NM_000535.7(PMS2):c.138T>G (p.Ser46Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 16, 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:: RCV002396661.2

Allele description [Variation Report for NM_000535.7(PMS2):c.138T>G (p.Ser46Arg)]

NM_000535.7(PMS2):c.138T>G (p.Ser46Arg)

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.138T>G (p.Ser46Arg)

HGVS:

NC_000007.14:g.6005917A>C
NG_008466.1:g.8190T>G
NG_050738.1:g.1667A>C
NM_000535.7:c.138T>GMANE SELECT
NM_001018040.1:c.-268T>G
NM_001322003.2:c.-268T>G
NM_001322004.2:c.-242-1859T>G
NM_001322005.2:c.-268T>G
NM_001322006.2:c.138T>G
NM_001322007.2:c.-78T>G
NM_001322008.2:c.-52-1859T>G
NM_001322009.2:c.-268T>G
NM_001322010.2:c.-242-1859T>G
NM_001322011.2:c.-747T>G
NM_001322012.2:c.-747T>G
NM_001322013.2:c.-268T>G
NM_001322014.2:c.138T>G
NM_001322015.2:c.-347T>G
NM_001406866.1:c.324T>G
NM_001406868.1:c.138T>G
NM_001406869.1:c.138T>G
NM_001406870.1:c.138T>G
NM_001406871.1:c.138T>G
NM_001406872.1:c.138T>G
NM_001406873.1:c.138T>G
NM_001406874.1:c.138T>G
NM_001406875.1:c.-347T>G
NM_001406876.1:c.-78T>G
NM_001406877.1:c.-347T>G
NM_001406878.1:c.-347T>G
NM_001406880.1:c.-294T>G
NM_001406882.1:c.-347T>G
NM_001406883.1:c.-78T>G
NM_001406884.1:c.138T>G
NM_001406885.1:c.138T>G
NM_001406886.1:c.138T>G
NM_001406887.1:c.-268T>G
NM_001406888.1:c.-215T>G
NM_001406889.1:c.-215T>G
NM_001406890.1:c.-258T>G
NM_001406891.1:c.-268T>G
NM_001406892.1:c.-215T>G
NM_001406893.1:c.-268T>G
NM_001406894.1:c.-215T>G
NM_001406896.1:c.-78T>G
NM_001406897.1:c.-268T>G
NM_001406898.1:c.-268T>G
NM_001406899.1:c.-215T>G
NM_001406900.1:c.-244T>G
NM_001406901.1:c.-78T>G
NM_001406902.1:c.-78T>G
NM_001406903.1:c.-78T>G
NM_001406904.1:c.-215T>G
NM_001406905.1:c.-268T>G
NM_001406906.1:c.-268T>G
NM_001406907.1:c.-215T>G
NM_001406908.1:c.-268T>G
NM_001406909.1:c.-215T>G
NM_001406910.1:c.-268T>G
NM_001406912.1:c.138T>G
NP_000526.1:p.Ser46Arg
NP_000526.2:p.Ser46Arg
NP_001308935.1:p.Ser46Arg
NP_001308943.1:p.Ser46Arg
NP_001393795.1:p.Ser108Arg
NP_001393797.1:p.Ser46Arg
NP_001393798.1:p.Ser46Arg
NP_001393799.1:p.Ser46Arg
NP_001393800.1:p.Ser46Arg
NP_001393801.1:p.Ser46Arg
NP_001393802.1:p.Ser46Arg
NP_001393803.1:p.Ser46Arg
NP_001393813.1:p.Ser46Arg
NP_001393814.1:p.Ser46Arg
NP_001393815.1:p.Ser46Arg
NP_001393841.1:p.Ser46Arg
LRG_161t1:c.138T>G
LRG_161:g.8190T>G
LRG_161p1:p.Ser46Arg
NC_000007.13:g.6045548A>C
NM_000535.5:c.138T>G
NR_003085.2:n.220T>G
NR_136154.1:n.225T>G

Protein change:

S108R

Molecular consequence:

NM_001322003.2:c.-268T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322005.2:c.-268T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322007.2:c.-78T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322009.2:c.-268T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322011.2:c.-747T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322012.2:c.-747T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322013.2:c.-268T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322015.2:c.-347T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322004.2:c.-242-1859T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322008.2:c.-52-1859T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001322010.2:c.-242-1859T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_000535.7:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406866.1:c.324T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406868.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406869.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406870.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406871.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406872.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406873.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406874.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406884.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406885.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406886.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001406912.1:c.138T>G - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.225T>G - 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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txid2927356[Organism:noexp] (1)
BioSample
UCE target enrichment of Aphidius sp.
UCE target enrichment of Aphidius sp.

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002700023	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jun 16, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002700023

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jun 16, 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, SCV002700023.2

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

Description

The p.S46R variant (also known as c.138T>G), located in coding exon 2 of the PMS2 gene, results from a T to G substitution at nucleotide position 138. The serine at codon 46 is replaced by arginine, an amino acid with dissimilar 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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