NM_000535.7(PMS2):c.2070A>T (p.Lys690Asn) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 27, 2014
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:: RCV000164198.1

Allele description [Variation Report for NM_000535.7(PMS2):c.2070A>T (p.Lys690Asn)]

NM_000535.7(PMS2):c.2070A>T (p.Lys690Asn)

Gene:

PMS2:PMS1 homolog 2, mismatch repair system component [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7p22.1

Genomic location:

Preferred name:

NM_000535.7(PMS2):c.2070A>T (p.Lys690Asn)

HGVS:

NC_000007.14:g.5982928T>A
NG_008466.1:g.31179A>T
NM_000535.7:c.2070A>TMANE SELECT
NM_001322003.2:c.1665A>T
NM_001322004.2:c.1665A>T
NM_001322005.2:c.1665A>T
NM_001322006.2:c.1914A>T
NM_001322007.2:c.1752A>T
NM_001322008.2:c.1752A>T
NM_001322009.2:c.1665A>T
NM_001322010.2:c.1509A>T
NM_001322011.2:c.1137A>T
NM_001322012.2:c.1137A>T
NM_001322013.2:c.1497A>T
NM_001322014.2:c.2070A>T
NM_001322015.2:c.1761A>T
NP_000526.2:p.Lys690Asn
NP_001308932.1:p.Lys555Asn
NP_001308933.1:p.Lys555Asn
NP_001308934.1:p.Lys555Asn
NP_001308935.1:p.Lys638Asn
NP_001308936.1:p.Lys584Asn
NP_001308937.1:p.Lys584Asn
NP_001308938.1:p.Lys555Asn
NP_001308939.1:p.Lys503Asn
NP_001308940.1:p.Lys379Asn
NP_001308941.1:p.Lys379Asn
NP_001308942.1:p.Lys499Asn
NP_001308943.1:p.Lys690Asn
NP_001308944.1:p.Lys587Asn
LRG_161t1:c.2070A>T
LRG_161:g.31179A>T
NC_000007.13:g.6022559T>A
NM_000535.5:c.2070A>T
NR_136154.1:n.2157A>T
p.K690N

Protein change:

K379N

Links:

dbSNP: rs786201749

NCBI 1000 Genomes Browser:

rs786201749

Molecular consequence:

NM_000535.7:c.2070A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.1665A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.1665A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.1665A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.1914A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.1752A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.1752A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.1665A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.1509A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.1137A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.1137A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.1497A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.2070A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.1761A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.2157A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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
SCV000214819	Ambry Genetics	criteria provided, single submitter (Ambry Autosomal Dominant and X-Linked criteria (10/2015))	Uncertain significance (Mar 27, 2014)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000214819

Ambry Genetics

criteria provided, single submitter

(Ambry Autosomal Dominant and X-Linked criteria (10/2015))

Uncertain significance
(Mar 27, 2014)

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	1	not provided	not provided	1	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV000214819.5

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

Description

The p.K690N variant (also known as c.2070A>T), located in coding exon 12 of the PMS2 gene, results from an A to T substitution at nucleotide position 2070. The lysine at codon 690 is replaced by asparagine, an amino acid with some similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. To date, this alteration has been detected with an allele frequency of approximately 0.006% (greater than 15000 alleles tested) in our clinical cohort (includes this individual). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be possibly damaging and deleterious by PolyPhen and SIFT in silico analyses, respectively. Since supporting evidence is limited at this time, the clinical significance of p.K690N remains unclear.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	1	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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