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NM_000535.7(PMS2):c.2276-113_2445+1596del AND Lynch syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 5, 2013
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV000076850.4

Allele description [Variation Report for NM_000535.7(PMS2):c.2276-113_2445+1596del]

NM_000535.7(PMS2):c.2276-113_2445+1596del

Gene:
PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7p22.1
Genomic location:
Preferred name:
NM_000535.7(PMS2):c.2276-113_2445+1596del
Other names:
p.Ala759Glyfs*8
HGVS:
  • NC_000007.14:g.5976004_5977882del
  • NG_008466.1:g.36237_38115del
  • NM_000535.7:c.2276-113_2445+1596delMANE SELECT
  • NM_001322003.2:c.1871-113_2040+1596del
  • NM_001322004.2:c.1871-113_2040+1596del
  • NM_001322005.2:c.1871-113_2040+1596del
  • NM_001322006.2:c.2120-113_2289+1596del
  • NM_001322007.2:c.1958-113_2127+1596del
  • NM_001322008.2:c.1958-113_2127+1596del
  • NM_001322009.2:c.1871-80_2073+1596del
  • NM_001322010.2:c.1715-113_1884+1596del
  • NM_001322011.2:c.1343-113_1512+1596del
  • NM_001322012.2:c.1343-113_1512+1596del
  • NM_001322013.2:c.1703-113_1872+1596del
  • NM_001322014.2:c.2276-80_2478+1596del
  • NM_001322015.2:c.1967-113_2136+1596del
  • LRG_161t1:c.2276-113_2445+1596del
  • LRG_161:g.36237_38115del
  • NC_000007.13:g.6015635_6017513del
  • NM_000535.5:c.2276-113_2445+1596del
  • NM_000535.7:c.2276-125_2445+1584delMANE SELECT
Note:
1879-nt deletion of exon 14 plus flanking intronic sequences in gene PMS2.
Links:
Molecular consequence:
  • NM_000535.7:c.2276-113_2445+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322003.2:c.1871-113_2040+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322004.2:c.1871-113_2040+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322005.2:c.1871-113_2040+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322006.2:c.2120-113_2289+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322007.2:c.1958-113_2127+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322008.2:c.1958-113_2127+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322009.2:c.1871-80_2073+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322010.2:c.1715-113_1884+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322011.2:c.1343-113_1512+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322012.2:c.1343-113_1512+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322013.2:c.1703-113_1872+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322014.2:c.2276-80_2478+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001322015.2:c.1967-113_2136+1596del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_000535.7:c.2276-113_2445+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322003.2:c.1871-113_2040+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322004.2:c.1871-113_2040+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322005.2:c.1871-113_2040+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322006.2:c.2120-113_2289+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322007.2:c.1958-113_2127+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322008.2:c.1958-113_2127+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322009.2:c.1871-80_2073+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322010.2:c.1715-113_1884+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322011.2:c.1343-113_1512+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322012.2:c.1343-113_1512+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322013.2:c.1703-113_1872+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322014.2:c.2276-80_2478+1596del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001322015.2:c.1967-113_2136+1596del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000108340International Society for Gastrointestinal Hereditary Tumours (InSiGHT)
reviewed by expert panel

(Guidelines v1.9)
Pathogenic
(Sep 5, 2013)
germlineresearch

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedresearch

Details of each submission

From International Society for Gastrointestinal Hereditary Tumours (InSiGHT), SCV000108340.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided

Description

Large deletion

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

Last Updated: Jun 9, 2024