NM_000535.7(PMS2):c.139_146del (p.Leu47fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 14, 2017
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:: RCV000575861.3

Allele description [Variation Report for NM_000535.7(PMS2):c.139_146del (p.Leu47fs)]

NM_000535.7(PMS2):c.139_146del (p.Leu47fs)

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.139_146del (p.Leu47fs)

HGVS:

NC_000007.14:g.6005909_6005916del
NG_008466.1:g.8191_8198del
NG_050738.1:g.1659_1666del
NM_000535.7:c.139_146delMANE SELECT
NM_001322003.2:c.-267_-260del
NM_001322004.2:c.-242-1858_-242-1851del
NM_001322005.2:c.-267_-260del
NM_001322006.2:c.139_146del
NM_001322007.2:c.-77_-70del
NM_001322008.2:c.-52-1858_-52-1851del
NM_001322009.2:c.-267_-260del
NM_001322010.2:c.-242-1858_-242-1851del
NM_001322011.2:c.-746_-739del
NM_001322012.2:c.-746_-739del
NM_001322013.2:c.-267_-260del
NM_001322014.2:c.139_146del
NM_001322015.2:c.-346_-339del
NP_000526.2:p.Leu47fs
NP_001308935.1:p.Leu47fs
NP_001308943.1:p.Leu47fs
LRG_161t1:c.139_146del
LRG_161:g.8191_8198del
NC_000007.13:g.6045540_6045547del
NM_000535.5:c.139_146delCTGGATGC
NR_136154.1:n.226_233del

Protein change:

L47fs

Links:

dbSNP: rs886039615

NCBI 1000 Genomes Browser:

rs886039615

Molecular consequence:

NM_001322003.2:c.-267_-260del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-267_-260del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-77_-70del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-267_-260del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-746_-739del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-746_-739del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-267_-260del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-346_-339del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000535.7:c.139_146del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.139_146del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.139_146del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.-242-1858_-242-1851del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1858_-52-1851del - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1858_-242-1851del - intron variant - [Sequence Ontology: SO:0001627]
NR_136154.1:n.226_233del - 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

Clear Turn Off Turn On

Homo sapiens mRNA; cDNA DKFZp686E0469 (from clone DKFZp686E0469); complete cds
Homo sapiens mRNA; cDNA DKFZp686E0469 (from clone DKFZp686E0469); complete cds
gi|34364915|emb|BX640796.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000663554	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Feb 14, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000663554

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Feb 14, 2017)

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, SCV000663554.5

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

Description

The c.139_146delCTGGATGC pathogenic mutation, located in coding exon 2 of the PMS2 gene, results from a deletion of 8 nucleotides at nucleotide positions 139 to 146, causing a translational frameshift with a predicted alternate stop codon (p.L47Wfs*4). 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: May 1, 2024

ClinVar

Relating variation to medicine