NM_000535.7(PMS2):c.1420G>T (p.Ala474Ser) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Jul 12, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000479914.2

Allele description [Variation Report for NM_000535.7(PMS2):c.1420G>T (p.Ala474Ser)]

NM_000535.7(PMS2):c.1420G>T (p.Ala474Ser)

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.1420G>T (p.Ala474Ser)
HGVS:
  • NC_000007.14:g.5987345C>A
  • NG_008466.1:g.26762G>T
  • NM_000535.7:c.1420G>TMANE SELECT
  • NM_001322003.2:c.1015G>T
  • NM_001322004.2:c.1015G>T
  • NM_001322005.2:c.1015G>T
  • NM_001322006.2:c.1264G>T
  • NM_001322007.2:c.1102G>T
  • NM_001322008.2:c.1102G>T
  • NM_001322009.2:c.1015G>T
  • NM_001322010.2:c.859G>T
  • NM_001322011.2:c.487G>T
  • NM_001322012.2:c.487G>T
  • NM_001322013.2:c.847G>T
  • NM_001322014.2:c.1420G>T
  • NM_001322015.2:c.1111G>T
  • NP_000526.2:p.Ala474Ser
  • NP_001308932.1:p.Ala339Ser
  • NP_001308933.1:p.Ala339Ser
  • NP_001308934.1:p.Ala339Ser
  • NP_001308935.1:p.Ala422Ser
  • NP_001308936.1:p.Ala368Ser
  • NP_001308937.1:p.Ala368Ser
  • NP_001308938.1:p.Ala339Ser
  • NP_001308939.1:p.Ala287Ser
  • NP_001308940.1:p.Ala163Ser
  • NP_001308941.1:p.Ala163Ser
  • NP_001308942.1:p.Ala283Ser
  • NP_001308943.1:p.Ala474Ser
  • NP_001308944.1:p.Ala371Ser
  • LRG_161t1:c.1420G>T
  • LRG_161:g.26762G>T
  • NC_000007.13:g.6026976C>A
  • NM_000535.5:c.1420G>T
  • NM_000535.6:c.1420G>T
  • NR_136154.1:n.1507G>T
  • p.A474S
Protein change:
A163S
Links:
dbSNP: rs373114291
NCBI 1000 Genomes Browser:
rs373114291
Molecular consequence:
  • NM_000535.7:c.1420G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.1015G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.1015G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.1015G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.1264G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.1102G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.1102G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.1015G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.859G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322011.2:c.487G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322012.2:c.487G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322013.2:c.847G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.1420G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.1111G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.1507G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000565404GeneDxcriteria provided, single submitter
Uncertain significance
(Jul 12, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000565404.4

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

Description

In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Observed in individuals with a history of a Lynch syndrome-associated tumor and/or polyps and other cancers (Yurgelun 2015, Zhang 2015, Blount 2018); This variant is associated with the following publications: (PMID: 29286535, 25980754, 26580448)

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

Last Updated: Nov 10, 2021

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