NM_000251.3(MSH2):c.116G>C (p.Arg39Pro) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 24, 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:: RCV000780435.1

Allele description [Variation Report for NM_000251.3(MSH2):c.116G>C (p.Arg39Pro)]

NM_000251.3(MSH2):c.116G>C (p.Arg39Pro)

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.116G>C (p.Arg39Pro)

HGVS:

NC_000002.12:g.47403307G>C
NG_007110.2:g.5184G>C
NM_000251.3:c.116G>CMANE SELECT
NM_001258281.1:c.-30-53G>C
NP_000242.1:p.Arg39Pro
NP_000242.1:p.Arg39Pro
LRG_218t1:c.116G>C
LRG_218:g.5184G>C
LRG_218p1:p.Arg39Pro
NC_000002.11:g.47630446G>C
NM_000251.1:c.116G>C
NM_000251.2:c.116G>C
p.R39P

Protein change:

R39P

Links:

dbSNP: rs587782759

NCBI 1000 Genomes Browser:

rs587782759

Molecular consequence:

NM_001258281.1:c.-30-53G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_000251.3:c.116G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000917683	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Jan 24, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000917683

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Jan 24, 2018)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Citations

PubMed

Cancer Susceptibility Gene Mutations in Individuals With Colorectal Cancer.

Yurgelun MB, Kulke MH, Fuchs CS, Allen BA, Uno H, Hornick JL, Ukaegbu CI, Brais LK, McNamara PG, Mayer RJ, Schrag D, Meyerhardt JA, Ng K, Kidd J, Singh N, Hartman AR, Wenstrup RJ, Syngal S.

J Clin Oncol. 2017 Apr 1;35(10):1086-1095. doi: 10.1200/JCO.2016.71.0012. Epub 2017 Jan 30.

PubMed [citation]

PMID:: 28135145
PMCID:: PMC5455355

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000917683.1

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

Description

Variant summary: The MSH2 c.116G>C (p.Arg39Pro) variant involves the alteration of a conserved nucleotide that leads to an amino acid substitution in the N-terminal mismatch-recognition domain (IPR007695, InterPro). 4/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 5/222394 control chromosomes at a frequency of 0.0000225, which does not exceed the estimated maximal expected allele frequency of a pathogenic MSH2 variant (0.0005683). The variant was reported in one individual with colorectal cancer, however without evidence for causality (Yurgelun 2017). In addition, one clinical diagnostic laboratory classified this variant as uncertain significance. Taken together, this variant is classified as VUS.

#	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: Sep 29, 2024

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