NM_000535.7(PMS2):c.1909C>T (p.Gln637Ter) AND Lynch syndrome

Clinical significance:Likely pathogenic (Last evaluated: Apr 13, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000590029.1

Allele description [Variation Report for NM_000535.7(PMS2):c.1909C>T (p.Gln637Ter)]

NM_000535.7(PMS2):c.1909C>T (p.Gln637Ter)

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.1909C>T (p.Gln637Ter)
HGVS:
  • NC_000007.14:g.5986856G>A
  • NG_008466.1:g.27251C>T
  • NM_000535.7:c.1909C>TMANE SELECT
  • NM_001322003.2:c.1504C>T
  • NM_001322004.2:c.1504C>T
  • NM_001322005.2:c.1504C>T
  • NM_001322006.2:c.1753C>T
  • NM_001322007.2:c.1591C>T
  • NM_001322008.2:c.1591C>T
  • NM_001322009.2:c.1504C>T
  • NM_001322010.2:c.1348C>T
  • NM_001322011.2:c.976C>T
  • NM_001322012.2:c.976C>T
  • NM_001322013.2:c.1336C>T
  • NM_001322014.2:c.1909C>T
  • NM_001322015.2:c.1600C>T
  • NP_000526.2:p.Gln637Ter
  • NP_001308932.1:p.Gln502Ter
  • NP_001308933.1:p.Gln502Ter
  • NP_001308934.1:p.Gln502Ter
  • NP_001308935.1:p.Gln585Ter
  • NP_001308936.1:p.Gln531Ter
  • NP_001308937.1:p.Gln531Ter
  • NP_001308938.1:p.Gln502Ter
  • NP_001308939.1:p.Gln450Ter
  • NP_001308940.1:p.Gln326Ter
  • NP_001308941.1:p.Gln326Ter
  • NP_001308942.1:p.Gln446Ter
  • NP_001308943.1:p.Gln637Ter
  • NP_001308944.1:p.Gln534Ter
  • LRG_161t1:c.1909C>T
  • LRG_161:g.27251C>T
  • NC_000007.13:g.6026487G>A
  • NM_000535.5:c.1909C>T
  • NM_000535.6:c.1909C>T
  • NR_136154.1:n.1996C>T
Protein change:
Q326*
Links:
dbSNP: rs1554297125
NCBI 1000 Genomes Browser:
rs1554297125
Molecular consequence:
  • NR_136154.1:n.1996C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000535.7:c.1909C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322003.2:c.1504C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322004.2:c.1504C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322005.2:c.1504C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322006.2:c.1753C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322007.2:c.1591C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322008.2:c.1591C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322009.2:c.1504C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322010.2:c.1348C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322011.2:c.976C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322012.2:c.976C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322013.2:c.1336C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322014.2:c.1909C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001322015.2:c.1600C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Lynch syndrome
Synonyms:
Familial nonpolyposis colon cancer
Identifiers:
MONDO: MONDO:0005835; MedGen: C4552100; OMIM: PS120435

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000697311Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Likely pathogenic
(Apr 13, 2016)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697311.1

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

Description

Variant summary: Variant affects a non-conserved nucleotide and results in a nonsense mutation predicted to cause a loss of normal protein function due to production of a truncated protein or by the absence of the protein product due to nonsense-mediated mRNA decay. It is absent from the large and broad cohorts of the ExAC project and to our knowledge, it was not reported in affected individuals either. Loss of function of PMS2 is a known mechanism of Lynch syndrome (GeneReviews), therefore, this nonsense variant was classified as Likely Pathogenic.

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

Last Updated: Oct 30, 2021

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