NM_000251.3(MSH2):c.689del (p.Ala230fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 23, 2020
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:: RCV002362304.2

Allele description [Variation Report for NM_000251.3(MSH2):c.689del (p.Ala230fs)]

NM_000251.3(MSH2):c.689del (p.Ala230fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.689del (p.Ala230fs)

HGVS:

NC_000002.12:g.47412457del
NG_007110.2:g.14334del
NM_000251.3:c.689delMANE SELECT
NM_001258281.1:c.491del
NM_001406631.1:c.689delC
NM_001406632.1:c.689delC
NM_001406633.1:c.689delC
NM_001406634.1:c.689delC
NM_001406635.1:c.689delC
NM_001406636.1:c.689delC
NM_001406637.1:c.689delC
NM_001406638.1:c.689delC
NM_001406639.1:c.689delC
NM_001406640.1:c.689delC
NM_001406641.1:c.689delC
NM_001406642.1:c.689delC
NM_001406643.1:c.689delC
NM_001406644.1:c.689delC
NM_001406645.1:c.689delC
NM_001406646.1:c.689delC
NM_001406647.1:c.689delC
NM_001406648.1:c.689delC
NM_001406649.1:c.689delC
NM_001406650.1:c.689delC
NM_001406651.1:c.689delC
NM_001406652.1:c.689delC
NM_001406653.1:c.629delC
NM_001406654.1:c.269delC
NM_001406655.1:c.689delC
NM_001406656.1:c.-307delC
NM_001406657.1:c.689delC
NM_001406658.1:c.-630delC
NM_001406659.1:c.-780delC
NM_001406660.1:c.-977delC
NM_001406661.1:c.-932delC
NM_001406662.1:c.-849delC
NM_001406666.1:c.689delC
NM_001406669.1:c.-780delC
NM_001406672.1:c.689delC
NM_001406674.1:c.689delC
NP_000242.1:p.Ala230Valfs
NP_000242.1:p.Ala230fs
NP_001245210.1:p.Ala164fs
NP_001393560.1:p.Ala230Valfs
NP_001393561.1:p.Ala230Valfs
NP_001393562.1:p.Ala230Valfs
NP_001393563.1:p.Ala230Valfs
NP_001393564.1:p.Ala230Valfs
NP_001393565.1:p.Ala230Valfs
NP_001393566.1:p.Ala230Valfs
NP_001393567.1:p.Ala230Valfs
NP_001393568.1:p.Ala230Valfs
NP_001393569.1:p.Ala230Valfs
NP_001393570.1:p.Ala230Valfs
NP_001393571.1:p.Ala230Valfs
NP_001393572.1:p.Ala230Valfs
NP_001393573.1:p.Ala230Valfs
NP_001393574.1:p.Ala230Valfs
NP_001393575.1:p.Ala230Valfs
NP_001393576.1:p.Ala230Valfs
NP_001393577.1:p.Ala230Valfs
NP_001393578.1:p.Ala230Valfs
NP_001393579.1:p.Ala230Valfs
NP_001393580.1:p.Ala230Valfs
NP_001393581.1:p.Ala230Valfs
NP_001393582.1:p.Ala210Valfs
NP_001393583.1:p.Ala90Valfs
NP_001393584.1:p.Ala230Valfs
NP_001393586.1:p.Ala230Valfs
NP_001393595.1:p.Ala230Valfs
NP_001393601.1:p.Ala230Valfs
NP_001393603.1:p.Ala230Valfs
LRG_218t1:c.689del
LRG_218:g.14334del
LRG_218p1:p.Ala230Valfs
NC_000002.11:g.47639596del
NM_000251.1:c.689delC
NM_000251.2:c.689delC
NR_176230.1:n.725delC
NR_176231.1:n.725delC
NR_176232.1:n.725delC
NR_176233.1:n.717delC
NR_176234.1:n.725delC
NR_176235.1:n.725delC
NR_176236.1:n.725delC
NR_176237.1:n.725delC
NR_176238.1:n.725delC
NR_176239.1:n.725delC
NR_176240.1:n.725delC
NR_176241.1:n.725delC
NR_176242.1:n.725delC
NR_176243.1:n.725delC
NR_176244.1:n.725delC
NR_176245.1:n.725delC
NR_176246.1:n.725delC
NR_176247.1:n.725delC
NR_176248.1:n.725delC
NR_176249.1:n.725delC
NR_176250.1:n.725delC

Protein change:

A164fs

Molecular consequence:

NM_000251.3:c.689del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258281.1:c.491del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406631.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406632.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406633.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406634.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406635.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406636.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406637.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406638.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406639.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406640.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406641.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406642.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406643.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406644.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406645.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406646.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406647.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406648.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406649.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406650.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406651.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406652.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406653.1:c.629delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406654.1:c.269delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406655.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406657.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406666.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406672.1:c.689delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001406674.1:c.689delC - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002661419	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Dec 23, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002661419

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Dec 23, 2020)

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, SCV002661419.2

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

Description

The c.689delC pathogenic mutation, located in coding exon 4 of the MSH2 gene, results from a deletion of one nucleotide at nucleotide position 689, causing a translational frameshift with a predicted alternate stop codon (p.A230Vfs*16). 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 1, 2024

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