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,459,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: MSH6 NM_000179.3 splice_acceptor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic reviewed by expert panel P:18
• Conservation: PhyloP100: 8.92

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 22 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 2-47804908-A-G is Pathogenic according to our data. Variant chr2-47804908-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 89391.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47804908-A-G is described in Lovd as [Likely_pathogenic]. Variant chr2-47804908-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSH6	NM_000179.3	c.3439-2A>G		splice_acceptor_variant		ENST00000234420.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSH6	ENST00000234420.11	c.3439-2A>G		splice_acceptor_variant		1	NM_000179.3	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1459678 Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1 AN XY: 726366

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: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:18

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jan 20, 2023	This variant disrupts a canonical splice-acceptor site and interferes with normal MSH6 mRNA splicing. It 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 Lynch syndrome or colorectal cancer (PMIDs: 25980754 (2015), 10537275 (1999)), endometrial cancer (PMIDs: 30612635 (2019), 29345684 (2018)), breast/ovarian cancer (PMID: 30128536 (2018)), and acute lymphoblastic leukemia (PMID: 34308104 (2021)). The variant also showed deleterious effects on protein function in a yeast-based complementation assay (PMID: 10537275 (1999)). Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 10, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 27, 2023	The MSH6 c.3439-2A>G variant (rs267608098), also known as IVS5-2A>G, has been described in the literature in individuals with colorectal cancer and families with Lynch syndrome (Baglietto 2010, Kolodner 1999, South 2009, Yurgelun 2015). It is reported as pathogenic by several laboratories in ClinVar (Variation ID: 89391) and is absent from the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. This variant abolishes the canonical splice acceptor site of intron 5, which is likely to disrupt gene function. Based on available information, this variant is considered pathogenic. References: Baglietto L et al. Risks of Lynch syndrome cancers for MSH6 mutation carriers. J Natl Cancer Inst. 2010;102(3):193-201. PMID: 20028993. Kolodner RD et al. Germ-line msh6 mutations in colorectal cancer families. Cancer Res. 1999;59(20):5068-74. PMID: 10537275. South CD et al. Immunohistochemistry staining for the mismatch repair proteins in the clinical care of patients with colorectal cancer. Genet Med. 2009;11(11):812-7. PMID: 19752738. Yurgelun MB et al. Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome. Gastroenterology. 2015 Sep;149(3):604-13.e20. PMID: 25980754. -
Pathogenic, no assertion criteria provided	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Feb 23, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 19, 2023	Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 10537275, 31447099, 20028993, 25980754, 28152038, 28514183, 18269114, 26866578, 22949387, 25561518, 30612635, 32719484, 34308104, 28888541) -

Lynch syndrome Pathogenic:3

Likely pathogenic, reviewed by expert panel	curation	International Society for Gastrointestinal Hereditary Tumours (InSiGHT)	Jun 21, 2019	Interrupts canonical donor splice site -
Pathogenic, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Oct 31, 2023	This variant causes an A to G nucleotide substitution at the -2 position of intron 5 of the MSH6 gene. An RNA functional study using RNA derived from a carrier individual has reported that this variant causes out-of-frame skipping of exon 6 (PMID: 22949379). This variant is expected to result in an absent or non-functional protein product. This variant has been observed in individuals affected with or suspected of having Lynch syndrome (PMID: 10537275, 25980754), colorectal cancer (PMID: 20028993), endometrial cancer (PMID: 29345684, 30612635), ovarian cancer (PMID: 30128536), and breast cancer (PMID: 30128536). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH6 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Oct 27, 2021	The c.3439-2A>G variant in MSH6 has been reported in 4 individuals with MSH6-associated cancers (Kolodner 1999 PMID: 10537275, Baglietto 2010 PMID: 20028993, , Long 2019 PMID: 30612635) and in 1 individual undergoing clinical genetic testing for Lynch Syndrome (Yurgelun 2015 PMID: 25980754) . It was absent from large population studies. This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. This was corroborated by a functional study using patient RNA that shows that this variant causes out-of-frame skipping of exon 6 (Thompson 2013 PMID: 22949379). Loss of function of the MSH6 gene is an established disease mechanism in autosomal dominant Lynch syndrome. In addition, this variant was classified as Likely Pathogenic on June 21, 2019 by the ClinGen-approved InSiGHT expert panel (ClinVar SCV000108071.2). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PVS1, PS3_Supporting, PM2_Supporting, PS4_Supporting. -

