NM_000535.7(PMS2):c.116del (p.Val39fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 1, 2021
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:: RCV002329147.2

Allele description [Variation Report for NM_000535.7(PMS2):c.116del (p.Val39fs)]

NM_000535.7(PMS2):c.116del (p.Val39fs)

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.116del (p.Val39fs)

HGVS:

NC_000007.14:g.6005939del
NG_008466.1:g.8168del
NG_050738.1:g.1689del
NM_000535.5:c.116del
NM_000535.7:c.116delMANE SELECT
NM_001322003.2:c.-290del
NM_001322004.2:c.-242-1881del
NM_001322005.2:c.-290del
NM_001322006.2:c.116del
NM_001322007.2:c.-100del
NM_001322008.2:c.-52-1881del
NM_001322009.2:c.-290del
NM_001322010.2:c.-242-1881del
NM_001322011.2:c.-769del
NM_001322012.2:c.-769del
NM_001322013.2:c.-290del
NM_001322014.2:c.116del
NM_001322015.2:c.-369del
NP_000526.2:p.Val39fs
NP_001308935.1:p.Val39fs
NP_001308943.1:p.Val39fs
LRG_161t1:c.116del
LRG_161:g.8168del
NC_000007.13:g.6045570del
NM_000535.5:c.116delT
NM_000535.6:c.116del
NR_136154.1:n.203del

Protein change:

V39fs

Links:

dbSNP: rs1064794152

NCBI 1000 Genomes Browser:

rs1064794152

Molecular consequence:

NM_001322003.2:c.-290del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-290del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-100del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-290del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-769del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-769del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-290del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-369del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000535.7:c.116del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.116del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.116del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.-242-1881del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1881del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1881del - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.203del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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RecName: Full=Chemokine-binding protein; Short=vCKBP; AltName: Full=35 kDa prote...
RecName: Full=Chemokine-binding protein; Short=vCKBP; AltName: Full=35 kDa protein; Flags: Precursor
gi|137559|sp|P19063.1|PG001_VACCL

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002631689	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Dec 1, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002631689

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Dec 1, 2021)

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 Ambry Genetics, SCV002631689.2

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

Description

The c.116delT pathogenic mutation, located in coding exon 2 of the PMS2 gene, results from a deletion of one nucleotide at nucleotide position 116, causing a translational frameshift with a predicted alternate stop codon (p.V39Efs*4). This variant has been identified in a proband(s) whose Lynch syndrome-associated tumor demonstrated loss of PMS2 expression by immunohistochemistry (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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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