NM_001126049.2(KLLN):c.-898G>A AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Aug 1, 2024
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:: RCV000586614.27

Allele description [Variation Report for NM_001126049.2(KLLN):c.-898G>A]

NM_001126049.2(KLLN):c.-898G>A

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.-898G>A

Other names:

NM_000314.6(PTEN):c.-1084C>T

HGVS:

NC_000010.11:g.87863385C>T
NG_007466.2:g.4948C>T
NG_033079.1:g.5053G>A
NG_183718.1:g.106C>T
NM_000314.8:c.-1085C>TMANE SELECT
NM_001126049.2:c.-898G>AMANE SELECT
LRG_1087t1:c.-898G>A
LRG_311t1:c.-1084C>T
LRG_1087:g.5053G>A
LRG_311:g.4948C>T
NC_000010.10:g.89623142C>T
NM_000314.4:c.-1084C>T
c.-1085C>T[hg19]

Links:

dbSNP: rs538728843

NCBI 1000 Genomes Browser:

rs538728843

Molecular consequence:

NM_001126049.2:c.-898G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000314.8:c.-1085C>T - upstream transcript variant - [Sequence Ontology: SO:0001986]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens forkhead box Q1 (FOXQ1), mRNA
Homo sapiens forkhead box Q1 (FOXQ1), mRNA
gi|1519312975|ref|NM_033260.4|

Nucleotide
forkhead box protein Q1 [Homo sapiens]
forkhead box protein Q1 [Homo sapiens]
gi|145309320|ref|NP_150285.3|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000149464	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Jan 4, 2017)	germline	clinical testing	Citation Link,
SCV000696525	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Feb 9, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV000780347	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Aug 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000149464

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Jan 4, 2017)

germline

clinical testing

Citation Link,

SCV000696525

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Feb 9, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV000780347

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Benign
(Aug 1, 2024)

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	80	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Outcomes of retesting BRCA negative patients using multigene panels.

Yadav S, Reeves A, Campian S, Paine A, Zakalik D.

Fam Cancer. 2017 Jul;16(3):319-328. doi: 10.1007/s10689-016-9956-7.

PubMed [citation]

PMID:: 27878467

Details of each submission

From GeneDx, SCV000149464.6

#	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: 25669429, 21417916, 17427195, 16773562, 12844284, 27884173, 27271787, 30528446, 33509259)

#	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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696525.1

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

Description

Variant summary: The PTEN variant c.-1084C>T (also known as c.-1085C>T) involves the alteration of a non-conserved nucleotide in the 5'UTR region. One in silico tool predicts a benign outcome for this variant. This variant was found in 28/5008 control chromosomes, predominantly observed in South Asians at a frequency of 0.0163599 (16/978). This frequency greatly exceeds the estimated maximal expected allele frequency of a pathogenic PTEN variant (0.0000063), suggesting this is likely a benign polymorphism found primarily in the populations of origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign/benign. Taken together, this variant is classified as benign.

#	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 CeGaT Center for Human Genetics Tuebingen, SCV000780347.29

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	80	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		80	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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