NM_000535.7(PMS2):c.2007-2_2007-1delinsCA AND Hereditary nonpolyposis colon cancer

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: May 14, 2020
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:: RCV001199875.1

Allele description [Variation Report for NM_000535.7(PMS2):c.2007-2_2007-1delinsCA]

NM_000535.7(PMS2):c.2007-2_2007-1delinsCA

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.2007-2_2007-1delinsCA

HGVS:

NC_000007.14:g.5982992_5982993delinsTG
NG_008466.1:g.31114_31115delinsCA
NM_000535.7:c.2007-2_2007-1delinsCAMANE SELECT
NM_001322003.2:c.1602-2_1602-1delinsCA
NM_001322004.2:c.1602-2_1602-1delinsCA
NM_001322005.2:c.1602-2_1602-1delinsCA
NM_001322006.2:c.1851-2_1851-1delinsCA
NM_001322007.2:c.1689-2_1689-1delinsCA
NM_001322008.2:c.1689-2_1689-1delinsCA
NM_001322009.2:c.1602-2_1602-1delinsCA
NM_001322010.2:c.1446-2_1446-1delinsCA
NM_001322011.2:c.1074-2_1074-1delinsCA
NM_001322012.2:c.1074-2_1074-1delinsCA
NM_001322013.2:c.1434-2_1434-1delinsCA
NM_001322014.2:c.2007-2_2007-1delinsCA
NM_001322015.2:c.1698-2_1698-1delinsCA
LRG_161:g.31114_31115delinsCA
NC_000007.13:g.6022623_6022624delinsTG
NM_000535.6:c.2007-2_2007-1delinsCA

Links:

dbSNP: rs1782473185

NCBI 1000 Genomes Browser:

rs1782473185

Molecular consequence:

NM_000535.7:c.2007-2_2007-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322003.2:c.1602-2_1602-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322004.2:c.1602-2_1602-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322005.2:c.1602-2_1602-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322006.2:c.1851-2_1851-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322007.2:c.1689-2_1689-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322008.2:c.1689-2_1689-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322009.2:c.1602-2_1602-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322010.2:c.1446-2_1446-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322011.2:c.1074-2_1074-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322012.2:c.1074-2_1074-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322013.2:c.1434-2_1434-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322014.2:c.2007-2_2007-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322015.2:c.1698-2_1698-1delinsCA - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Hereditary nonpolyposis colon cancer (HNPCC)
Synonyms:: Hereditary nonpolyposis colorectal cancer; Familial nonpolyposis colon cancer; Hereditary Nonpolyposis Colorectal Cancer Syndrome
Identifiers:: MONDO: MONDO:0018630; MedGen: C1333990; OMIM: PS120435

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001370626	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (May 14, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001370626

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(May 14, 2020)

germline

clinical testing

Citation Link

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001370626.1

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

Description

Variant summary: PMS2 c.2007-2_2007-1delinsCA is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a canonical 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 158418 control chromosomes. To our knowledge, no occurrence of c.2007-2_2007-1delinsCA in individuals affected with Lynch Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely 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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