NM_000535.7(PMS2):c.514G>A (p.Glu172Lys) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 26, 2020
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:: RCV000217866.4

Allele description [Variation Report for NM_000535.7(PMS2):c.514G>A (p.Glu172Lys)]

NM_000535.7(PMS2):c.514G>A (p.Glu172Lys)

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.514G>A (p.Glu172Lys)

HGVS:

NC_000007.14:g.6002476C>T
NG_008466.1:g.11631G>A
NM_000535.7:c.514G>AMANE SELECT
NM_001322003.2:c.109G>A
NM_001322004.2:c.109G>A
NM_001322005.2:c.109G>A
NM_001322006.2:c.514G>A
NM_001322007.2:c.196G>A
NM_001322008.2:c.196G>A
NM_001322009.2:c.109G>A
NM_001322010.2:c.109G>A
NM_001322011.2:c.-371G>A
NM_001322012.2:c.-371G>A
NM_001322013.2:c.109G>A
NM_001322014.2:c.514G>A
NM_001322015.2:c.205G>A
NP_000526.2:p.Glu172Lys
NP_001308932.1:p.Glu37Lys
NP_001308933.1:p.Glu37Lys
NP_001308934.1:p.Glu37Lys
NP_001308935.1:p.Glu172Lys
NP_001308936.1:p.Glu66Lys
NP_001308937.1:p.Glu66Lys
NP_001308938.1:p.Glu37Lys
NP_001308939.1:p.Glu37Lys
NP_001308942.1:p.Glu37Lys
NP_001308943.1:p.Glu172Lys
NP_001308944.1:p.Glu69Lys
LRG_161t1:c.514G>A
LRG_161:g.11631G>A
NC_000007.13:g.6042107C>T
NM_000535.5:c.514G>A
NR_136154.1:n.601G>A

Protein change:

E172K

Links:

dbSNP: rs876660196

NCBI 1000 Genomes Browser:

rs876660196

Molecular consequence:

NM_001322011.2:c.-371G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-371G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000535.7:c.514G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.109G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.109G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.109G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.514G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.196G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.196G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.109G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.109G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.109G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.514G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.205G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.601G>A - 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
SCV000277409	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Feb 26, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000277409

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Feb 26, 2020)

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, SCV000277409.7

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

Description

The p.E172K variant (also known as c.514G>A), located in coding exon 5 of the PMS2 gene, results from a G to A substitution at nucleotide position 514. The glutamic acid at codon 172 is replaced by lysine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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

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