NM_000251.3(MSH2):c.2708A>T (p.Asn903Ile) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 11, 2022
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:: RCV003038298.3

Allele description [Variation Report for NM_000251.3(MSH2):c.2708A>T (p.Asn903Ile)]

NM_000251.3(MSH2):c.2708A>T (p.Asn903Ile)

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.2708A>T (p.Asn903Ile)

HGVS:

NC_000002.12:g.47482852A>T
NG_007110.2:g.84729A>T
NM_000251.3:c.2708A>TMANE SELECT
NM_001258281.1:c.2510A>T
NM_001406638.1:c.2747A>T
NM_001406641.1:c.2708A>T
NM_001406649.1:c.2558A>T
NM_001406650.1:c.2558A>T
NM_001406658.1:c.1352A>T
NM_001406659.1:c.1352A>T
NM_001406660.1:c.1352A>T
NM_001406661.1:c.1352A>T
NM_001406662.1:c.1352A>T
NP_000242.1:p.Asn903Ile
NP_000242.1:p.Asn903Ile
NP_001245210.1:p.Asn837Ile
NP_001393567.1:p.Asn916Ile
NP_001393570.1:p.Asn903Ile
NP_001393578.1:p.Asn853Ile
NP_001393579.1:p.Asn853Ile
NP_001393587.1:p.Asn451Ile
NP_001393588.1:p.Asn451Ile
NP_001393589.1:p.Asn451Ile
NP_001393590.1:p.Asn451Ile
NP_001393591.1:p.Asn451Ile
LRG_218t1:c.2708A>T
LRG_218:g.84729A>T
LRG_218p1:p.Asn903Ile
NC_000002.11:g.47709991A>T
NM_000251.2:c.2708A>T
NR_176235.1:n.2744A>T
NR_176237.1:n.2744A>T
NR_176239.1:n.2744A>T
NR_176242.1:n.2744A>T
NR_176250.1:n.2484A>T

Protein change:

N451I

Molecular consequence:

NM_000251.3:c.2708A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001258281.1:c.2510A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406638.1:c.2747A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406641.1:c.2708A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406649.1:c.2558A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406650.1:c.2558A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406658.1:c.1352A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406659.1:c.1352A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406660.1:c.1352A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406661.1:c.1352A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001406662.1:c.1352A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary nonpolyposis colorectal neoplasms
Identifiers:: MeSH: D003123; MedGen: C0009405

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003325953	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 11, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003325953

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 11, 2022)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003325953.2

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

Description

This sequence change replaces asparagine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 903 of the MSH2 protein (p.Asn903Ile). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MSH2 protein function. This variant has not been reported in the literature in individuals affected with MSH2-related conditions. This variant is not present in population databases (gnomAD no frequency).

#	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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