NM_001126049.2(KLLN):c.-794_-783del AND not provided

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Jan 1, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000506666.28

Allele description [Variation Report for NM_001126049.2(KLLN):c.-794_-783del]

NM_001126049.2(KLLN):c.-794_-783del

Genes:

PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
KLLN:killin, p53 regulated DNA replication inhibitor [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_001126049.2(KLLN):c.-794_-783del

Other names:

NM_000314.6(PTEN):c.-1195_-1184delAAGCCGCAGCAA

HGVS:

NC_000010.11:g.87863274_87863285del
NG_007466.2:g.4837_4848del
NG_033079.1:g.5157_5168del
NM_000314.4:c.-1196_-1185del
NM_001126049.2:c.-794_-783delMANE SELECT
LRG_1087t1:c.-794_-783del
LRG_311t1:c.-1196_-1185del
LRG_1087:g.5157_5168del
LRG_311:g.4837_4848del
NC_000010.10:g.89623027_89623038del
NC_000010.10:g.89623031_89623042del
NM_000314.4:c.-1195_-1184delAAGCCGCAGCAA
NM_000314.4:c.-1196_-1185del
NM_000314.4:c.-1196_-1185del12
NM_000314.4:c.-1196_-1185del12
NM_001126049.2:c.-794_-783delTGCGGCTTTTGCMANE SELECT
c.-1196_-1185delAAGCCGCAGCAA[hg19]

Links:

dbSNP: rs587781340

NCBI 1000 Genomes Browser:

rs587781340

Molecular consequence:

NM_001126049.2:c.-794_-783del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000222146	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Mar 26, 2019)	germline	clinical testing	Citation Link,
SCV000602111	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely benign (May 16, 2022)	unknown	clinical testing	PubMed (4) [See all records that cite these PMIDs] 21532617, 21194675, 25669429, 26467025
SCV001148032	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Jan 1, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000222146

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Mar 26, 2019)

germline

clinical testing

Citation Link,

SCV000602111

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely benign
(May 16, 2022)

unknown

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV001148032

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Benign
(Jan 1, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	6	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Differential regulation of PTEN expression by androgen receptor in prostate and breast cancers.

Wang Y, Romigh T, He X, Tan MH, Orloff MS, Silverman RH, Heston WD, Eng C.

Oncogene. 2011 Oct 20;30(42):4327-38. doi: 10.1038/onc.2011.144. Epub 2011 May 2.

PubMed [citation]

PMID:: 21532617

A clinical scoring system for selection of patients for PTEN mutation testing is proposed on the basis of a prospective study of 3042 probands.

Tan MH, Mester J, Peterson C, Yang Y, Chen JL, Rybicki LA, Milas K, Pederson H, Remzi B, Orloff MS, Eng C.

Am J Hum Genet. 2011 Jan 7;88(1):42-56. doi: 10.1016/j.ajhg.2010.11.013. Epub 2010 Dec 30.

PubMed [citation]

PMID:: 21194675
PMCID:: PMC3014373

See all PubMed Citations (4)

Details of each submission

From GeneDx, SCV000222146.10

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

Description

This variant is associated with the following publications: (PMID: 21194675, 21956414, 25669429, 28821472, 28157521, 21532617)

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000602111.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV001148032.25

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	6	not provided	not provided	clinical testing	not provided

Description

KLLN: BS1, BS2; PTEN: BS1, BS2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		6	not provided	not provided	not provided

Last Updated: Aug 4, 2024

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