NM_000251.3(MSH2):c.1859T>C (p.Val620Ala) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 31, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002414882.2

Allele description [Variation Report for NM_000251.3(MSH2):c.1859T>C (p.Val620Ala)]

NM_000251.3(MSH2):c.1859T>C (p.Val620Ala)

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.1859T>C (p.Val620Ala)

HGVS:

NC_000002.12:g.47475124T>C
NG_007110.2:g.77001T>C
NM_000251.3:c.1859T>CMANE SELECT
NM_001258281.1:c.1661T>C
NM_001406631.1:c.1859T>C
NM_001406632.1:c.1859T>C
NM_001406633.1:c.1859T>C
NM_001406634.1:c.1859T>C
NM_001406635.1:c.1859T>C
NM_001406636.1:c.1826T>C
NM_001406637.1:c.1859T>C
NM_001406638.1:c.1898T>C
NM_001406639.1:c.1859T>C
NM_001406640.1:c.1859T>C
NM_001406641.1:c.1859T>C
NM_001406642.1:c.1859T>C
NM_001406643.1:c.1859T>C
NM_001406644.1:c.1859T>C
NM_001406645.1:c.1859T>C
NM_001406646.1:c.1859T>C
NM_001406647.1:c.1709T>C
NM_001406648.1:c.1859T>C
NM_001406649.1:c.1709T>C
NM_001406650.1:c.1709T>C
NM_001406651.1:c.1709T>C
NM_001406652.1:c.1709T>C
NM_001406653.1:c.1799T>C
NM_001406654.1:c.1439T>C
NM_001406655.1:c.1859T>C
NM_001406656.1:c.962T>C
NM_001406657.1:c.*69T>C
NM_001406658.1:c.503T>C
NM_001406659.1:c.503T>C
NM_001406660.1:c.503T>C
NM_001406661.1:c.503T>C
NM_001406662.1:c.503T>C
NM_001406669.1:c.503T>C
NM_001406674.1:c.1859T>C
NP_000242.1:p.Val620Ala
NP_000242.1:p.Val620Ala
NP_001245210.1:p.Val554Ala
NP_001393560.1:p.Val620Ala
NP_001393561.1:p.Val620Ala
NP_001393562.1:p.Val620Ala
NP_001393563.1:p.Val620Ala
NP_001393564.1:p.Val620Ala
NP_001393565.1:p.Val609Ala
NP_001393566.1:p.Val620Ala
NP_001393567.1:p.Val633Ala
NP_001393568.1:p.Val620Ala
NP_001393569.1:p.Val620Ala
NP_001393570.1:p.Val620Ala
NP_001393571.1:p.Val620Ala
NP_001393572.1:p.Val620Ala
NP_001393573.1:p.Val620Ala
NP_001393574.1:p.Val620Ala
NP_001393575.1:p.Val620Ala
NP_001393576.1:p.Val570Ala
NP_001393577.1:p.Val620Ala
NP_001393578.1:p.Val570Ala
NP_001393579.1:p.Val570Ala
NP_001393580.1:p.Val570Ala
NP_001393581.1:p.Val570Ala
NP_001393582.1:p.Val600Ala
NP_001393583.1:p.Val480Ala
NP_001393584.1:p.Val620Ala
NP_001393585.1:p.Val321Ala
NP_001393587.1:p.Val168Ala
NP_001393588.1:p.Val168Ala
NP_001393589.1:p.Val168Ala
NP_001393590.1:p.Val168Ala
NP_001393591.1:p.Val168Ala
NP_001393598.1:p.Val168Ala
NP_001393603.1:p.Val620Ala
LRG_218t1:c.1859T>C
LRG_218:g.77001T>C
LRG_218p1:p.Val620Ala
NC_000002.11:g.47702263T>C
NM_000251.1:c.1859T>C
NM_000251.2:c.1859T>C
NR_176230.1:n.1895T>C
NR_176231.1:n.1895T>C
NR_176232.1:n.1895T>C
NR_176233.1:n.1737T>C
NR_176234.1:n.1895T>C
NR_176235.1:n.1895T>C
NR_176236.1:n.1895T>C
NR_176237.1:n.1895T>C
NR_176238.1:n.2028T>C
NR_176239.1:n.1895T>C
NR_176240.1:n.1895T>C
NR_176241.1:n.1895T>C
NR_176242.1:n.1895T>C
NR_176243.1:n.1745T>C
NR_176244.1:n.1895T>C
NR_176245.1:n.1895T>C
NR_176246.1:n.1895T>C
NR_176247.1:n.1895T>C
NR_176248.1:n.1895T>C
NR_176249.1:n.2125T>C
NR_176250.1:n.1635T>C

Protein change:

V168A

Molecular consequence:

NM_000251.3:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001258281.1:c.1661T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406631.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406632.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406633.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406634.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406635.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406636.1:c.1826T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406637.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406638.1:c.1898T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406639.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406640.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406641.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406642.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406643.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406644.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406645.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406646.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406647.1:c.1709T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406648.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406649.1:c.1709T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406650.1:c.1709T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406651.1:c.1709T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406652.1:c.1709T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406653.1:c.1799T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406654.1:c.1439T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406655.1:c.1859T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406656.1:c.962T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406658.1:c.503T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406659.1:c.503T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406660.1:c.503T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406661.1:c.503T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406662.1:c.503T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406669.1:c.503T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406674.1:c.1859T>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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002724074	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 31, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002724074

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 31, 2018)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV002724074.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The p.V620A variant (also known as c.1859T>C), located in coding exon 12 of the MSH2 gene, results from a T to C substitution at nucleotide position 1859. The valine at codon 620 is replaced by alanine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. In addition, this alteration is predicted to be deleterious by MAPP-MMR in silico analyses (Chao EC et al. Hum. Mutat. 2008 Jun;29:852-60). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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