NM_000251.3(MSH2):c.266T>C (p.Val89Ala) AND Hereditary cancer-predisposing syndrome

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Nov 22, 2023
Review status:: criteria provided, conflicting classifications

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000215101.13

Allele description [Variation Report for NM_000251.3(MSH2):c.266T>C (p.Val89Ala)]

NM_000251.3(MSH2):c.266T>C (p.Val89Ala)

Gene:

MSH2:mutS homolog 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.266T>C (p.Val89Ala)

HGVS:

NC_000002.12:g.47408455T>C
NG_007110.2:g.10332T>C
NM_000251.3:c.266T>CMANE SELECT
NM_001258281.1:c.68T>C
NP_000242.1:p.Val89Ala
NP_000242.1:p.Val89Ala
NP_001245210.1:p.Val23Ala
LRG_218t1:c.266T>C
LRG_218:g.10332T>C
LRG_218p1:p.Val89Ala
NC_000002.11:g.47635594T>C
NM_000251.1:c.266T>C
NM_000251.2:c.266T>C

Protein change:

V23A

Links:

dbSNP: rs876659747

NCBI 1000 Genomes Browser:

rs876659747

Molecular consequence:

NM_000251.3:c.266T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001258281.1:c.68T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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Transcriptional factor B3 family protein [Arabidopsis thaliana]
Transcriptional factor B3 family protein [Arabidopsis thaliana]
gi|30689117|ref|NP_194896.2|

Protein
GPRIN3 AND (alive[prop]) (562)
Gene
L1TD1 AND (alive[prop]) (186)
Gene
Gm29788 predicted gene, 29788 [Mus musculus]
Gm29788 predicted gene, 29788 [Mus musculus]
Gene ID:101056148

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000276538	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Aug 11, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 28580595, 31386297, 31666926, 33357406 Citation Link,
SCV000906757	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 22, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 28580595, 31386297, 31391288, 35449176, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000276538

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Benign
(Aug 11, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV000906757

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 22, 2023)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Germline mutations in cancer-predisposition genes in patients with biliary tract cancer.

Terashima T, Umemoto K, Takahashi H, Hosoi H, Takai E, Kondo S, Sakamoto Y, Mitsunaga S, Ohno I, Hashimoto Y, Sasaki M, Ikeda M, Shimada K, Kaneko S, Yachida S, Sugano K, Okusaka T, Morizane C.

Oncotarget. 2019 Oct 15;10(57):5949-5957. doi: 10.18632/oncotarget.27224.

PubMed [citation]

PMID:: 31666926
PMCID:: PMC6800267

Massively parallel functional testing of MSH2 missense variants conferring Lynch syndrome risk.

Jia X, Burugula BB, Chen V, Lemons RM, Jayakody S, Maksutova M, Kitzman JO.

Am J Hum Genet. 2021 Jan 7;108(1):163-175. doi: 10.1016/j.ajhg.2020.12.003. Epub 2020 Dec 23.

PubMed [citation]

PMID:: 33357406
PMCID:: PMC7820803

See all PubMed Citations (7)

Details of each submission

From Ambry Genetics, SCV000276538.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Color Diagnostics, LLC DBA Color Health, SCV000906757.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This missense variant replaces valine with alanine at codon 89 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). This variant has been reported in individuals affected with breast cancer (PMID: 28580595, 35449176), and in several individuals affected with unspecified cancer (PMID: 31386297, 31391288). This variant has also been identified in 3/282588 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 15, 2024

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