NM_000535.7(PMS2):c.2569G>C (p.Gly857Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 29, 2024
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:: RCV000566001.4

Allele description [Variation Report for NM_000535.7(PMS2):c.2569G>C (p.Gly857Arg)]

NM_000535.7(PMS2):c.2569G>C (p.Gly857Arg)

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.2569G>C (p.Gly857Arg)

HGVS:

NC_000007.14:g.5973419C>G
NG_008466.1:g.40688G>C
NM_000535.7:c.2569G>CMANE SELECT
NM_001322003.2:c.2164G>C
NM_001322004.2:c.2164G>C
NM_001322005.2:c.2164G>C
NM_001322006.2:c.2413G>C
NM_001322007.2:c.2251G>C
NM_001322008.2:c.2251G>C
NM_001322009.2:c.2197G>C
NM_001322010.2:c.2008G>C
NM_001322011.2:c.1636G>C
NM_001322012.2:c.1636G>C
NM_001322013.2:c.1996G>C
NM_001322014.2:c.2602G>C
NM_001322015.2:c.2260G>C
NP_000526.2:p.Gly857Arg
NP_001308932.1:p.Gly722Arg
NP_001308933.1:p.Gly722Arg
NP_001308934.1:p.Gly722Arg
NP_001308935.1:p.Gly805Arg
NP_001308936.1:p.Gly751Arg
NP_001308937.1:p.Gly751Arg
NP_001308938.1:p.Gly733Arg
NP_001308939.1:p.Gly670Arg
NP_001308940.1:p.Gly546Arg
NP_001308941.1:p.Gly546Arg
NP_001308942.1:p.Gly666Arg
NP_001308943.1:p.Gly868Arg
NP_001308944.1:p.Gly754Arg
LRG_161t1:c.2569G>C
LRG_161:g.40688G>C
NC_000007.13:g.6013050C>G
NM_000535.5:c.2569G>C
NR_136154.1:n.2613G>C

Protein change:

G546R

Links:

dbSNP: rs750820328

NCBI 1000 Genomes Browser:

rs750820328

Molecular consequence:

NM_000535.7:c.2569G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322003.2:c.2164G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322004.2:c.2164G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322005.2:c.2164G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322006.2:c.2413G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322007.2:c.2251G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322008.2:c.2251G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322009.2:c.2197G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322010.2:c.2008G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322011.2:c.1636G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322012.2:c.1636G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322013.2:c.1996G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322014.2:c.2602G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001322015.2:c.2260G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_136154.1:n.2613G>C - 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
SCV000670866	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Feb 29, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000670866

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Feb 29, 2024)

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, SCV000670866.5

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

Description

The p.G857R variant (also known as c.2569G>C), located in coding exon 15 of the PMS2 gene, results from a G to C substitution at nucleotide position 2569. The glycine at codon 857 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, 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 7, 2024

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