rs63751004

chr2-47416365-G-Achr2-47416365-G-Cchr2-47416365-G-T

Variant summary

Our verdict is Pathogenic. Variant got 26 ACMG points: 26P and 0B. PS1_Very_Strong PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000251.3(MSH2):c.1012G>A(p.Gly338Arg) 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. 13/20 in silico tools predict a damaging 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 Likely pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G338E) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MSH2 NM_000251.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4 U:1
• Conservation: PhyloP100: 9.81

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 26 ACMG points.

• PS1: Transcript NM_000251.3 (MSH2) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar as 232810
• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 7 benign, 16 uncertain in NM_000251.3
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr2-47416366-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 90504.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.993
• PP5: Variant 2-47416365-G-A is Pathogenic according to our data. Variant chr2-47416365-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 90503.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-47416365-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSH2	NM_000251.3	c.1012G>A	p.Gly338Arg	missense_variant	6/16	ENST00000233146.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSH2	ENST00000233146.7	c.1012G>A	p.Gly338Arg	missense_variant	6/16	1	NM_000251.3	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4 Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Lynch syndrome 1 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Feb 06, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Aug 09, 2023	This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [Myriad internal data]. This variant is expected to disrupt protein structure [Myriad internal data]. -

Hereditary nonpolyposis colorectal neoplasms Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Sep 09, 2020

This sequence change replaces glycine with arginine at codon 338 of the MSH2 protein (p.Gly338Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 16736289, Invitae). Also, a different variant (c.1012G>C) giving rise to the same protein effect observed here (p.Gly338Arg) has been determined to be pathogenic (PMID: 16736289, 23612316, 17720936, external communication, Invitae). This suggests that this variant is also likely to be causative of disease. ClinVar contains an entry for this variant (Variation ID: 90503). An algorithm developed specifically for the MSH2 gene suggests that this missense change is likely to be deleterious (PMID: 22290698). However, this prediction has not been confirmed by published functional studies and its clinical significance is uncertain. For these reasons, this variant has been classified as Pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 13, 2022

The p.G338R pathogenic mutation (also known as c.1012G>A), located in coding exon 6 of the MSH2 gene, results from a G to A substitution at nucleotide position 1012. The glycine at codon 338 is replaced by arginine, an amino acid with dissimilar properties. This alteration was identified in a Belgian patient with suspected HNPCC and MSS colorectal cancer demonstrating normal IHC staining (Spaepen M et al. Fam. Cancer 2006;5:179-89). A different nucleotide substitution (c.1012G>C) resulting in the same amino acid change (p.G338R) was identified in patients with family histories that met Amsterdam II criteria and/or displayed absent MSH2 protein expression in their tumors (Ambry internal data; Moline J et al. Gynecol. Oncol. 2013 Jul;130:121-6). One study aimed at testing the function of the MSH2 yeast equivalent (p.G350R) of this variant determined mismatch repair efficiency was deficient in a mutator assay, protein expression was only 1% of wild type (100%), and interaction with MSH6 in a yeast two-hybrid was lost (Gammie AE et al. Genetics, 2007 Oct;177:707-21). A splicing assay using mini gene constructs demonstrated a 40% decrease in exon 6 inclusion in two of three cell lines transfected with this variant (G1012A) (Lastella P et al. BMC Genomics, 2006 Sep;7:243). In a massively parallel cell-based functional assay testing susceptibility to a DNA damaging agent, 6-thioguanine (6-TG), this variant was reported to be functionally deleterious (Jia X et al. Am J Hum Genet, 2021 01;108:163-175). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Carcinoma of colon Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The MSH2 p.Gly338Arg variant was identified in multiple studies using prediction models and/or functional assays to determine the pathogenicity of the variant; overall the results were inconclusive. An equivalent variant in the yeast MSH2 homolog was created and found to be expressed at 1% of the level of wild type MSH2 and was identified to have lost interaction with all MSH2 partners (Gammie 2007). Two published in silico prediction tools classified the variant as deleterious (Chao 2008, Ali 2012). Two studies utilized exon splice enhancer (ESE)-Finder to identify 3 ESEs within MSH2 which were predicted to be lost due to the c.1012G>A variant (Zhu 2013, Lastella 2006). Transfection of this variant into two out of three different cell lines displayed an exon exclusion event, however overall the splicing defect was inconclusive (Lastella 2006). The variant was also identified in dbSNP (ID: rs63751004) as “With Uncertain significance allele”, Clinvitae database (classification uncertain significance), “Mismatch Repair Genes Variant Database”, “MMR Gene Unclassified Variants Database”, InSiGHT Colon Cancer Gene Variant Database (LOVD) 15x as unknown, ClinVar database (classification uncertain significance by InSIGHT, reviewed by an expert panel); and was not identified in 1000 Genomes Project, NHLBI GO Exome Sequencing Project, Exome Aggregation Consortium database (March 14, 2016), COSMIC, Zhejiang Colon Cancer Database (LOVD), Canadian Open Genetics Repository database and UMD. The p.Gly338 residue is conserved across mammals and other organisms, and 5 of 5 computational analysis software (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) shows a difference in splicing, but this information is not very predictive of pathogenicity. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.59	D
BayesDel_noAF	Pathogenic	0.61
Cadd	Pathogenic	30
Dann	Pathogenic	1.0
DEOGEN2	Pathogenic	0.94	D;.;.;.
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.97
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.97	D;D;D;D
M_CAP	Pathogenic	0.81	D
MetaRNN	Pathogenic	0.99	D;D;D;D
MetaSVM	Pathogenic	0.96	D
MutationAssessor	Pathogenic	3.5	H;.;.;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Pathogenic	0.85	D
PROVEAN	Pathogenic	-7.8	D;D;.;D
REVEL	Pathogenic	0.97
Sift	Pathogenic	0.0	D;D;.;D
Sift4G	Uncertain	0.0020	D;D;.;D
Polyphen		1.0	D;.;.;D
Vest4		0.98
MutPred		0.96		Gain of MoRF binding (P = 0.0256);.;Gain of MoRF binding (P = 0.0256);Gain of MoRF binding (P = 0.0256);
MVP		0.99
MPC		0.033
ClinPred		1.0	D
GERP RS		5.6
Varity_R		0.99
gMVP		0.89

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: rs63751004; hg19: chr2-47643504; COSMIC: COSV99253467;