NM_000535.7(PMS2):c.537+1del AND Lynch syndrome 4

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Oct 6, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV003449191.2

Allele description [Variation Report for NM_000535.7(PMS2):c.537+1del]

NM_000535.7(PMS2):c.537+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.537+1del

HGVS:

NC_000007.14:g.6002453del
NG_008466.1:g.11655del
NM_000535.7:c.537+1delMANE SELECT
NM_001322003.2:c.132+1del
NM_001322004.2:c.132+1del
NM_001322005.2:c.132+1del
NM_001322006.2:c.537+1del
NM_001322007.2:c.219+1del
NM_001322008.2:c.219+1del
NM_001322009.2:c.132+1del
NM_001322010.2:c.132+1del
NM_001322011.2:c.-348+1del
NM_001322012.2:c.-348+1del
NM_001322013.2:c.132+1del
NM_001322014.2:c.537+1del
NM_001322015.2:c.228+1del
NM_001406866.1:c.723+1del
NM_001406868.1:c.561+1del
NM_001406869.1:c.537+1del
NM_001406870.1:c.537+1del
NM_001406871.1:c.537+1del
NM_001406872.1:c.537+1del
NM_001406873.1:c.537+1del
NM_001406874.1:c.537+1del
NM_001406875.1:c.228+1del
NM_001406876.1:c.219+1del
NM_001406877.1:c.228+1del
NM_001406878.1:c.228+1del
NM_001406879.1:c.228+1del
NM_001406880.1:c.228+1del
NM_001406881.1:c.228+1del
NM_001406882.1:c.228+1del
NM_001406883.1:c.219+1del
NM_001406884.1:c.537+1del
NM_001406885.1:c.250+1520del
NM_001406886.1:c.537+1del
NM_001406887.1:c.132+1del
NM_001406888.1:c.132+1del
NM_001406889.1:c.132+1del
NM_001406890.1:c.132+1del
NM_001406891.1:c.132+1del
NM_001406892.1:c.132+1del
NM_001406893.1:c.132+1del
NM_001406894.1:c.132+1del
NM_001406895.1:c.132+1del
NM_001406896.1:c.132+1del
NM_001406897.1:c.132+1del
NM_001406898.1:c.132+1del
NM_001406899.1:c.132+1del
NM_001406900.1:c.228+1del
NM_001406901.1:c.219+1del
NM_001406902.1:c.219+1del
NM_001406903.1:c.219+1del
NM_001406904.1:c.132+1del
NM_001406905.1:c.132+1del
NM_001406906.1:c.132+1del
NM_001406907.1:c.132+1del
NM_001406908.1:c.132+1del
NM_001406909.1:c.132+1del
NM_001406910.1:c.132+1del
NM_001406911.1:c.132+1del
NM_001406912.1:c.537+1del
LRG_161t1:c.537+1del
LRG_161:g.11655del
NC_000007.13:g.6042083del
NC_000007.13:g.6042084del
NM_000535.5:c.537+1del
NM_000535.5:c.537+1delG
NM_000535.6:c.537+1delG

Links:

dbSNP: rs1064793868

NCBI 1000 Genomes Browser:

rs1064793868

Molecular consequence:

NM_001406885.1:c.250+1520del - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322003.2:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322004.2:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322005.2:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322006.2:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322007.2:c.219+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322008.2:c.219+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322009.2:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322010.2:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322011.2:c.-348+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322012.2:c.-348+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322013.2:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322014.2:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001322015.2:c.228+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406866.1:c.723+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406868.1:c.561+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406869.1:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406870.1:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406871.1:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406872.1:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406873.1:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406874.1:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406875.1:c.228+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406876.1:c.219+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406877.1:c.228+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406878.1:c.228+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406879.1:c.228+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406880.1:c.228+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406881.1:c.228+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406882.1:c.228+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406883.1:c.219+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406884.1:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406886.1:c.537+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406887.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406888.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406889.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406890.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406891.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406892.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406893.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406894.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406895.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406896.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406897.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406898.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406899.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406900.1:c.228+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406901.1:c.219+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406902.1:c.219+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406903.1:c.219+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406904.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406905.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406906.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406907.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406908.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406909.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406910.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406911.1:c.132+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406912.1:c.537+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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004187642	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely pathogenic (Sep 19, 2023)	unknown	clinical testing	Citation Link,
SCV004205406	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 6, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004187642

Myriad Genetics, Inc.

criteria provided, single submitter

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

Likely pathogenic
(Sep 19, 2023)

unknown

clinical testing

Citation Link,

SCV004205406

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 6, 2023)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Citations

PubMed

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 Myriad Genetics, Inc., SCV004187642.1

#	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

From Baylor Genetics, SCV004205406.1

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

#	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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