NM_000535.7(PMS2):c.2127C>T (p.Phe709=) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Likely benign(2);Uncertain significance(1) (Last evaluated: Mar 1, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000588071.8

Allele description [Variation Report for NM_000535.7(PMS2):c.2127C>T (p.Phe709=)]

NM_000535.7(PMS2):c.2127C>T (p.Phe709=)

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.2127C>T (p.Phe709=)
HGVS:
  • NC_000007.14:g.5982871G>A
  • NG_008466.1:g.31236C>T
  • NM_000535.7:c.2127C>TMANE SELECT
  • NM_001322003.2:c.1722C>T
  • NM_001322004.2:c.1722C>T
  • NM_001322005.2:c.1722C>T
  • NM_001322006.2:c.1971C>T
  • NM_001322007.2:c.1809C>T
  • NM_001322008.2:c.1809C>T
  • NM_001322009.2:c.1722C>T
  • NM_001322010.2:c.1566C>T
  • NM_001322011.2:c.1194C>T
  • NM_001322012.2:c.1194C>T
  • NM_001322013.2:c.1554C>T
  • NM_001322014.2:c.2127C>T
  • NM_001322015.2:c.1818C>T
  • NP_000526.2:p.Phe709=
  • NP_001308932.1:p.Phe574=
  • NP_001308933.1:p.Phe574=
  • NP_001308934.1:p.Phe574=
  • NP_001308935.1:p.Phe657=
  • NP_001308936.1:p.Phe603=
  • NP_001308937.1:p.Phe603=
  • NP_001308938.1:p.Phe574=
  • NP_001308939.1:p.Phe522=
  • NP_001308940.1:p.Phe398=
  • NP_001308941.1:p.Phe398=
  • NP_001308942.1:p.Phe518=
  • NP_001308943.1:p.Phe709=
  • NP_001308944.1:p.Phe606=
  • LRG_161t1:c.2127C>T
  • LRG_161:g.31236C>T
  • NC_000007.13:g.6022502G>A
  • NM_000535.5:c.2127C>T
  • NM_000535.6:c.2127C>T
  • NR_136154.1:n.2214C>T
Links:
dbSNP: rs199943748
NCBI 1000 Genomes Browser:
rs199943748
Molecular consequence:
  • NR_136154.1:n.2214C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000535.7:c.2127C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322003.2:c.1722C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322004.2:c.1722C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322005.2:c.1722C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322006.2:c.1971C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322007.2:c.1809C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322008.2:c.1809C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322009.2:c.1722C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322010.2:c.1566C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322011.2:c.1194C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322012.2:c.1194C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322013.2:c.1554C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322014.2:c.2127C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001322015.2:c.1818C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
2

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000225529EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Feb 18, 2015)
germlineclinical testing

Citation Link,

SCV000806198PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Likely benign
(Sep 25, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001747498CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Likely benign
(Mar 1, 2021)
germlineclinical testing

Citation Link,

SCV001870716GeneDxcriteria provided, single submitter
Benign
(Mar 3, 2015)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000225529.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From PreventionGenetics,PreventionGenetics, SCV000806198.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001747498.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV001870716.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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