NM_000535.7(PMS2):c.2007-1_2009del AND Lynch syndrome 4

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 21, 2023
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:: RCV003452394.1

Allele description [Variation Report for NM_000535.7(PMS2):c.2007-1_2009del]

NM_000535.7(PMS2):c.2007-1_2009del

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.2007-1_2009del

HGVS:

NC_000007.14:g.5982990_5982993del
NG_008466.1:g.31115_31118del
NM_000535.7:c.2007-1_2009delMANE SELECT
NM_001322003.2:c.1602-1_1604del
NM_001322004.2:c.1602-1_1604del
NM_001322005.2:c.1602-1_1604del
NM_001322006.2:c.1851-1_1853del
NM_001322007.2:c.1689-1_1691del
NM_001322008.2:c.1689-1_1691del
NM_001322009.2:c.1602-1_1604del
NM_001322010.2:c.1446-1_1448del
NM_001322011.2:c.1074-1_1076del
NM_001322012.2:c.1074-1_1076del
NM_001322013.2:c.1434-1_1436del
NM_001322014.2:c.2007-1_2009del
NM_001322015.2:c.1698-1_1700del
NM_001406866.1:c.2193-1_2195del
NM_001406868.1:c.2031-1_2033del
NM_001406869.1:c.1899-1_1901del
NM_001406870.1:c.1851-1_1853del
NM_001406871.1:c.2007-1_2009del
NM_001406872.1:c.2006+3767_2006+3770del
NM_001406873.1:c.1809-1_1811del
NM_001406874.1:c.1839-1_1841del
NM_001406875.1:c.1698-1_1700del
NM_001406876.1:c.1689-1_1691del
NM_001406877.1:c.1698-1_1700del
NM_001406878.1:c.1698-1_1700del
NM_001406879.1:c.1698-1_1700del
NM_001406880.1:c.1698-1_1700del
NM_001406881.1:c.1698-1_1700del
NM_001406882.1:c.1698-1_1700del
NM_001406883.1:c.1689-1_1691del
NM_001406884.1:c.1683-1_1685del
NM_001406885.1:c.1671-1_1673del
NM_001406886.1:c.1641-1_1643del
NM_001406887.1:c.1602-1_1604del
NM_001406888.1:c.1602-1_1604del
NM_001406889.1:c.1602-1_1604del
NM_001406890.1:c.1602-1_1604del
NM_001406891.1:c.1602-1_1604del
NM_001406892.1:c.1602-1_1604del
NM_001406893.1:c.1602-1_1604del
NM_001406894.1:c.1602-1_1604del
NM_001406895.1:c.1602-1_1604del
NM_001406896.1:c.1602-1_1604del
NM_001406897.1:c.1602-1_1604del
NM_001406898.1:c.1602-1_1604del
NM_001406899.1:c.1602-1_1604del
NM_001406900.1:c.1542-1_1544del
NM_001406901.1:c.1533-1_1535del
NM_001406902.1:c.1533-1_1535del
NM_001406903.1:c.1688+3767_1688+3770del
NM_001406904.1:c.1494-1_1496del
NM_001406905.1:c.1494-1_1496del
NM_001406906.1:c.1446-1_1448del
NM_001406907.1:c.1446-1_1448del
NM_001406908.1:c.1601+3767_1601+3770del
NM_001406909.1:c.1434-1_1436del
NM_001406910.1:c.1601+3767_1601+3770del
NM_001406911.1:c.1236-1_1238del
NM_001406912.1:c.804-1_806del
LRG_161:g.31115_31118del
NC_000007.13:g.6022621_6022624del

Molecular consequence:

NM_001406872.1:c.2006+3767_2006+3770del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406903.1:c.1688+3767_1688+3770del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406908.1:c.1601+3767_1601+3770del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406910.1:c.1601+3767_1601+3770del - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.2007-1_2009del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322003.2:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322004.2:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322005.2:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322006.2:c.1851-1_1853del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322007.2:c.1689-1_1691del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322008.2:c.1689-1_1691del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322009.2:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322010.2:c.1446-1_1448del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322011.2:c.1074-1_1076del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322012.2:c.1074-1_1076del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322013.2:c.1434-1_1436del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322014.2:c.2007-1_2009del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001322015.2:c.1698-1_1700del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406866.1:c.2193-1_2195del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406868.1:c.2031-1_2033del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406869.1:c.1899-1_1901del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406870.1:c.1851-1_1853del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406871.1:c.2007-1_2009del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406873.1:c.1809-1_1811del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406874.1:c.1839-1_1841del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406875.1:c.1698-1_1700del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406876.1:c.1689-1_1691del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406877.1:c.1698-1_1700del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406878.1:c.1698-1_1700del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406879.1:c.1698-1_1700del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406880.1:c.1698-1_1700del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406881.1:c.1698-1_1700del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406882.1:c.1698-1_1700del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406883.1:c.1689-1_1691del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406884.1:c.1683-1_1685del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406885.1:c.1671-1_1673del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406886.1:c.1641-1_1643del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406887.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406888.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406889.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406890.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406891.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406892.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406893.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406894.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406895.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406896.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406897.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406898.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406899.1:c.1602-1_1604del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406900.1:c.1542-1_1544del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406901.1:c.1533-1_1535del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406902.1:c.1533-1_1535del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406904.1:c.1494-1_1496del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406905.1:c.1494-1_1496del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406906.1:c.1446-1_1448del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406907.1:c.1446-1_1448del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406909.1:c.1434-1_1436del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406911.1:c.1236-1_1238del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001406912.1:c.804-1_806del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Lynch syndrome 4 (LYNCH4)
Synonyms:: Colorectal cancer, hereditary nonpolyposis, type 4; Hereditary non-polyposis colorectal cancer, type 4
Identifiers:: MONDO: MONDO:0013699; MedGen: C1838333; Orphanet: 144; OMIM: 614337

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PREDICTED: mitochondrial basic amino acids transporter [Mandrillus leucophaeus]
PREDICTED: mitochondrial basic amino acids transporter [Mandrillus leucophaeus]
gi|795194128|ref|XP_011847030.1|

Protein
AVT71_gp27 [Bacillus phage 250]
AVT71_gp27 [Bacillus phage 250]
Gene ID:26645764

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004187652	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely pathogenic (Sep 21, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004187652

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Likely pathogenic
(Sep 21, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Myriad Genetics, Inc., SCV004187652.1

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

Description

This variant is considered likely pathogenic. This variant occurs within a consensus splice junction and is predicted to result in abnormal mRNA splicing of either an out-of-frame exon or an in-frame exon necessary for protein stability and/or normal function.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 30, 2023

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