rs587779971

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM1BP6

The ENST00000233146.7(MSH2):ā€‹c.362A>Gā€‹(p.Tyr121Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000624 in 1,602,528 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y121N) has been classified as Uncertain significance.

Frequency

Genomes: š‘“ 0.000013 ( 0 hom., cov: 31)
Exomes š‘“: 0.0000055 ( 0 hom. )

Consequence

MSH2
ENST00000233146.7 missense

Scores

1
11
7

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:7B:2

Conservation

PhyloP100: 0.540
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM1
In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 6 benign, 15 uncertain in ENST00000233146.7
BP6
Variant 2-47408551-A-G is Benign according to our data. Variant chr2-47408551-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 127643.We mark this variant Likely_benign, oryginal submissions are: {Benign=2, Uncertain_significance=7}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MSH2NM_000251.3 linkuse as main transcriptc.362A>G p.Tyr121Cys missense_variant 2/16 ENST00000233146.7 NP_000242.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MSH2ENST00000233146.7 linkuse as main transcriptc.362A>G p.Tyr121Cys missense_variant 2/161 NM_000251.3 ENSP00000233146 P1P43246-1

Frequencies

GnomAD3 genomes
AF:
0.0000131
AC:
2
AN:
152204
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000319
AC:
8
AN:
250740
Hom.:
0
AF XY:
0.0000221
AC XY:
3
AN XY:
135502
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000203
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:
0.000164
GnomAD4 exome
AF:
0.00000552
AC:
8
AN:
1450324
Hom.:
0
Cov.:
29
AF XY:
0.00000554
AC XY:
4
AN XY:
721962
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000134
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
AF:
0.0000131
AC:
2
AN:
152204
Hom.:
0
Cov.:
31
AF XY:
0.0000269
AC XY:
2
AN XY:
74362
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000113
ExAC
AF:
0.0000165
AC:
2

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:7Benign:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:3
Uncertain significance, criteria provided, single submitterclinical testingARUP Laboratories, Molecular Genetics and Genomics, ARUP LaboratoriesJul 27, 2017The MSH2 c.362A>G;p.Tyr121Cys variant has been published in the medical literature in at least one individual suspected of having hereditary cancer (Mu 2016). The variant is listed in the ClinVar database (Variation ID: 127643) and the dbSNP variant database (rs587779971) with an allele frequency of 0.003253 percent (9/276636 alleles) in the Genome Aggregation Database. The amino acid at this position is located in the mismatch binding domain (Lutzen 2008), but the amino acid is weakly conserved and computational algorithms do not reach a consensus as to the effect of this variant (AlignGVGD: C15, SIFT: Tolerated, MutationTaster: disease causing). However, this variant occurs near an exon/intron boundary and splicing prediction programs (SpliceSiteFinder-like, MaxEntScan, NNSplice, GeneSplicer, Human Splicing Finder) predict this variant may alter splicing. Considering available information, there is insufficient evidence to classify the variant at this time. Pathogenic MSH2 variants are causative for Lynch syndrome (MIM#120435). References Lutzen A et al. Functional analysis of HNPCC-related missense mutations in MSH2. Mutat Res. 2008 Oct 14;645(1-2):44-55. Mu W et al. Sanger Confirmation Is Required to Achieve Optimal Sensitivity and Specificity in Next-Generation Sequencing Panel Testing. J Mol Diagn. 2016 Nov;18(6):923-932. -
Uncertain significance, criteria provided, single submitterclinical testingGeneDxApr 25, 2024In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in a patient with juvenile polyposis syndrome who also harbored a canonical splice variant in SMAD4 (PMID: 36359527); Published functional study demonstrates mismatch repair activity similar to wild-type (PMID: 33357406); This variant is associated with the following publications: (PMID: 25318351, 27720647, 36359527, 33357406, 18822302, 21120944, 24326041, 30584090) -
Uncertain significance, criteria provided, single submitterclinical testingMayo Clinic Laboratories, Mayo ClinicDec 19, 2022- -
Hereditary cancer-predisposing syndrome Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitterclinical testingColor Diagnostics, LLC DBA Color HealthAug 09, 2023This missense variant replaces tyrosine with cysteine at codon 121 of the MSH2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). This variant does not impact MSH2 function in a 6-thioguanine sensitivity assay in haploid human cells (internally defined LOF score threshold <= -1.32, PMID: 33357406). To our knowledge, this variant has not been reported in individuals affected with MSH2-related disorders in the literature. This variant has been identified in 9/282148 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Benign, criteria provided, single submitterclinical testingAmbry GeneticsSep 30, 2022This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpSep 29, 2023Variant summary: MSH2 c.362A>G (p.Tyr121Cys) 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 five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 250740 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.362A>G has been reported in the literature in individuals affected with breast and ovarian cancer without strong evidence for causality (examples: Harismendy_2013 and Li_2019). These report(s) do not provide unequivocal conclusions about association of the variant with Lynch Syndrome. 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: 24326041, 30584090). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=4) and benign (n=2). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Lynch syndrome 1 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingDivision of Medical Genetics, University of WashingtonJan 22, 2020This variant has been reported in the literature as identified on hereditary cancer gene panel testing (Mu 2016). This variant has an overall allele frequency of 0.00003 in the Broad Institute gnomAD Browser (https://gnomad.broadinstitute.org/). In silico analyses indicate that this variant does not alter protein structure/function. Thus, it is unknown at this time whether this variant increases cancer risk. BP4 -
Lynch syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAll of Us Research Program, National Institutes of HealthDec 14, 2023This missense variant replaces tyrosine with cysteine at codon 121 of the MSH2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). This variant does not impact MSH2 function in a 6-thioguanine sensitivity assay in haploid human cells (internally defined LOF score threshold <= -1.32, PMID: 33357406). To our knowledge, this variant has not been reported in individuals affected with MSH2-related disorders in the literature. This variant has been identified in 9/282148 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Hereditary nonpolyposis colorectal neoplasms Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 19, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.079
BayesDel_addAF
Benign
-0.0023
T
BayesDel_noAF
Uncertain
0.040
CADD
Benign
21
DANN
Uncertain
0.98
DEOGEN2
Uncertain
0.76
D;D;.;.;.
Eigen
Benign
-0.25
Eigen_PC
Benign
-0.33
FATHMM_MKL
Uncertain
0.82
D
LIST_S2
Uncertain
0.92
D;D;D;D;D
M_CAP
Uncertain
0.11
D
MetaRNN
Uncertain
0.56
D;D;D;D;D
MetaSVM
Uncertain
0.22
D
MutationAssessor
Uncertain
2.6
M;.;.;.;.
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.63
T
PROVEAN
Uncertain
-4.1
D;D;D;.;D
REVEL
Pathogenic
0.68
Sift
Benign
0.071
T;D;T;.;T
Sift4G
Benign
0.17
T;T;T;.;T
Polyphen
0.90
P;.;.;.;D
Vest4
0.30
MutPred
0.68
Gain of methylation at K122 (P = 0.0197);.;.;Gain of methylation at K122 (P = 0.0197);Gain of methylation at K122 (P = 0.0197);
MVP
0.86
MPC
0.022
ClinPred
0.57
D
GERP RS
0.97
Varity_R
0.61
gMVP
0.65

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.12
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs587779971; hg19: chr2-47635690; API