NM_000535.7(PMS2):c.1144+1del AND Lynch syndrome 4

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 20, 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:: RCV003450001.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1144+1del]

NM_000535.7(PMS2):c.1144+1del

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.1144+1del

HGVS:

NC_000007.14:g.5989800del
NG_008466.1:g.24308del
NM_000535.7:c.1144+1delMANE SELECT
NM_001322003.2:c.739+1del
NM_001322004.2:c.739+1del
NM_001322005.2:c.739+1del
NM_001322006.2:c.988+2174del
NM_001322007.2:c.826+1del
NM_001322008.2:c.826+1del
NM_001322009.2:c.739+1del
NM_001322010.2:c.583+2174del
NM_001322011.2:c.211+1del
NM_001322012.2:c.211+1del
NM_001322013.2:c.571+1del
NM_001322014.2:c.1144+1del
NM_001322015.2:c.835+1del
NM_001406866.1:c.1330+1del
NM_001406868.1:c.1168+1del
NM_001406869.1:c.1036+1del
NM_001406870.1:c.988+2174del
NM_001406871.1:c.1144+1del
NM_001406872.1:c.1144+1del
NM_001406873.1:c.946+1del
NM_001406874.1:c.976+1del
NM_001406875.1:c.835+1del
NM_001406876.1:c.826+1del
NM_001406877.1:c.835+1del
NM_001406878.1:c.835+1del
NM_001406879.1:c.835+1del
NM_001406880.1:c.835+1del
NM_001406881.1:c.835+1del
NM_001406882.1:c.835+1del
NM_001406883.1:c.826+1del
NM_001406884.1:c.820+2174del
NM_001406885.1:c.808+1del
NM_001406886.1:c.778+1del
NM_001406887.1:c.739+1del
NM_001406888.1:c.739+1del
NM_001406889.1:c.739+1del
NM_001406890.1:c.739+1del
NM_001406891.1:c.739+1del
NM_001406892.1:c.739+1del
NM_001406893.1:c.739+1del
NM_001406894.1:c.739+1del
NM_001406895.1:c.739+1del
NM_001406896.1:c.739+1del
NM_001406897.1:c.739+1del
NM_001406898.1:c.739+1del
NM_001406899.1:c.739+1del
NM_001406900.1:c.679+2174del
NM_001406901.1:c.670+2174del
NM_001406902.1:c.670+2174del
NM_001406903.1:c.826+1del
NM_001406904.1:c.631+1del
NM_001406905.1:c.631+1del
NM_001406906.1:c.583+2174del
NM_001406907.1:c.583+2174del
NM_001406908.1:c.739+1del
NM_001406909.1:c.571+1del
NM_001406910.1:c.739+1del
NM_001406911.1:c.373+1del
NM_001406912.1:c.804-6808del
LRG_161t1:c.1144+1del
LRG_161:g.24308del
NC_000007.13:g.6029430del
NC_000007.13:g.6029431del
NM_000535.5:c.1144+1delG

Links:

dbSNP: rs2128746842

NCBI 1000 Genomes Browser:

rs2128746842

Molecular consequence:

NM_001322006.2:c.988+2174del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.583+2174del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406870.1:c.988+2174del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406884.1:c.820+2174del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406900.1:c.679+2174del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406901.1:c.670+2174del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406902.1:c.670+2174del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406906.1:c.583+2174del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406907.1:c.583+2174del - intron variant - [Sequence Ontology: SO:0001627]
NM_001406912.1:c.804-6808del - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322003.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322004.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322005.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322007.2:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322008.2:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322009.2:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322011.2:c.211+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322012.2:c.211+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322013.2:c.571+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322014.2:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322015.2:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406866.1:c.1330+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406868.1:c.1168+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406869.1:c.1036+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406871.1:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406872.1:c.1144+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406873.1:c.946+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406874.1:c.976+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406875.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406876.1:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406877.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406878.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406879.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406880.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406881.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406882.1:c.835+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406883.1:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406885.1:c.808+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406886.1:c.778+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406887.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406888.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406889.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406890.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406891.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406892.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406893.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406894.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406895.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406896.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406897.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406898.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406899.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406903.1:c.826+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406904.1:c.631+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406905.1:c.631+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406908.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406909.1:c.571+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406910.1:c.739+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406911.1:c.373+1del - splice donor variant - [Sequence Ontology: SO:0001575]

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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gi|1993674918|gb|MT226322.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004187656	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely pathogenic (Sep 20, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004187656

Myriad Genetics, Inc.

criteria provided, single submitter

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

Likely pathogenic
(Sep 20, 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., SCV004187656.1

#	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: Sep 29, 2024

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