NC_000002.11:g.(?_47630331)_(47672806_?)del AND Hereditary nonpolyposis colorectal neoplasms

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 9, 2021
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:: RCV001963286.3

Allele description [Variation Report for NC_000002.11:g.(?_47630331)_(47672806_?)del]

NC_000002.11:g.(?_47630331)_(47672806_?)del

Gene:: MSH2:mutS homolog 2 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 2p21
Genomic location:: Chr2: 47630331 - 47672806 (on Assembly GRCh37)
Preferred name:: NC_000002.11:g.(?_47630331)_(47672806_?)del
HGVS:: NC_000002.11:g.(?_47630331)_(47672806_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Hereditary nonpolyposis colorectal neoplasms
Identifiers:: MeSH: D003123; MedGen: C0009405

Recent activity

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UI-R-CV1-bsc-e-05-0-UI.s1 UI-R-CV1 Rattus norvegicus cDNA clone UI-R-CV1-bsc-e-0...
UI-R-CV1-bsc-e-05-0-UI.s1 UI-R-CV1 Rattus norvegicus cDNA clone UI-R-CV1-bsc-e-05-0-UI 3', mRNA sequence
gi|13268956|gnl|dbEST|8093173|gb|BG 9.1|

Nucleotide
RecName: Full=Elongation factor 1-alpha 2; Short=EF-1-alpha-2; AltName: Full=Euk...
RecName: Full=Elongation factor 1-alpha 2; Short=EF-1-alpha-2; AltName: Full=Eukaryotic elongation factor 1 A-2; Short=eEF1A-2; AltName: Full=Statin-S1
gi|544231|sp|Q05639.1|EF1A2_HUMAN

Protein
TRNAS-GCU [Panthera tigris]
TRNAS-GCU [Panthera tigris]
Gene ID:122237592

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002244042	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 9, 2021)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 15849733, 24362816, 16143124, 16941473, 11830542, 16736289, 15713769, 24323032, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002244042

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 9, 2021)

germline

clinical testing

PubMed (9)
[See all records that cite these PMIDs]

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

Spectrum and frequencies of mutations in MSH2 and MLH1 identified in 1,721 German families suspected of hereditary nonpolyposis colorectal cancer.

Mangold E, Pagenstecher C, Friedl W, Mathiak M, Buettner R, Engel C, Loeffler M, Holinski-Feder E, Müller-Koch Y, Keller G, Schackert HK, Krüger S, Goecke T, Moeslein G, Kloor M, Gebert J, Kunstmann E, Schulmann K, Rüschoff J, Propping P.

Int J Cancer. 2005 Sep 20;116(5):692-702.

PubMed [citation]

PMID:: 15849733

Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database.

Thompson BA, Spurdle AB, Plazzer JP, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, Farrell MP, Farrington SM, Frayling IM, Frebourg T, Goldgar DE, Heinen CD, Holinski-Feder E, Kohonen-Corish M, Robinson KL, Leung SY, et al.

Nat Genet. 2014 Feb;46(2):107-115. doi: 10.1038/ng.2854. Epub 2013 Dec 22.

PubMed [citation]

PMID:: 24362816
PMCID:: PMC4294709

See all PubMed Citations (9)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002244042.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 1-8 of the MSH2 gene, which includes the initiator codon. If EPCAM has been tested and no copy number events are reported for it, then the 5' boundary of this event lies between the EPCAM and MSH2 genes. If EPCAM has not been tested, the 5' end of this event is unknown as it extends beyond the assayed region of this test. The 3' boundary is likely confined to intron 8 of the MSH2 gene. This is expected to result in an absent or disrupted protein product. Loss-of-function variants in MSH2 are known to be pathogenic (PMID: 15849733, 24362816). Similar deletions ‚Äãhave been observed in individual(s) with clinical features of Lynch syndrome (PMID: 16143124, 16941473, 11830542, 16736289, 15713769, 24323032). For these reasons, this variant has been classified as Pathogenic.

#	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: Sep 29, 2024

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