2-47403261-C-T

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1 PM2

The NM_000251.3(MSH2):c.70C>T(p.Gln24Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000207 in 1,447,728 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. Q24Q) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: MSH2 NM_000251.3 stop_gained
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:3 B:1
• Conservation: PhyloP100: 1.91

Genes affected

MSH2 (HGNC:7325): (mutS homolog 2) This locus is frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). When cloned, it was discovered to be a human homolog of the E. coli mismatch repair gene mutS, consistent with the characteristic alterations in microsatellite sequences (RER+ phenotype) found in HNPCC. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 1360 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSH2	NM_000251.3	c.70C>T	p.Gln24Ter	stop_gained	1/16	ENST00000233146.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSH2	ENST00000233146.7	c.70C>T	p.Gln24Ter	stop_gained	1/16	1	NM_000251.3	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000454 AC: 1 AN: 220192 Hom.: 0 AF XY: 0.00000832 AC XY: 1 AN XY: 120146

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000323

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000207 AC: 3 AN: 1447728 Hom.: 0 Cov.: 31 AF XY: 0.00000139 AC XY: 1 AN XY: 719042

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000238

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: 0.00000181

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:3 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jul 20, 2023	Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation; however a downstream in-frame ATG could serve as an alternate initiator codonwhich may result in a smaller, yet still functional, protein (Kets et al., 2009; Cyr et al., 2012; Jia et al., 2020); Observed in individuals with endometrial cancer and primary peritoneal cancer (Roberts et al., 2018); This variant is associated with the following publications: (PMID: 26681312, 29345684, 30322717, 21837758, 33357406, 18781192, 34426522, 31068090, 9718327, 29922827) -
Pathogenic, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The MSH2 p.Gln24X variant was not identified in the literature. The variant was identified in dbSNP (ID: rs587779976) as “Pathogenic”, Clinvitae database (as pathogenic), and ClinVar (as pathogenic). The variant was not found in COSMIC, “Mismatch Repair Genes Variant Database”, “MMR Gene Unclassified Variants Database”, InSiGHT Colon Cancer Gene Variant Database (LOVD), Zhejiang Colon Cancer Database (LOVD), GeneInsight - COGR database, and UMD. The p.Gln24X variant leads to a premature stop codon at position 24, which is predicted to lead to a truncated or absent protein and loss of function. Loss of function variants of the MSH2 gene are an established mechanism of disease in Lynch syndrome and this is the type of variant expected to cause the disorder. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Ambry Genetics	Oct 18, 2023	The p.Q24* variant (also known as c.70C>T), located in coding exon 1 of the MSH2 gene, results from a C to T substitution at nucleotide position 70. This changes the amino acid from a glutamine to a stop codon within coding exon 1. The predicted stop codon occurs within the first 150 nucleotides of the MSH2 gene. This alteration may escape nonsense-mediated mRNA decay and/or be rescued by re-initiation through use of a downstream, in-frame AUG at codon 26 (Farrington SM et al. Am J Hum Genet, 1998 Sep;63:749-59; Kets CM et al. Eur J Hum Genet, 2009 Feb;17:159-64; Rivas et al. Science. 2015 May 8;348(6235):666-9; Lindeboom et al. Nat Genet. 2016 Oct;48(10):1112-8; Rhee et al. Sci Rep. 2017 May 10;7(1):1653). The exact functional effect of this alteration is unknown; however, MutS alpha complexes formed using recombinantly expressed wild type MSH6 and MSH2 with a deletion of the first 25 amino acids of the protein, demonstrated partially retained function in several biochemical assays that measured ATP binding, ATPase activity, mismatch binding, and sliding clamp formation (Cyr JL et al. Mol Carcinog, 2012 Aug;51:647-58). This alteration was identified in a patient diagnosed with both endometrial and peritoneal cancers (Susswein LR et al. Genet. Med. 2016 08;18:823-32). This variant was also identified once in a cohort of women with ovarian cancer undergoing multigene panel testing, once in a cohort of women undergoing multigene panel testing for hereditary cancer risk, and in a proband diagnosed with colorectal cancer at age 41 with a family history of colorectal cancer in one first degree relative (Carter NJ et al. Gynecol Oncol, 2018 12;151:481-488; Roberts ME et al. Genet Med, 2018 10;20:1167-1174; Ricci MT et al. Tumori, 2019 Aug;105:338-352). In addition, this variant has been identified in a proband whose colorectal tumor demonstrated normal staining for MSH2, MLH1, and MSH6 proteins on immunohistochemistry (Ambry internal data). Since supporting evidence is conflicting at this time, the clinical significance of this alteration remains unclear. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Jun 02, 2023	This variant changes 1 nucleotide in exon 1 of the MSH2 gene, creating a premature translation stop signal. However this variant may escape nonsense-mediated mRNA decay due to secondary initiation at one of multiple downstream AUG start codons. Experimental studies have shown that a protein with a deletion of 25 amino acids of the N-terminal domain has been observed as partially functional (PMID: 21837758). An alternative MSH2 transcript (NM_001258281) lacking the first 66 amino acids of the primary transcript, is expressed at similar or higher levels in human tissues (https://gnomad.broadinstitute.org/). Premature stop codons located in close proximity to the canonical Met1 start codon often show a decrease in nonsense-mediated mRNA decay efficiency (PMID: 27618451). Missense variants impacting the start codon at Met1 are classified as VUS (ClinVar Variation ID: 90832, 90833, 230889). This variant has been reported in individuals affected with endometrial and peritoneal cancer (PMID: 26681312), ovarian cancer (PMID: 30322717), and early-onset colorectal cancer (PMID: 31068090). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of MSH2 function is a known mechanism of disease (clinicalgenome.org). The clinical impact of truncations in MSH2 prior to a secondary in-frame methionine at amino acid residue 26 is not fully understood at this time. Until further functional and clinical evidence is obtained, based on the evidence available this variant is classified as Likely Pathogenic. -

