NM_000535.7(PMS2):c.2123del (p.Asn708fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 10, 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:: RCV002422488.2

Allele description [Variation Report for NM_000535.7(PMS2):c.2123del (p.Asn708fs)]

NM_000535.7(PMS2):c.2123del (p.Asn708fs)

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.2123del (p.Asn708fs)

HGVS:

NC_000007.14:g.5982876del
NG_008466.1:g.31232del
NM_000535.7:c.2123delMANE SELECT
NM_001322003.2:c.1718del
NM_001322004.2:c.1718del
NM_001322005.2:c.1718del
NM_001322006.2:c.1967del
NM_001322007.2:c.1805del
NM_001322008.2:c.1805del
NM_001322009.2:c.1718del
NM_001322010.2:c.1562del
NM_001322011.2:c.1190del
NM_001322012.2:c.1190del
NM_001322013.2:c.1550del
NM_001322014.2:c.2123del
NM_001322015.2:c.1814del
NP_000526.2:p.Asn708fs
NP_001308932.1:p.Asn573fs
NP_001308933.1:p.Asn573fs
NP_001308934.1:p.Asn573fs
NP_001308935.1:p.Asn656fs
NP_001308936.1:p.Asn602fs
NP_001308937.1:p.Asn602fs
NP_001308938.1:p.Asn573fs
NP_001308939.1:p.Asn521fs
NP_001308940.1:p.Asn397fs
NP_001308941.1:p.Asn397fs
NP_001308942.1:p.Asn517fs
NP_001308943.1:p.Asn708fs
NP_001308944.1:p.Asn605fs
LRG_161t1:c.2123del
LRG_161:g.31232del
NC_000007.13:g.6022506del
NC_000007.13:g.6022507del
NM_000535.5:c.2123delA
NR_136154.1:n.2210del

Protein change:

N397fs

Links:

dbSNP: rs781078805

NCBI 1000 Genomes Browser:

rs781078805

Molecular consequence:

NM_000535.7:c.2123del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322003.2:c.1718del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322004.2:c.1718del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322005.2:c.1718del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322006.2:c.1967del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322007.2:c.1805del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322008.2:c.1805del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322009.2:c.1718del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322010.2:c.1562del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322011.2:c.1190del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322012.2:c.1190del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322013.2:c.1550del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322014.2:c.2123del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001322015.2:c.1814del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_136154.1:n.2210del - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002729933	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Jan 10, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002729933

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Jan 10, 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, SCV002729933.2

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

Description

The c.2123delA pathogenic mutation, located in coding exon 12 of the PMS2 gene, results from a deletion of one nucleotide at nucleotide position 2123, causing a translational frameshift with a predicted alternate stop codon (p.N708Tfs*17). 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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