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NM_000535.7(PMS2):c.55G>T (p.Asp19Tyr) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 25, 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:
RCV002346284.2

Allele description [Variation Report for NM_000535.7(PMS2):c.55G>T (p.Asp19Tyr)]

NM_000535.7(PMS2):c.55G>T (p.Asp19Tyr)

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.55G>T (p.Asp19Tyr)
HGVS:
  • NC_000007.14:g.6006000C>A
  • NG_008466.1:g.8107G>T
  • NG_050738.1:g.1750C>A
  • NM_000535.7:c.55G>TMANE SELECT
  • NM_001322003.2:c.-351G>T
  • NM_001322004.2:c.-242-1942G>T
  • NM_001322005.2:c.-351G>T
  • NM_001322006.2:c.55G>T
  • NM_001322007.2:c.-161G>T
  • NM_001322008.2:c.-52-1942G>T
  • NM_001322009.2:c.-351G>T
  • NM_001322010.2:c.-242-1942G>T
  • NM_001322011.2:c.-830G>T
  • NM_001322012.2:c.-830G>T
  • NM_001322013.2:c.-351G>T
  • NM_001322014.2:c.55G>T
  • NM_001322015.2:c.-430G>T
  • NP_000526.2:p.Asp19Tyr
  • NP_001308935.1:p.Asp19Tyr
  • NP_001308943.1:p.Asp19Tyr
  • LRG_161t1:c.55G>T
  • LRG_161:g.8107G>T
  • NC_000007.13:g.6045631C>A
  • NM_000535.5:c.55G>T
  • NR_136154.1:n.142G>T
Protein change:
D19Y
Links:
dbSNP: rs1554306568
NCBI 1000 Genomes Browser:
rs1554306568
Molecular consequence:
  • NM_001322003.2:c.-351G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322005.2:c.-351G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322007.2:c.-161G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322009.2:c.-351G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322011.2:c.-830G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322012.2:c.-830G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322013.2:c.-351G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322015.2:c.-430G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322004.2:c.-242-1942G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322008.2:c.-52-1942G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322010.2:c.-242-1942G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000535.7:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322006.2:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322014.2:c.55G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136154.1:n.142G>T - 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
SCV002648276Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Oct 25, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV002648276.2

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

Description

The p.D19Y variant (also known as c.55G>T), located in coding exon 2 of the PMS2 gene, results from a G to T substitution at nucleotide position 55. The aspartic acid at codon 19 is replaced by tyrosine, an amino acid with highly dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious 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

Last Updated: Sep 29, 2024