chr2-47410209-T-A

Variant names:

• chr2-47410209-T-A
• rs63750126
• NM_000251.3:c.482T>A

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2 PP3_Strong PP5_Very_Strong

The NM_001406656.1(MSH2):​c.-514T>A variant causes a 5 prime UTR premature start codon gain 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. Variant has been reported in ClinVar as Pathogenic (★★★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: MSH2 NM_001406656.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Pathogenic reviewed by expert panel P:3
• Conservation: PhyloP100: 7.93

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 14 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.983
• PP5: Variant 2-47410209-T-A is Pathogenic according to our data. Variant chr2-47410209-T-A is described in ClinVar as [Pathogenic]. Clinvar id is 91104.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47410209-T-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSH2	NM_000251.3	c.482T>A	p.Val161Asp	missense_variant	Exon 3 of 16	ENST00000233146.7	NP_000242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSH2	ENST00000233146.7	c.482T>A	p.Val161Asp	missense_variant	Exon 3 of 16	1	NM_000251.3	ENSP00000233146.2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3

Revision: reviewed by expert panel

Submissions by phenotype

Lynch syndrome 1 Pathogenic:2

Mar 09, 2018

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

Class 5 - Pathogenic Classification using multifactorial probability: 0.9977 -

Jul 27, 2023

Myriad Genetics, Inc.

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely pathogenic. This variant is expected to disrupt protein structure [Myriad internal data]. Functional studies indicate this variant impacts protein function [PMID: 17101317, 26951660]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 15849733, 28785832]. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Jun 13, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.V161D pathogenic mutation (also known as c.482T>A), located in coding exon 3 of the MSH2 gene, results from a T to A substitution at nucleotide position 482. The valine at codon 161 is replaced by aspartic acid, an amino acid with highly dissimilar properties. In one study, this variant was detected in an individual diagnosed with colorectal cancer at 52 years of age who met Amsterdam I criteria for Lynch syndrome and tumor demonstrated high microsatellite instability (MSI-H) with negative staining for MSH2 on immunohistochemistry (IHC). An in vitro MMR assay revealed that this variant protein was completely deficient in MMR activity (Ollila S et al. Gastroenterology 2006 Nov; 131(5):1408-17). This alteration was also reported by an Italian group in a family that met Amsterdam II criteria for Lynch syndrome and the alteration segregated in three affected family members. The proband and her mother had Lynch-associated tumors that demonstrated MSI-H and absent MSH2/MSH6 staining on IHC. Furthermore, the MSH2 V161D protein showed an abnormal subcellular localization pattern compared to wild type MSH2 protein (Bianchi F et al. Fam. Cancer, 2018 Apr;17:215-224). In another study, the MSH2 V161D protein showed deficient mismatch repair activity using a genetic screen in mouse embryonic stem cells, reduced protein expression, and increased microsatellite instability compared to wild type MSH2 protein (Houlleberghs H et al. Proc. Natl. Acad. Sci. U.S.A., 2016 Apr;113:4128-33). 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 Jan;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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.49	D
BayesDel_noAF	Pathogenic	0.46
CADD	Pathogenic	31
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.95	D;D;.;.;.
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.85
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.97	D;D;D;D;D
M_CAP	Pathogenic	0.32	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D
MetaSVM	Pathogenic	0.95	D
MutationAssessor	Pathogenic	3.2	M;.;.;.;.
PrimateAI	Benign	0.40	T
PROVEAN	Pathogenic	-6.4	D;D;D;.;D
REVEL	Pathogenic	0.96
Sift	Pathogenic	0.0	D;D;D;.;D
Sift4G	Pathogenic	0.0	D;D;D;.;D
Polyphen		1.0	D;.;.;.;D
Vest4		0.96
MutPred		0.89		Gain of disorder (P = 0.0098);.;.;Gain of disorder (P = 0.0098);Gain of disorder (P = 0.0098);
MVP		0.97
MPC		0.029
ClinPred		1.0	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		1.0
gMVP		0.95

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs63750126; hg19: chr2-47637348;