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NM_001126049.2(KLLN):c.-956G>T AND PTEN hamartoma tumor syndrome

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Nov 9, 2016
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:
RCV000710301.2

Allele description

NM_001126049.2(KLLN):c.-956G>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.-956G>T
HGVS:
  • NC_000010.11:g.87863443C>A
  • NG_007466.2:g.5006C>A
  • NG_033079.1:g.4995G>T
  • NM_001126049.1:c.-956G>T
  • NM_001126049.2:c.-956G>TMANE SELECT
  • LRG_1087t1:c.-956G>T
  • LRG_311t1:c.-1026C>A
  • LRG_1087:g.4995G>T
  • LRG_311:g.5006C>A
  • NC_000010.10:g.89623200C>A
  • NM_000314.4:c.-1026C>A
  • NM_000314.5:c.-1026C>A
  • c.-1027C>A[hg19]
Links:
dbSNP: rs34149102
NCBI 1000 Genomes Browser:
rs34149102
Molecular consequence:
  • NM_001126049.2:c.-956G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001126049.1:c.-956G>T - upstream transcript variant - [Sequence Ontology: SO:0001986]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000840478ClinGen PTEN Variant Curation Expert Panel
reviewed by expert panel

(ClinGen PTEN ACMG Specifications v1)		Likely benign
(Nov 9, 2016) 		germlinecuration

ClinGen_PTEN_ACMG_Specifications_v1.pdf,

Citation Link,

SCV001138116Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)		Likely benign
(May 28, 2019) 		unknownclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From ClinGen PTEN Variant Curation Expert Panel, SCV000840478.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

PTEN c.-1026C>A (NC_000010.10:g.89623200C>A) meets criteria to be classified as likely benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). Please see a summary of the rules and criteria codes in the 'PTEN ACMG Specifications Summary' document (assertion method column). BS1: Allele frequency of 0.0056 (0.56%, 173/30,898 alleles) in the gnomAD cohort. (PMID 27535533) BS2_P: Meets criteria for BS2 (observed in the homozygous state in at least one healthy or PHTS-unaffected individual) but BS1 is also applied. (Internal laboratory contributor(s) SCV000171228.5) BP5: Variant found in multiple cases with alternate molecular basis for disease. (Internal laboratory contributor(s) SCV000171228.5)

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

From Mendelics, SCV001138116.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 24, 2021