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NM_000535.7(PMS2):c.1924G>A (p.Glu642Lys) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jul 1, 2022
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001013714.5

Allele description [Variation Report for NM_000535.7(PMS2):c.1924G>A (p.Glu642Lys)]

NM_000535.7(PMS2):c.1924G>A (p.Glu642Lys)

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.1924G>A (p.Glu642Lys)
HGVS:
  • NC_000007.14:g.5986841C>T
  • NG_008466.1:g.27266G>A
  • NM_000535.6:c.1924G>A
  • NM_000535.7:c.1924G>AMANE SELECT
  • NM_001322003.2:c.1519G>A
  • NM_001322004.2:c.1519G>A
  • NM_001322005.2:c.1519G>A
  • NM_001322006.2:c.1768G>A
  • NM_001322007.2:c.1606G>A
  • NM_001322008.2:c.1606G>A
  • NM_001322009.2:c.1519G>A
  • NM_001322010.2:c.1363G>A
  • NM_001322011.2:c.991G>A
  • NM_001322012.2:c.991G>A
  • NM_001322013.2:c.1351G>A
  • NM_001322014.2:c.1924G>A
  • NM_001322015.2:c.1615G>A
  • NP_000526.2:p.Glu642Lys
  • NP_001308932.1:p.Glu507Lys
  • NP_001308933.1:p.Glu507Lys
  • NP_001308934.1:p.Glu507Lys
  • NP_001308935.1:p.Glu590Lys
  • NP_001308936.1:p.Glu536Lys
  • NP_001308937.1:p.Glu536Lys
  • NP_001308938.1:p.Glu507Lys
  • NP_001308939.1:p.Glu455Lys
  • NP_001308940.1:p.Glu331Lys
  • NP_001308941.1:p.Glu331Lys
  • NP_001308942.1:p.Glu451Lys
  • NP_001308943.1:p.Glu642Lys
  • NP_001308944.1:p.Glu539Lys
  • LRG_161t1:c.1924G>A
  • LRG_161:g.27266G>A
  • NC_000007.13:g.6026472C>T
  • NM_000535.5:c.1924G>A
  • NR_136154.1:n.2011G>A
Protein change:
E331K
Links:
dbSNP: rs752772040
NCBI 1000 Genomes Browser:
rs752772040
Molecular consequence:
  • NM_000535.7:c.1924G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322003.2:c.1519G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322004.2:c.1519G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322005.2:c.1519G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.1768G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322007.2:c.1606G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322008.2:c.1606G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322009.2:c.1519G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322010.2:c.1363G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322011.2:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322012.2:c.991G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322013.2:c.1351G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.1924G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322015.2:c.1615G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.2011G>A - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001174335Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Jul 1, 2022) 		germlineclinical testing

Citation Link,

SCV002530241Sema4, Sema4
criteria provided, single submitter

(Sema4 Curation Guidelines)		Uncertain significance
(Feb 10, 2022) 		germlinecuration

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV001174335.4

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

Description

The p.E642K variant (also known as c.1924G>A), located in coding exon 11 of the PMS2 gene, results from a G to A substitution at nucleotide position 1924. The glutamic acid at codon 642 is replaced by lysine, an amino acid with similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

From Sema4, Sema4, SCV002530241.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024