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NM_000314.4(PTEN):c.-1290C>T AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 13, 2016
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:
RCV000215358.11

Allele description [Variation Report for NM_000314.4(PTEN):c.-1290C>T]

NM_000314.4(PTEN):c.-1290C>T

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_000314.4(PTEN):c.-1290C>T
HGVS:
  • NC_000010.11:g.87863179C>T
  • NG_007466.2:g.4742C>T
  • NG_033079.1:g.5259G>A
  • NM_001126049.2:c.-692G>AMANE SELECT
  • LRG_1087t1:c.-692G>A
  • LRG_311t1:c.-1290C>T
  • LRG_1087:g.5259G>A
  • LRG_311:g.4742C>T
  • NC_000010.10:g.89622936C>T
  • NM_000314.4:c.-1290C>T
Links:
dbSNP: rs542360599
NCBI 1000 Genomes Browser:
rs542360599
Molecular consequence:
  • NM_001126049.2:c.-692G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000279638GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Oct 13, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000279638.4

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

Description

This variant is denoted PTEN c.-1291C>T, and describes a nucleotide substitution 1291 base pairs upstream of the ATG translational start site in the PTEN promoter region. The surrounding sequence, with the base that is substituted in braces, is TCCT{C/T}CACC. This variant, also called c.-1290C>T using alternate numbering, has not been published in the literature to our knowledge. Variants within the PTEN core promoter region (c.-798 to c.-1238) have been observed in individuals with features of Cowden syndrome (Zhou 2003). While the c.-1291C>T variant is outside of this core promoter region, it could still have an effect on transcription and, possibly, PTEN protein levels. Based on currently available information, it is unclear whether PTEN c.-1291C>T is pathogenic or benign. We consider it to be a variant of uncertain significance.

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

Last Updated: Nov 3, 2024