NM_000251.3(MSH2):c.2078del (p.Cys693fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 30, 2021
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:: RCV002422244.2

Allele description [Variation Report for NM_000251.3(MSH2):c.2078del (p.Cys693fs)]

NM_000251.3(MSH2):c.2078del (p.Cys693fs)

Gene:

MSH2:mutS homolog 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.2078del (p.Cys693fs)

HGVS:

NC_000002.12:g.47476439del
NG_007110.2:g.78316del
NM_000251.3:c.2078delMANE SELECT
NM_001258281.1:c.1880del
NM_001406631.1:c.2078delG
NM_001406632.1:c.2078delG
NM_001406633.1:c.2078delG
NM_001406634.1:c.2078delG
NM_001406635.1:c.2078delG
NM_001406636.1:c.2045delG
NM_001406637.1:c.2078delG
NM_001406638.1:c.2117delG
NM_001406639.1:c.2078delG
NM_001406640.1:c.2078delG
NM_001406641.1:c.2078delG
NM_001406642.1:c.2078delG
NM_001406643.1:c.2078delG
NM_001406644.1:c.2078delG
NM_001406645.1:c.2078delG
NM_001406646.1:c.2078delG
NM_001406647.1:c.1928delG
NM_001406648.1:c.2078delG
NM_001406649.1:c.1928delG
NM_001406650.1:c.1928delG
NM_001406651.1:c.1928delG
NM_001406652.1:c.1928delG
NM_001406653.1:c.2018delG
NM_001406654.1:c.1658delG
NM_001406656.1:c.1181delG
NM_001406658.1:c.722delG
NM_001406659.1:c.722delG
NM_001406660.1:c.722delG
NM_001406661.1:c.722delG
NM_001406662.1:c.722delG
NM_001406669.1:c.722delG
NM_001406674.1:c.2078delG
NP_000242.1:p.Cys693Phefs
NP_000242.1:p.Cys693fs
NP_001245210.1:p.Cys627fs
NP_001393560.1:p.Cys693Phefs
NP_001393561.1:p.Cys693Phefs
NP_001393562.1:p.Cys693Phefs
NP_001393563.1:p.Cys693Phefs
NP_001393564.1:p.Cys693Phefs
NP_001393565.1:p.Cys682Phefs
NP_001393566.1:p.Cys693Phefs
NP_001393567.1:p.Cys706Phefs
NP_001393568.1:p.Cys693Phefs
NP_001393569.1:p.Cys693Phefs
NP_001393570.1:p.Cys693Phefs
NP_001393571.1:p.Cys693Phefs
NP_001393572.1:p.Cys693Phefs
NP_001393573.1:p.Cys693Phefs
NP_001393574.1:p.Cys693Phefs
NP_001393575.1:p.Cys693Phefs
NP_001393576.1:p.Cys643Phefs
NP_001393577.1:p.Cys693Phefs
NP_001393578.1:p.Cys643Phefs
NP_001393579.1:p.Cys643Phefs
NP_001393580.1:p.Cys643Phefs
NP_001393581.1:p.Cys643Phefs
NP_001393582.1:p.Cys673Phefs
NP_001393583.1:p.Cys553Phefs
NP_001393585.1:p.Cys394Phefs
NP_001393587.1:p.Cys241Phefs
NP_001393588.1:p.Cys241Phefs
NP_001393589.1:p.Cys241Phefs
NP_001393590.1:p.Cys241Phefs
NP_001393591.1:p.Cys241Phefs
NP_001393598.1:p.Cys241Phefs
NP_001393603.1:p.Cys693Phefs
LRG_218t1:c.2078del
LRG_218:g.78316del
LRG_218p1:p.Cys693Phefs
NC_000002.11:g.47703578del
NM_000251.1:c.2078delG
NM_000251.2:c.2078delG
NR_176230.1:n.2114delG
NR_176231.1:n.2114delG
NR_176232.1:n.2114delG
NR_176233.1:n.1956delG
NR_176234.1:n.2114delG
NR_176235.1:n.2114delG
NR_176236.1:n.2114delG
NR_176237.1:n.2114delG
NR_176238.1:n.2247delG
NR_176239.1:n.2114delG
NR_176241.1:n.2114delG
NR_176242.1:n.2114delG
NR_176243.1:n.1964delG
NR_176244.1:n.2114delG
NR_176245.1:n.2114delG
NR_176246.1:n.2114delG
NR_176247.1:n.2114delG
NR_176248.1:n.2114delG
NR_176249.1:n.2344delG
NR_176250.1:n.1854delG

Protein change:

C627fs

Molecular consequence:

NM_000251.3:c.2078del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258281.1:c.1880del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406631.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406632.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406633.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406634.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406635.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406636.1:c.2045delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406637.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406638.1:c.2117delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406639.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406640.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406641.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406642.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406643.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406644.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406645.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406646.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406647.1:c.1928delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406648.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406649.1:c.1928delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406650.1:c.1928delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406651.1:c.1928delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406652.1:c.1928delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406653.1:c.2018delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406654.1:c.1658delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406656.1:c.1181delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406658.1:c.722delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406659.1:c.722delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406660.1:c.722delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406661.1:c.722delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406662.1:c.722delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406669.1:c.722delG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406674.1:c.2078delG - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

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PREDICTED: Ursus americanus sarcoglycan delta (SGCD), transcript variant X2, mRN...
PREDICTED: Ursus americanus sarcoglycan delta (SGCD), transcript variant X2, mRNA
gi|2176657282|ref|XM_045791977.1|

Nucleotide
Salmonella enterica subsp. enterica serovar Senftenberg strain Sf1 SpeC (speC) g...
Salmonella enterica subsp. enterica serovar Senftenberg strain Sf1 SpeC (speC) gene, partial cds
gi|82706403|gb|DQ285520.1|

Nucleotide
Org.one project - Puerto Rican Parrot
Org.one project - Puerto Rican Parrot
Org.one project - Puerto Rican Parrot

BioProject
Salmonella enterica subsp. enterica serovar Infantis strain In1 SpeC (speC) gene...
Salmonella enterica subsp. enterica serovar Infantis strain In1 SpeC (speC) gene, partial cds
gi|82706409|gb|DQ285523.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002727750	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Jun 30, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002727750

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Jun 30, 2021)

germline

clinical testing

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

Details of each submission

From Ambry Genetics, SCV002727750.2

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

Description

The c.2078delG pathogenic mutation, located in coding exon 13 of the MSH2 gene, results from a deletion of one nucleotide at nucleotide position 2078, causing a translational frameshift with a predicted alternate stop codon (p.C693Ffs*17). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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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