NM_000251.3(MSH2):c.673A>C (p.Thr225Pro) AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 1, 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:: RCV003858465.2

Allele description [Variation Report for NM_000251.3(MSH2):c.673A>C (p.Thr225Pro)]

NM_000251.3(MSH2):c.673A>C (p.Thr225Pro)

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.673A>C (p.Thr225Pro)

HGVS:

NC_000002.12:g.47412441A>C
NG_007110.2:g.14318A>C
NM_000251.3:c.673A>CMANE SELECT
NM_001258281.1:c.475A>C
NM_001406631.1:c.673A>C
NM_001406632.1:c.673A>C
NM_001406633.1:c.673A>C
NM_001406634.1:c.673A>C
NM_001406635.1:c.673A>C
NM_001406636.1:c.673A>C
NM_001406637.1:c.673A>C
NM_001406638.1:c.673A>C
NM_001406639.1:c.673A>C
NM_001406640.1:c.673A>C
NM_001406641.1:c.673A>C
NM_001406642.1:c.673A>C
NM_001406643.1:c.673A>C
NM_001406644.1:c.673A>C
NM_001406645.1:c.673A>C
NM_001406646.1:c.673A>C
NM_001406647.1:c.673A>C
NM_001406648.1:c.673A>C
NM_001406649.1:c.673A>C
NM_001406650.1:c.673A>C
NM_001406651.1:c.673A>C
NM_001406652.1:c.673A>C
NM_001406653.1:c.613A>C
NM_001406654.1:c.253A>C
NM_001406655.1:c.673A>C
NM_001406656.1:c.-323A>C
NM_001406657.1:c.673A>C
NM_001406658.1:c.-646A>C
NM_001406659.1:c.-796A>C
NM_001406660.1:c.-993A>C
NM_001406661.1:c.-948A>C
NM_001406662.1:c.-865A>C
NM_001406666.1:c.673A>C
NM_001406669.1:c.-796A>C
NM_001406672.1:c.673A>C
NM_001406674.1:c.673A>C
NP_000242.1:p.Thr225Pro
NP_000242.1:p.Thr225Pro
NP_001245210.1:p.Thr159Pro
NP_001393560.1:p.Thr225Pro
NP_001393561.1:p.Thr225Pro
NP_001393562.1:p.Thr225Pro
NP_001393563.1:p.Thr225Pro
NP_001393564.1:p.Thr225Pro
NP_001393565.1:p.Thr225Pro
NP_001393566.1:p.Thr225Pro
NP_001393567.1:p.Thr225Pro
NP_001393568.1:p.Thr225Pro
NP_001393569.1:p.Thr225Pro
NP_001393570.1:p.Thr225Pro
NP_001393571.1:p.Thr225Pro
NP_001393572.1:p.Thr225Pro
NP_001393573.1:p.Thr225Pro
NP_001393574.1:p.Thr225Pro
NP_001393575.1:p.Thr225Pro
NP_001393576.1:p.Thr225Pro
NP_001393577.1:p.Thr225Pro
NP_001393578.1:p.Thr225Pro
NP_001393579.1:p.Thr225Pro
NP_001393580.1:p.Thr225Pro
NP_001393581.1:p.Thr225Pro
NP_001393582.1:p.Thr205Pro
NP_001393583.1:p.Thr85Pro
NP_001393584.1:p.Thr225Pro
NP_001393586.1:p.Thr225Pro
NP_001393595.1:p.Thr225Pro
NP_001393601.1:p.Thr225Pro
NP_001393603.1:p.Thr225Pro
LRG_218t1:c.673A>C
LRG_218:g.14318A>C
LRG_218p1:p.Thr225Pro
NC_000002.11:g.47639580A>C
NM_000251.2:c.673A>C
NR_176230.1:n.709A>C
NR_176231.1:n.709A>C
NR_176232.1:n.709A>C
NR_176233.1:n.701A>C
NR_176234.1:n.709A>C
NR_176235.1:n.709A>C
NR_176236.1:n.709A>C
NR_176237.1:n.709A>C
NR_176238.1:n.709A>C
NR_176239.1:n.709A>C
NR_176240.1:n.709A>C
NR_176241.1:n.709A>C
NR_176242.1:n.709A>C
NR_176243.1:n.709A>C
NR_176244.1:n.709A>C
NR_176245.1:n.709A>C
NR_176246.1:n.709A>C
NR_176247.1:n.709A>C
NR_176248.1:n.709A>C
NR_176249.1:n.709A>C
NR_176250.1:n.709A>C

Protein change:

T159P

Molecular consequence:

NM_001406656.1:c.-323A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406658.1:c.-646A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406659.1:c.-796A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406660.1:c.-993A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406661.1:c.-948A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406662.1:c.-865A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001406669.1:c.-796A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000251.3:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001258281.1:c.475A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406631.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406632.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406633.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406634.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406635.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406636.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406637.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406638.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406639.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406640.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406641.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406642.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406643.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406644.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406645.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406646.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406647.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406648.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406649.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406650.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406651.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406652.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406653.1:c.613A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406654.1:c.253A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406655.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406657.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406666.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406672.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001406674.1:c.673A>C - missense variant - [Sequence Ontology: SO:0001583]
NR_176230.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176231.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176232.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176233.1:n.701A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176234.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176235.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176236.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176237.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176238.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176239.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176240.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176241.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176242.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176243.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176244.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176245.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176246.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176247.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176248.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176249.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176250.1:n.709A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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UNVERIFIED: Cheilinus trilobatus isolate KHU-16 cytochrome oxidase subunit 1-like gene, partial sequence; mitochondrial
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004655770	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 1, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 33357406, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004655770

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 1, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

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, SCV004655770.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

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 performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 33357406) indicates that this missense variant is expected to disrupt MSH2 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). This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 225 of the MSH2 protein (p.Thr225Pro).

#	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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