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NM_000314.6(PTEN):c.-1243G>A AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 10, 2022
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:
RCV000115561.18

Allele description [Variation Report for NM_000314.6(PTEN):c.-1243G>A]

NM_000314.6(PTEN):c.-1243G>A

Genes:
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
KLLN:killin, p53 regulated DNA replication inhibitor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NM_000314.6(PTEN):c.-1243G>A
HGVS:
  • NC_000010.11:g.87863226G>A
  • NG_007466.2:g.4789G>A
  • NG_033079.1:g.5212C>T
  • NM_001126049.2:c.-739C>TMANE SELECT
  • LRG_1087t1:c.-739C>T
  • LRG_311t1:c.-1243G>A
  • LRG_1087:g.5212C>T
  • LRG_311:g.4789G>A
  • NC_000010.10:g.89622983G>A
  • NM_000314.4:c.-1243G>A
  • NM_000314.6:c.-1243G>A
  • NM_001126049.1:c.-739C>T
Links:
dbSNP: rs727502790
NCBI 1000 Genomes Browser:
rs727502790
Molecular consequence:
  • NM_001126049.2:c.-739C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

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
SCV000187616Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Jun 10, 2022) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

KLLN epigenotype-phenotype associations in Cowden syndrome.

Nizialek EA, Mester JL, Dhiman VK, Smiraglia DJ, Eng C.

Eur J Hum Genet. 2015 Nov;23(11):1538-43. doi: 10.1038/ejhg.2015.8. Epub 2015 Feb 11.

PubMed [citation]
PMID:
25669429
PMCID:
PMC4613489

Details of each submission

From Ambry Genetics, SCV000187616.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The c.-1243G>A variant is located in the 5' untranslated region (5'UTR) of the PTEN gene. This variant results from a G to A substitution 1243 nucleotides upstream from the first translated codon. This variant is located in the promoter region of the PTEN gene, but its potential impact on PTEN regulation has not yet been investigated (Zhou XP et al. Am. J. Hum. Genet. 2003 Aug;73:404-11). This variant, referred to as c.-1242G>A, has been detected in a cohort of patients who met clinical diagnostic criteria for Cowden syndrome (CS) or relaxed clinical diagnostic criteria for CS-like (Nizialek EA et al. Eur. J. Hum. Genet. 2015 Nov;23:1538-43). This nucleotide position is highly conserved on limited sequence alignment. 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: Nov 3, 2024