NM_000251.3(MSH2):c.2459-1G>A AND Lynch syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 1, 2018
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:: RCV000465186.4

Allele description [Variation Report for NM_000251.3(MSH2):c.2459-1G>A]

NM_000251.3(MSH2):c.2459-1G>A

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.2459-1G>A

HGVS:

NC_000002.12:g.47480695G>A
NG_007110.2:g.82572G>A
NM_000251.3:c.2459-1G>AMANE SELECT
NM_001258281.1:c.2261-1G>A
NM_001406631.1:c.2459-1G>A
NM_001406632.1:c.2459-1G>A
NM_001406633.1:c.2459-1G>A
NM_001406634.1:c.2459-1G>A
NM_001406635.1:c.2459-1G>A
NM_001406636.1:c.2426-1G>A
NM_001406637.1:c.2459-1G>A
NM_001406638.1:c.2498-1G>A
NM_001406639.1:c.2459-1G>A
NM_001406640.1:c.2459-1G>A
NM_001406641.1:c.2459-1G>A
NM_001406642.1:c.2459-1G>A
NM_001406643.1:c.2459-1G>A
NM_001406644.1:c.2459-1G>A
NM_001406645.1:c.2459-1G>A
NM_001406646.1:c.2459-1G>A
NM_001406647.1:c.2309-1G>A
NM_001406648.1:c.2459-1G>A
NM_001406649.1:c.2309-1G>A
NM_001406650.1:c.2309-1G>A
NM_001406651.1:c.2309-1G>A
NM_001406652.1:c.2309-1G>A
NM_001406653.1:c.2399-1G>A
NM_001406654.1:c.2039-1G>A
NM_001406656.1:c.1562-1G>A
NM_001406658.1:c.1103-1G>A
NM_001406659.1:c.1103-1G>A
NM_001406660.1:c.1103-1G>A
NM_001406661.1:c.1103-1G>A
NM_001406662.1:c.1103-1G>A
NM_001406669.1:c.1103-1G>A
NM_001406674.1:c.2459-1G>A
LRG_218t1:c.2459-1G>A
LRG_218:g.82572G>A
NC_000002.11:g.47707834G>A
NM_000251.1:c.2459-1G>A
NM_000251.2:c.2459-1G>A

Links:

dbSNP: rs1060501991

NCBI 1000 Genomes Browser:

rs1060501991

Molecular consequence:

NM_000251.3:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001258281.1:c.2261-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406631.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406632.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406633.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406634.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406635.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406636.1:c.2426-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406637.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406638.1:c.2498-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406639.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406640.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406641.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406642.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406643.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406644.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406645.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406646.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406647.1:c.2309-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406648.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406649.1:c.2309-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406650.1:c.2309-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406651.1:c.2309-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406652.1:c.2309-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406653.1:c.2399-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406654.1:c.2039-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406656.1:c.1562-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406658.1:c.1103-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406659.1:c.1103-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406660.1:c.1103-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406661.1:c.1103-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406662.1:c.1103-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406669.1:c.1103-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406674.1:c.2459-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Lynch syndrome
Identifiers:: MONDO: MONDO:0005835; MedGen: C4552100

Recent activity

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NADH dehydrogenase subunit 6 (mitochondrion) [Parasphaerasclera valdiviae]
NADH dehydrogenase subunit 6 (mitochondrion) [Parasphaerasclera valdiviae]
gi|2190896806|gb|UKP87991.1|

Protein
Octocorallia MutS-like protein (MutS) gene, partial cds; mitochondrial.
Octocorallia MutS-like protein (MutS) gene, partial cds; mitochondrial.
PopSet: 428765395

PopSet
uncharacterized protein LOC111009921 isoform X1 [Momordica charantia]
uncharacterized protein LOC111009921 isoform X1 [Momordica charantia]
gi|1229771822|ref|XP_022138850.1|

Protein
uncharacterized protein LOC102615854 [Citrus sinensis]
uncharacterized protein LOC102615854 [Citrus sinensis]
gi|568871483|ref|XP_006488913.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000887428	University of Washington Department of Laboratory Medicine, University of Washington	criteria provided, single submitter (Shirts BH et al. (Am J Hum Genet 2018))	Likely pathogenic (May 1, 2018)	somatic	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

SCV000887428

University of Washington Department of Laboratory Medicine, University of Washington

criteria provided, single submitter

(Shirts BH et al. (Am J Hum Genet 2018))

Likely pathogenic
(May 1, 2018)

somatic

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	somatic	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Using Somatic Mutations from Tumors to Classify Variants in Mismatch Repair Genes.

Shirts BH, Konnick EQ, Upham S, Walsh T, Ranola JMO, Jacobson AL, King MC, Pearlman R, Hampel H, Pritchard CC.

Am J Hum Genet. 2018 Jul 5;103(1):19-29. doi: 10.1016/j.ajhg.2018.05.001. Epub 2018 Jun 7.

PubMed [citation]

PMID:: 29887214
PMCID:: PMC6035155

Details of each submission

From University of Washington Department of Laboratory Medicine, University of Washington, SCV000887428.1

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

Description

MSH2 NM_000251.2:c.2459-1G>A has a 98.7% probability of pathogenicity based on combining prior probability from public data with likelihood ratios of 1.56 and 1.56 to 1, generated from evidence of seeing this as a somatic mutation in two independent tumors without loss of heterozygosity at the MSH2 locus. See Shirts et al 2018, PMID 29887214.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	somatic	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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