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:: RCV000710301.12

Allele description [Variation Report for NM_001126049.2(KLLN):c.-956G>T]

NM_001126049.2(KLLN):c.-956G>T

Genes:

PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
LOC130004273:ATAC-STARR-seq lymphoblastoid silent region 2585 [Gene]
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
NG_183718.1:g.164C>A
NM_000314.4:c.-1026C>A
NM_000314.6:c.-1026C>A
NM_001126049.2:c.-956G>TMANE SELECT
NM_001304717.4:c.-507C>A
NM_001304718.1:c.-1731C>A
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_000314.5:c.-1026C>A
NM_001126049.1:c.-956G>T
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]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000840478	Clingen PTEN Variant Curation Expert Panel, Clingen	reviewed by expert panel (ClinGen PTEN ACMG Specifications v1)	Likely benign (Nov 9, 2016)	germline	curation	ClinGen_PTEN_ACMG_Specifications_v1.pdf, Citation Link,
SCV001138116	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Likely benign (May 28, 2019)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000840478

Clingen PTEN Variant Curation Expert Panel, Clingen

reviewed by expert panel

(ClinGen PTEN ACMG Specifications v1)

Likely benign
(Nov 9, 2016)

germline

curation

ClinGen_PTEN_ACMG_Specifications_v1.pdf,

Citation Link,

SCV001138116

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Likely benign
(May 28, 2019)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

Details of each submission

From Clingen PTEN Variant Curation Expert Panel, Clingen, SCV000840478.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not 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)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mendelics, SCV001138116.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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