NM_000251.3(MSH2):c.478_479del (p.Gln160fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 16, 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:: RCV004039438.1

Allele description [Variation Report for NM_000251.3(MSH2):c.478_479del (p.Gln160fs)]

NM_000251.3(MSH2):c.478_479del (p.Gln160fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p21

Genomic location:

Preferred name:

NM_000251.3(MSH2):c.478_479del (p.Gln160fs)

HGVS:

NC_000002.12:g.47410205_47410206del
NG_007110.2:g.12082_12083del
NM_000251.1:c.478_479delCA
NM_000251.3:c.478_479delMANE SELECT
NM_001258281.1:c.280_281del
NP_000242.1:p.Gln160fs
NP_001245210.1:p.Gln94fs
LRG_218t1:c.478_479del
LRG_218:g.12082_12083del
NC_000002.11:g.47637344_47637345del
NM_000251.2:c.478_479delCA

Protein change:

Q160fs

Links:

dbSNP: rs2104025532

NCBI 1000 Genomes Browser:

rs2104025532

Molecular consequence:

NM_000251.3:c.478_479del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001258281.1:c.280_281del - 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
SCV005033562	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Nov 16, 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

SCV005033562

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Nov 16, 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

Lynch syndrome: influence of additional susceptibility variants on cancer risk.

Vibert R, Hasnaoui J, Perrier A, Lefebvre A, Colas C, Dhooge M, Basset N, Chansavang A, Desseignes C, Duval A, Farelly S, Hamzaoui N, Laurent-Puig P, Metras J, Moliere D, Muleris M, Netter J, Touat M, Bielle F, Labreche K, Nicolle R, Perkins G, et al.

Eur J Hum Genet. 2023 Sep;31(9):1078-1082. doi: 10.1038/s41431-023-01367-z. Epub 2023 Apr 24.

PubMed [citation]

PMID:: 37088804
PMCID:: PMC10474080

Details of each submission

From Ambry Genetics, SCV005033562.1

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

Description

The c.478_479delCA pathogenic mutation, located in coding exon 3 of the MSH2 gene, results from a deletion of two nucleotides at nucleotide positions 478 to 479, causing a translational frameshift with a predicted alternate stop codon (p.Q160Gfs*17). This alteration was detected in a patient with colon cancer at age 16 (Vibert R et al. Eur J Hum Genet, 2023 Sep;31:1078-1082). In addition to the clinical data presented in the literature, 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: Jun 9, 2024

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