NM_000251.3(MSH2):c.541A>G (p.Asn181Asp) AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Aug 21, 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:: RCV002349468.3

Allele description [Variation Report for NM_000251.3(MSH2):c.541A>G (p.Asn181Asp)]

NM_000251.3(MSH2):c.541A>G (p.Asn181Asp)

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.541A>G (p.Asn181Asp)

HGVS:

NC_000002.12:g.47410268A>G
NG_007110.2:g.12145A>G
NM_000251.3:c.541A>GMANE SELECT
NM_001258281.1:c.343A>G
NM_001406631.1:c.541A>G
NM_001406632.1:c.541A>G
NM_001406633.1:c.541A>G
NM_001406634.1:c.541A>G
NM_001406635.1:c.541A>G
NM_001406636.1:c.541A>G
NM_001406637.1:c.541A>G
NM_001406638.1:c.541A>G
NM_001406639.1:c.541A>G
NM_001406640.1:c.541A>G
NM_001406641.1:c.541A>G
NM_001406642.1:c.541A>G
NM_001406643.1:c.541A>G
NM_001406644.1:c.541A>G
NM_001406645.1:c.541A>G
NM_001406646.1:c.541A>G
NM_001406647.1:c.541A>G
NM_001406648.1:c.541A>G
NM_001406649.1:c.541A>G
NM_001406650.1:c.541A>G
NM_001406651.1:c.541A>G
NM_001406652.1:c.541A>G
NM_001406653.1:c.481A>G
NM_001406654.1:c.121A>G
NM_001406655.1:c.541A>G
NM_001406656.1:c.-455A>G
NM_001406657.1:c.541A>G
NM_001406658.1:c.-778A>G
NM_001406659.1:c.-928A>G
NM_001406660.1:c.-1125A>G
NM_001406661.1:c.-1080A>G
NM_001406662.1:c.-997A>G
NM_001406666.1:c.541A>G
NM_001406669.1:c.-928A>G
NM_001406672.1:c.541A>G
NM_001406674.1:c.541A>G
NP_000242.1:p.Asn181Asp
NP_000242.1:p.Asn181Asp
NP_001245210.1:p.Asn115Asp
NP_001393560.1:p.Asn181Asp
NP_001393561.1:p.Asn181Asp
NP_001393562.1:p.Asn181Asp
NP_001393563.1:p.Asn181Asp
NP_001393564.1:p.Asn181Asp
NP_001393565.1:p.Asn181Asp
NP_001393566.1:p.Asn181Asp
NP_001393567.1:p.Asn181Asp
NP_001393568.1:p.Asn181Asp
NP_001393569.1:p.Asn181Asp
NP_001393570.1:p.Asn181Asp
NP_001393571.1:p.Asn181Asp
NP_001393572.1:p.Asn181Asp
NP_001393573.1:p.Asn181Asp
NP_001393574.1:p.Asn181Asp
NP_001393575.1:p.Asn181Asp
NP_001393576.1:p.Asn181Asp
NP_001393577.1:p.Asn181Asp
NP_001393578.1:p.Asn181Asp
NP_001393579.1:p.Asn181Asp
NP_001393580.1:p.Asn181Asp
NP_001393581.1:p.Asn181Asp
NP_001393582.1:p.Asn161Asp
NP_001393583.1:p.Asn41Asp
NP_001393584.1:p.Asn181Asp
NP_001393586.1:p.Asn181Asp
NP_001393595.1:p.Asn181Asp
NP_001393601.1:p.Asn181Asp
NP_001393603.1:p.Asn181Asp
LRG_218t1:c.541A>G
LRG_218:g.12145A>G
LRG_218p1:p.Asn181Asp
NC_000002.11:g.47637407A>G
NM_000251.1:c.541A>G
NM_000251.2:c.541A>G
NR_176230.1:n.577A>G
NR_176231.1:n.577A>G
NR_176232.1:n.577A>G
NR_176233.1:n.569A>G
NR_176234.1:n.577A>G
NR_176235.1:n.577A>G
NR_176236.1:n.577A>G
NR_176237.1:n.577A>G
NR_176238.1:n.577A>G
NR_176239.1:n.577A>G
NR_176240.1:n.577A>G
NR_176241.1:n.577A>G
NR_176242.1:n.577A>G
NR_176243.1:n.577A>G
NR_176244.1:n.577A>G
NR_176245.1:n.577A>G
NR_176246.1:n.577A>G
NR_176247.1:n.577A>G
NR_176248.1:n.577A>G
NR_176249.1:n.577A>G
NR_176250.1:n.577A>G

Protein change:

N115D

Molecular consequence:

NM_000251.3:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001258281.1:c.343A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406631.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406632.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406633.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406634.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406635.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406636.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406637.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406638.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406639.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406640.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406641.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406642.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406643.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406644.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406645.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406646.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406647.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406648.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406649.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406650.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406651.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406652.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406653.1:c.481A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406654.1:c.121A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406655.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406657.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406666.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406672.1:c.541A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406674.1:c.541A>G - 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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gi|9706838|gnl|dbEST|5684558|gb|BE5 .1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002649342	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Aug 21, 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

SCV002649342

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Aug 21, 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, SCV002649342.3

#	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: Sep 29, 2024

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