NM_000251.3(MSH2):c.709A>T (p.Ile237Phe) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Nov 17, 2023
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:: RCV004522967.1

Allele description [Variation Report for NM_000251.3(MSH2):c.709A>T (p.Ile237Phe)]

NM_000251.3(MSH2):c.709A>T (p.Ile237Phe)

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.709A>T (p.Ile237Phe)

HGVS:

NC_000002.12:g.47412477A>T
NG_007110.2:g.14354A>T
NM_000251.3:c.709A>TMANE SELECT
NM_001258281.1:c.511A>T
NM_001406631.1:c.709A>T
NM_001406632.1:c.709A>T
NM_001406633.1:c.709A>T
NM_001406634.1:c.709A>T
NM_001406635.1:c.709A>T
NM_001406636.1:c.709A>T
NM_001406637.1:c.709A>T
NM_001406638.1:c.709A>T
NM_001406639.1:c.709A>T
NM_001406640.1:c.709A>T
NM_001406641.1:c.709A>T
NM_001406642.1:c.709A>T
NM_001406643.1:c.709A>T
NM_001406644.1:c.709A>T
NM_001406645.1:c.709A>T
NM_001406646.1:c.709A>T
NM_001406647.1:c.709A>T
NM_001406648.1:c.709A>T
NM_001406649.1:c.709A>T
NM_001406650.1:c.709A>T
NM_001406651.1:c.709A>T
NM_001406652.1:c.709A>T
NM_001406653.1:c.649A>T
NM_001406654.1:c.289A>T
NM_001406655.1:c.709A>T
NM_001406656.1:c.-287A>T
NM_001406657.1:c.709A>T
NM_001406658.1:c.-610A>T
NM_001406659.1:c.-760A>T
NM_001406660.1:c.-957A>T
NM_001406661.1:c.-912A>T
NM_001406662.1:c.-829A>T
NM_001406666.1:c.709A>T
NM_001406669.1:c.-760A>T
NM_001406672.1:c.709A>T
NM_001406674.1:c.709A>T
NP_000242.1:p.Ile237Phe
NP_000242.1:p.Ile237Phe
NP_001245210.1:p.Ile171Phe
NP_001393560.1:p.Ile237Phe
NP_001393561.1:p.Ile237Phe
NP_001393562.1:p.Ile237Phe
NP_001393563.1:p.Ile237Phe
NP_001393564.1:p.Ile237Phe
NP_001393565.1:p.Ile237Phe
NP_001393566.1:p.Ile237Phe
NP_001393567.1:p.Ile237Phe
NP_001393568.1:p.Ile237Phe
NP_001393569.1:p.Ile237Phe
NP_001393570.1:p.Ile237Phe
NP_001393571.1:p.Ile237Phe
NP_001393572.1:p.Ile237Phe
NP_001393573.1:p.Ile237Phe
NP_001393574.1:p.Ile237Phe
NP_001393575.1:p.Ile237Phe
NP_001393576.1:p.Ile237Phe
NP_001393577.1:p.Ile237Phe
NP_001393578.1:p.Ile237Phe
NP_001393579.1:p.Ile237Phe
NP_001393580.1:p.Ile237Phe
NP_001393581.1:p.Ile237Phe
NP_001393582.1:p.Ile217Phe
NP_001393583.1:p.Ile97Phe
NP_001393584.1:p.Ile237Phe
NP_001393586.1:p.Ile237Phe
NP_001393595.1:p.Ile237Phe
NP_001393601.1:p.Ile237Phe
NP_001393603.1:p.Ile237Phe
LRG_218t1:c.709A>T
LRG_218:g.14354A>T
LRG_218p1:p.Ile237Phe
NC_000002.11:g.47639616A>T
NM_000251.1:c.709A>T
NM_000251.2:c.709A>T
NR_176230.1:n.745A>T
NR_176231.1:n.745A>T
NR_176232.1:n.745A>T
NR_176233.1:n.737A>T
NR_176234.1:n.745A>T
NR_176235.1:n.745A>T
NR_176236.1:n.745A>T
NR_176237.1:n.745A>T
NR_176238.1:n.745A>T
NR_176239.1:n.745A>T
NR_176240.1:n.745A>T
NR_176241.1:n.745A>T
NR_176242.1:n.745A>T
NR_176243.1:n.745A>T
NR_176244.1:n.745A>T
NR_176245.1:n.745A>T
NR_176246.1:n.745A>T
NR_176247.1:n.745A>T
NR_176248.1:n.745A>T
NR_176249.1:n.745A>T
NR_176250.1:n.745A>T

Protein change:

I171F

Molecular consequence:

NM_001406656.1:c.-287A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406658.1:c.-610A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406659.1:c.-760A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406660.1:c.-957A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406661.1:c.-912A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406662.1:c.-829A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406669.1:c.-760A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000251.3:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001258281.1:c.511A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406631.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406632.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406633.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406634.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406635.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406636.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406637.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406638.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406639.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406640.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406641.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406642.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406643.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406644.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406645.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406646.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406647.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406648.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406649.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406650.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406651.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406652.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406653.1:c.649A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406654.1:c.289A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406655.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406657.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406666.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406672.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406674.1:c.709A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_176230.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176231.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176232.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176233.1:n.737A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176234.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176235.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176236.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176237.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176238.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176239.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176240.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176241.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176242.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176243.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176244.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176245.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176246.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176247.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176248.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176249.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176250.1:n.745A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Saccharomyces cerevisiae S288C Lot5p (LOT5), partial mRNA
Saccharomyces cerevisiae S288C Lot5p (LOT5), partial mRNA
gi|296146204|ref|NM_001179749.1|

Nucleotide
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Homologene neighbors for GEO Profiles (Select 126243491) (0)
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Homologene neighbors for GEO Profiles (Select 126257456) (0)
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Homologene neighbors for GEO Profiles (Select 62325239) (0)
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005033565	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Nov 17, 2023)	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

SCV005033565

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Nov 17, 2023)

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

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

Details of each submission

From Ambry Genetics, SCV005033565.1

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

Description

This alteration is classified as likely 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

Last Updated: May 7, 2024

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