NM_000535.7(PMS2):c.2521del (p.Trp841fs) AND Lynch syndrome 4

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 10, 2024
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:: RCV004567811.1

Allele description [Variation Report for NM_000535.7(PMS2):c.2521del (p.Trp841fs)]

NM_000535.7(PMS2):c.2521del (p.Trp841fs)

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.2521del (p.Trp841fs)

HGVS:

NC_000007.14:g.5973467del
NG_008466.1:g.40640del
NM_000535.7:c.2521delMANE SELECT
NM_001322003.2:c.2116del
NM_001322004.2:c.2116del
NM_001322005.2:c.2116del
NM_001322006.2:c.2365del
NM_001322007.2:c.2203del
NM_001322008.2:c.2203del
NM_001322009.2:c.2149del
NM_001322010.2:c.1960del
NM_001322011.2:c.1588del
NM_001322012.2:c.1588del
NM_001322013.2:c.1948del
NM_001322014.2:c.2554del
NM_001322015.2:c.2212del
NP_000526.2:p.Trp841fs
NP_001308932.1:p.Trp706fs
NP_001308933.1:p.Trp706fs
NP_001308934.1:p.Trp706fs
NP_001308935.1:p.Trp789fs
NP_001308936.1:p.Trp735fs
NP_001308937.1:p.Trp735fs
NP_001308938.1:p.Trp717fs
NP_001308939.1:p.Trp654fs
NP_001308940.1:p.Trp530fs
NP_001308941.1:p.Trp530fs
NP_001308942.1:p.Trp650fs
NP_001308943.1:p.Trp852fs
NP_001308944.1:p.Trp738fs
LRG_161t1:c.2521del
LRG_161:g.40640del
NC_000007.13:g.6013098del
NM_000535.5:c.2521del
NM_000535.5:c.2521delT
NM_000535.6:c.2521del
NR_136154.1:n.2565del
p.Trp841fs

Protein change:

W530fs

Links:

dbSNP: rs886039646

NCBI 1000 Genomes Browser:

rs886039646

Molecular consequence:

NM_000535.7:c.2521del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322003.2:c.2116del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.2116del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322005.2:c.2116del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.2365del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.2203del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322008.2:c.2203del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322009.2:c.2149del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322010.2:c.1960del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322011.2:c.1588del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322012.2:c.1588del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322013.2:c.1948del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.2554del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322015.2:c.2212del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_136154.1:n.2565del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV005056403	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 10, 2024)	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

SCV005056403

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 10, 2024)

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 Baylor Genetics, SCV005056403.1

#	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: Nov 3, 2024

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