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NM_000535.7(PMS2):c.2276-113_2445+1596del AND Lynch syndrome 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 8, 2022
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:
RCV002305444.4

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 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002600097Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Nov 8, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Diagnostic and therapeutic challenges of glioblastoma as an initial malignancy of constitutional mismatch repair deficiency (CMMRD): two case reports and a literature review.

Onishi S, Yamasaki F, Kuraoka K, Taguchi A, Takayasu T, Akagi K, Hinoi T.

BMC Med Genomics. 2023 Jan 16;16(1):6. doi: 10.1186/s12920-022-01403-9. Review.

PubMed [citation]
PMID:
36647049
PMCID:
PMC9843912

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, SCV002600097.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providedclinical testing PubMed (2)

Description

This sequence change is frameshift variant introducing Premature Termination Codon. This variant has been detected in patients who developed MSI-H glioblastoma at age 10 or younger, along with another variant, PMS2(NM_000535.7): c.241G>T (p.Glu81*, phase unknown). The patient is considered constitutional mismatch repair deficiency (CMMRD).

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

Last Updated: Jun 9, 2024