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NM_000535.7(PMS2):c.58C>T (p.Arg20Trp) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 5, 2023
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:
RCV001562874.6

Allele description [Variation Report for NM_000535.7(PMS2):c.58C>T (p.Arg20Trp)]

NM_000535.7(PMS2):c.58C>T (p.Arg20Trp)

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.58C>T (p.Arg20Trp)
HGVS:
  • NC_000007.14:g.6005997G>A
  • NG_008466.1:g.8110C>T
  • NG_050738.1:g.1747G>A
  • NM_000535.7:c.58C>TMANE SELECT
  • NM_001322003.2:c.-348C>T
  • NM_001322004.2:c.-242-1939C>T
  • NM_001322005.2:c.-348C>T
  • NM_001322006.2:c.58C>T
  • NM_001322007.2:c.-158C>T
  • NM_001322008.2:c.-52-1939C>T
  • NM_001322009.2:c.-348C>T
  • NM_001322010.2:c.-242-1939C>T
  • NM_001322011.2:c.-827C>T
  • NM_001322012.2:c.-827C>T
  • NM_001322013.2:c.-348C>T
  • NM_001322014.2:c.58C>T
  • NM_001322015.2:c.-427C>T
  • NP_000526.2:p.Arg20Trp
  • NP_001308935.1:p.Arg20Trp
  • NP_001308943.1:p.Arg20Trp
  • LRG_161t1:c.58C>T
  • LRG_161:g.8110C>T
  • NC_000007.13:g.6045628G>A
  • NM_000535.5:c.58C>T
  • NM_000535.6:c.58C>T
  • NR_136154.1:n.145C>T
Protein change:
R20W
Links:
dbSNP: rs573374779
NCBI 1000 Genomes Browser:
rs573374779
Molecular consequence:
  • NM_001322003.2:c.-348C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322005.2:c.-348C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322007.2:c.-158C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322009.2:c.-348C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322011.2:c.-827C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-827C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322013.2:c.-348C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322015.2:c.-427C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322004.2:c.-242-1939C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322008.2:c.-52-1939C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322010.2:c.-242-1939C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.58C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.58C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.58C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.145C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001785711GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Uncertain significance
(Sep 5, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV001785711.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Identified in patients with Lynch syndrome-associated cancers/polyps or breast cancer (Yurgelun et al., 2015; Chan et al., 2018; Zhang et al., 2023); This variant is associated with the following publications: (PMID: 25980754, 30093976, 11574484, 18768816, 36627197, 21239990)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024