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

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 8, 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:: RCV003453475.1

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

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

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>C

HGVS:

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

Links:

dbSNP: rs1060501991

NCBI 1000 Genomes Browser:

rs1060501991

Molecular consequence:

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

Condition(s)

Name:: Lynch syndrome 1
Synonyms:: COLON CANCER, FAMILIAL NONPOLYPOSIS, TYPE 1; MSH2-Related Hereditary Non-Polyposis Colon Cancer; Lynch syndrome I; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007356; MedGen: C2936783; Orphanet: 144; OMIM: 120435

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gi|1992403746|gb|QRY27453.1|

Protein
Homologene neighbors for GEO Profiles (Select 104740828) (0)
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Profile neighbors for GEO Profiles (Select 104733922) (199)
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Homologene neighbors for GEO Profiles (Select 104736525) (0)
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Chromosome neighbors for GEO Profiles (Select 104738224) (20)
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004186730	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely pathogenic (Aug 8, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004186730

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Likely pathogenic
(Aug 8, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Myriad Genetics, Inc., SCV004186730.1

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

Description

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.

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

Last Updated: Sep 29, 2024

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