Lynch syndrome 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Myriad Genetics, Inc.

Jul 26, 2023

This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation. -

Lynch syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Oct 27, 2021

The p.Gln24X variant in MSH2 has been reported in at least 1 individual with an MSH2-associated cancer (Susswein 2016 PMID: 26681312, Carter 2018 PMID: 30322717). It has also been reported by other clinical laboratories in ClinVar (Variation ID: 127652) and has been identified in 0.003% (1/30994) of Latino/Admixed American chromosomes by gnomAD (http://gnomad.broadinstitute.org). This nonsense variant leads to a premature termination codon at position 24, which is predicted to lead to a truncated or absent protein. Loss of function of the MSH2 gene is an established disease mechanism in autosomal dominant Lynch syndrome. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PVS1, PM2_Supporting. -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Nov 03, 2023

Variant summary: MSH2 c.70C>T (p.Gln24X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The next downstream in-frame ATG start site is at codon 26. Other truncating variants upstram of the potential new start codon have been classified as pathogenic by our laboratory, and in ClinVar, and HGMD. However, studies in patients with start-loss variants and functional studies involving a truncated Msh2 variant lacking the first 25 amino acids suggest that utilization of an alternative downstream start codon allows retention of functional, albeit reduced, activity (PMIDs: 9718327, 18781192, 21837758). The variant allele was found at a frequency of 4.5e-06 in 220192 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.70C>T has been reported in the literature in individuals affected with Lynch Syndrome-associated cancers (e.g., Susswein_2016, Carter_2018, Ricci_2019). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 30322717, 31068090, 26681312). Four submitters have reported clinical-significance assessments for this variant to ClinVar after 2014. Multiple submitters reported the variant with conflicting assessments (uncertain significance, n = 2; likely benign, n = 1; pathogenic, n = 1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -

Hereditary nonpolyposis colorectal neoplasms Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jan 21, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.55	D
BayesDel_noAF	Pathogenic	0.55
Cadd	Pathogenic	40
Dann	Uncertain	1.0
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.41
FATHMM_MKL	Uncertain	0.78	D
MutationTaster	Benign	1.0	A;A;D
Vest4		0.67
GERP RS		3.5
RBP_binding_hub_radar		1.0
RBP_regulation_power_radar		2.8

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: rs587779976; hg19: chr2-47630400;