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NM_001126049.2(KLLN):c.-792C>T AND PTEN hamartoma tumor syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 23, 2020
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV001172263.10

Allele description [Variation Report for NM_001126049.2(KLLN):c.-792C>T]

NM_001126049.2(KLLN):c.-792C>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_001126049.2(KLLN):c.-792C>T
Other names:
NM_001126049.1(KLLN):c.-792C>T; NM_000314.6(PTEN):c.-1190G>A
HGVS:
  • NC_000010.11:g.87863279G>A
  • NG_007466.2:g.4842G>A
  • NG_033079.1:g.5159C>T
  • NM_001126049.2:c.-792C>TMANE SELECT
  • LRG_1087t1:c.-792C>T
  • LRG_311t1:c.-1190G>A
  • LRG_1087:g.5159C>T
  • LRG_311:g.4842G>A
  • NC_000010.10:g.89623036G>A
  • NC_000010.10:g.89623036G>A
  • NM_000314.4:c.-1190G>A
  • NM_000314.8:c.-1191G>AMANE SELECT
  • c.-1191G>A[hg19]
Links:
dbSNP: rs587779982
NCBI 1000 Genomes Browser:
rs587779982
Molecular consequence:
  • NM_001126049.2:c.-792C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Name:
PTEN hamartoma tumor syndrome (PHTS)
Synonyms:
PTEN Hamartomatous Tumour Syndrome
Identifiers:
MONDO: MONDO:0017623; MeSH: D006223; MedGen: C1959582

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001335278Clingen PTEN Variant Curation Expert Panel, Clingen
reviewed by expert panel

(ClinGen PTEN ACMG Specifications v2)		Uncertain significance
(Mar 23, 2020) 		germlinecuration

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 providedcuration

Citations

PubMed

Analysis of protein-coding genetic variation in 60,706 humans.

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, et al.

Nature. 2016 Aug 18;536(7616):285-91. doi: 10.1038/nature19057.

PubMed [citation]
PMID:
27535533
PMCID:
PMC5018207

Details of each submission

From Clingen PTEN Variant Curation Expert Panel, Clingen, SCV001335278.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

PTEN c.-1190G>A (NC_000010.10:g.89623036) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the "PTEN ACMG Specifications Summary" document (assertion method column). BS1_P: Allele frequency of 0.0009189 (0.09189%, 8/8706 alleles) in the African subpopulation of the gnomAD cohort. (PMID 27535533)

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

Last Updated: Nov 3, 2024