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NM_000251.2(MSH2):c.(?_-1)_1076+?del AND Lynch syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 27, 2015
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:
RCV000199211.1

Allele description

NM_000251.2(MSH2):c.(?_-1)_1076+?del

Gene:
MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p21
Genomic location:
Preferred name:
NM_000251.2(MSH2):c.(?_-1)_1076+?del
HGVS:
  • NC_000002.12:g.(?_47403191)_(47416429_?)del
  • LRG_218t1:c.(?_-1)_1076+?del
  • NC_000002.11:g.(?_47630330)_(47643568_?)del
  • NM_000251.2:c.(?_-1)_1076+?del

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000253795Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 27, 2015) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000253795.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change is a gross deletion of the genomic region encompassing exons 1-6 of the MSH2 gene. This deletion includes the translation initiation methionine and extends beyond both edges of the assayed region, and therefore the 5' and 3' boundaries of this event are not known. It is expected to result in a disrupted or absent protein product. Deletions of exons 1-6 have been reported in several affected patients and families, and are clearly defined as Lynch syndrome causative alleles (PMID: 15942939, 16086322, 16143124). A particular deletion of exons 1-6 of the MSH2 gene is a known founder mutation in the North American population (PMID: 12658575, 16143124, 14871915). Because the breakpoints of this deletion are unknown, it is uncertain whether or not the sequence change identified in this patient is that founder mutation. For these reasons, this sequence change has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 26, 2023