Hereditary cancer-predisposing syndrome Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jan 18, 2023	This variant causes an A to G nucleotide substitution at the -2 position of intron 5 of the MSH6 gene. An RNA functional study using RNA derived from a carrier individual has reported that this variant causes out-of-frame skipping of exon 6 (PMID: 22949379). This variant is expected to result in an absent or non-functional protein product. This variant has been observed in individuals affected with or suspected of having Lynch syndrome (PMID: 10537275, 25980754), colorectal cancer (PMID: 20028993), endometrial cancer (PMID: 29345684, 30612635), ovarian cancer (PMID: 30128536), and breast cancer (PMID: 30128536). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH6 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	curation	Sema4, Sema4	Nov 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Dec 19, 2022	The c.3439-2A>G intronic pathogenic mutation results from an A to G substitution two nucleotides before coding exon 6 in the MSH6 gene. This variant has been identified in a proband(s) who met Amsterdam I/II criteria for Lynch syndrome and/or whose tumor(s) demonstrated loss of MSH6 expression by immunohistochemistry (Kolodner RD et al. Cancer Res, 1999 Oct;59:5068-74; Ambry internal data). This mutation was also identified in two additional patients with a history of Lynch/HNPCC-associated cancers and/or polyps and was reported in a cohort of patients diagnosed with endometrial cancer or complex atypical hyperplasia (Yurgelun MB et al. Gastroenterology, 2015 Sep;149:604-13.e20; Long B et al. Gynecol Oncol, 2019 01;152:20-25). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site. RNA studies have demonstrated this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This alteration was predicted to cause skipping of coding exon 6, and a deletion of this region in yeast resulted in complete loss of MSH6 function (Kolodner RD et al. Cancer Res, 1999 Oct;59:5068-74). In addition to the clinical data presented in the literature, alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -

Lynch syndrome 5 Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Counsyl	Jan 04, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Mar 29, 2023	This variant is considered pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function. 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]. -

Carcinoma of colon Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The MSH6 c.3439-2A>G variant was identified in 3 of 3026 proband chromosomes (frequency: 0.001) from individuals or families with Lynch Syndrome (Kolodner 1999, Biaglietto 2009, Yurgelun 2015). The variant was identified in dbSNP (rs267608098) as “with likely pathogenic, pathogenic allele” and ClinVar (interpreted as "pathogenic" by Invitae and 8 others and "likely pathogenic" by 3 laboratories). The variant was not identified in UMD-LSDB. The variant was not identified in the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The c.3439-2A>G variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, 4 out of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predicted a greater than 10% difference in splicing. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. -

Breast and/or ovarian cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Aug 28, 2019

- -

Hereditary nonpolyposis colon cancer Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

May 19, 2021

Variant summary: MSH6 c.3439-2A>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes a 3 prime acceptor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Kolodner_1999). The variant was absent in 251432 control chromosomes (gnomAD). c.3439-2A>G has been reported in the literature in individuals affected with Lynch Syndrome (e.g. Kolodner_1999, Baglietto_2010, Yurgelun_2015). These data indicate that the variant is likely to be associated with disease. Eleven 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 pathogenic/likely pathogenic. 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 31, 2024

This sequence change affects an acceptor splice site in intron 5 of the MSH6 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with clinical features of Lynch syndrome (PMID: 10537275, 20028993, 25980754; Invitae). This variant is also known as IVS5-2A>G. ClinVar contains an entry for this variant (Variation ID: 89391). Studies have shown that disruption of this splice site results in exon 6 skipping and introduces a premature termination codon (Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

Endometrial carcinoma Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Feb 15, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.33	D
BayesDel_noAF	Pathogenic	0.24
CADD	Pathogenic	31
DANN	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.94
FATHMM_MKL	Pathogenic	0.99	D
MutationTaster	Benign	1.0	D;D;D;D
GERP RS		5.2

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AL_spliceai		1.0		Position offset: 2

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

Publications

LitVar

Other links and lift over

dbSNP: rs267608098; hg19: chr2-48032047;