2-47403402-G-C

Position:

• chr2-47403402-G-C

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PVS1 PM2_Supporting PP4_Strong

This summary comes from the ClinGen Evidence Repository: The MSH2 (NM_000251.3):c.211G>C variant affects the last G of exon 1. mRNA assays using RNA derived from patient constitutional biological samples indicates that the variant allele results in a splicing aberration (with evidence that the variant allele produces no full-length/reference transcript) leading to a premature stop codon (PVS1). It was identified in 4 CRC/EC tumours showing loss of MSH2/MSH6 expression in >2 families (PP4_strong). It was absent in gnomAD v2.1, v3.1 and v4.1 datasets (PM2_Supporting). In summary, this variant meets the criteria to be classified as pathogenic for Lynch Syndrome, based on the MMR gene specific ACMG/AMP criteria established by the ClinGen InSiGHT Hereditary Colorectal Cancer/ Polyposis VCEP: PVS1, PP4_Strong, and PM2_Sup (VCEP specifications version 1). LINK:https://erepo.genome.network/evrepo/ui/classification/CA020066/MONDO:0005835/137

• Frequency: Genomes: not found (cov: 33)
• Consequence: MSH2 ENST00000233146.7 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 4.37

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 13 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSH2	NM_000251.3	c.211G>C	p.Gly71Arg	missense_variant, splice_region_variant	1/16	ENST00000233146.7	NP_000242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSH2	ENST00000233146.7	c.211G>C	p.Gly71Arg	missense_variant, splice_region_variant	1/16	1	NM_000251.3	ENSP00000233146	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Lynch syndrome 1 Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Jun 13, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genomics Laboratory, Washington University in St. Louis	Oct 14, 2023	The MSH2 c.211G>C (p.Gly71Arg) variant has been reported in two individuals affected with Lynch syndrome (Vargas-Parra GM et al., PMID: 28577310). This variant is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. This variant falls on the last nucleotide of exon 1, which is part of the consensus splice site for this exon. Functional studies show that the variant results in a partial deletion of exon 1, which is predicted to generate a truncated protein (p.Tyr66Serfs*10), and impacts protein function (Vargas-Parra GM et al., PMID: 28577310). Computational predictors indicate that this variant would alter splicing, evidence that correlates to an impact of this variant on MSH2 function. This variant has been reported in the ClinVar database as a likely pathogenic variant by five submitters and pathogenic by one submitter. Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Jul 26, 2023	This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [Myriad internal data]. -

Hereditary cancer-predisposing syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Sep 07, 2023	The c.211G>C pathogenic mutation (also known as p.G71R), located in coding exon 1 of the MSH2 gene, results from a G to C substitution at nucleotide position 211. The amino acid change results in glycine to arginine at codon 71, an amino acid with dissimilar properties. However, this change occurs in the last base pair of coding exon 1, which makes it likely to have some effect on normal mRNA splicing. In one study, this variant was detected in two unrelated individuals diagnosed with early-onset colon cancer, whose tumors showed loss of MSH2/MSH6 protein expression by immunohistochemistry (IHC). Both families met Bethesda criteria and this variant was not detected in 188 controls. Further RNA studies indicated that this variant led to a partial deletion of exon 1, resulting in a premature truncation of MSH2 (Vargas-Parra GM et al. Int J Cancer, 2017 Oct;141:1365-1380). This variant has been identified in a proband who met Amsterdam II criteria for Lynch syndrome and tumor demonstrated loss of MSH2/MSH6 expression by IHC (Ambry internal data). This variant has also been identified in multiple probands whose Lynch syndrome-associated tumor demonstrated high microsatellite instability and/or loss of MSH2 or MSH2/MSH6 expression by IHC (Ambry internal data). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site; however, direct evidence is insufficient at this time (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 11, 2022	This missense variant replaces glycine with arginine at codon 71 of the MSH2 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). An RNA assay detect two aberrant splice products but the splicing defect was incomplete (PMID: 28577310). This variant has been reported in individuals affected with suspected Lynch syndrome (PMID: 28577310, ClinVar: SCV000187139, SCV000625353), or breast cancer (PMID: 32522261). It has been shown that this variant segregates with disease (PMID: 28577310). 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 Likely Pathogenic. -

Carcinoma of colon Pathogenic:1

Likely pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The p.Gly71Arg variant has not been reported in the literature nor previously identified by our laboratory. The variant occurs in the last base of exon 1. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In-silico or computational prediction software (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predicts a greater than 10% difference in splicing in 4 out of 5 different programs. This residue is conserved in mammals but not in lower organisms, and computational analyses (SIFT, AlignGVGD) do not suggest a high likelihood of impact to the protein. However, the information from these software analyses is not predictive enough to rule out pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time, although we would lean towards a more pathogenic role for this variant. This variant is classified as Predicted Pathogenic. -

Lynch syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

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

Jan 14, 2020

Variant summary: MSH2 c.211G>C (p.Gly71Arg) results in a non-conservative amino acid change located in the DNA mismatch repair protein MutS-like, N-terminal domain (IPR007695) of the encoded protein sequence. Four of four in-silico tools predict a damaging effect of the variant on protein function and weakens a 5' donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing and results in aberrant transcript which is predicted to generate a truncated protein (p.Tyr66Serfs*10) (Vargas-Parra_2017). The variant was absent in 218268 control chromosomes (gnomAD). c.211G>C has been reported in the literature in individuals affected with Lynch Syndrome, including one family suggesting co-segregation of the variant and the disease (Vargas-Parra_2017). Three ClinVar submitters (evaluation after 2014) cite the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

May 15, 2019

Not found in the total gnomAD dataset, and the data is high quality (0/221594 chr). Found in at least one symptomatic patient in literature. Predicted to negatively affect a known splice site. Assessment of experimental evidence suggests this variant results in abnormal protein function. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 14, 2024

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 71 of the MSH2 protein (p.Gly71Arg). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of Lynch syndrome and/or breast cancer (PMID: 28577310, 32522261; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 142708). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this missense change results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 35676339). The resulting mRNA is expected to undergo nonsense-mediated decay. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.52
BayesDel_addAF	Pathogenic	0.30	D
BayesDel_noAF	Pathogenic	0.20
CADD	Pathogenic	36
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.61	D;T;.;.;.
Eigen	Uncertain	0.50
Eigen_PC	Uncertain	0.49
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.93	D;D;D;D;D
MetaRNN	Uncertain	0.74	D;D;D;D;D
MetaSVM	Pathogenic	0.90	D
MutationAssessor	Uncertain	2.9	M;.;.;.;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Uncertain	0.69	T
PROVEAN	Uncertain	-3.5	D;D;D;.;D
REVEL	Pathogenic	0.73
Sift	Benign	0.074	T;D;D;.;T
Sift4G	Uncertain	0.019	D;D;D;.;D
Polyphen		0.11	B;.;.;.;D
Vest4		0.39
MutPred		0.53		Gain of MoRF binding (P = 0.0334);.;.;Gain of MoRF binding (P = 0.0334);Gain of MoRF binding (P = 0.0334);
MVP		0.89
MPC		0.0079
ClinPred		0.98	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.9
Varity_R		0.75
gMVP		0.45

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.65		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.65		Position offset: -17
DS_DL_spliceai		0.46		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs587782659; hg19: chr2-47630541;