NM_001126049.2(KLLN):c.-914_-889del AND Hereditary cancer-predisposing syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jun 9, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000169828.16

Allele description [Variation Report for NM_001126049.2(KLLN):c.-914_-889del]

NM_001126049.2(KLLN):c.-914_-889del

Genes:

LOC130004273:ATAC-STARR-seq lymphoblastoid silent region 2585 [Gene]
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.-914_-889del

HGVS:

NC_000010.11:g.87863382_87863407del
NG_007466.2:g.4945_4970del
NG_033079.1:g.5037_5062del
NG_183718.1:g.103_128del
NM_001126049.2:c.-914_-889delMANE SELECT
LRG_1087t1:c.-914_-889del
LRG_311t1:c.-1087_-1062del
LRG_1087:g.5037_5062del
LRG_311:g.4945_4970del
NC_000010.10:g.89623139_89623164del
NM_000314.4:c.-1087_-1062delGCTCGCACCCAGAGCTACCGCTCTGC
NM_000314.4:c.-1088_-1063del
NM_000314.6:c.-1088_-1063del26
c.-1088_-1063delGCTCGCACCCAGAGCTACCGCTCTGC[hg19]

Links:

dbSNP: rs786203072

NCBI 1000 Genomes Browser:

rs786203072

Molecular consequence:

NM_001126049.2:c.-914_-889del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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metallothionein-1 [Mus musculus]
metallothionein-1 [Mus musculus]
gi|7305285|ref|NP_038630.1|

Protein
MAG TPA: 50S ribosomal protein L28 [Candidatus Limivicinus faecipullorum]
MAG TPA: 50S ribosomal protein L28 [Candidatus Limivicinus faecipullorum]
tpg|HIR86915.1||gnl|WGS:DVHY|IAC00_

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000216993	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Jun 9, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000216993

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Jun 9, 2020)

germline

clinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

Germline PTEN promoter mutations and deletions in Cowden/Bannayan-Riley-Ruvalcaba syndrome result in aberrant PTEN protein and dysregulation of the phosphoinositol-3-kinase/Akt pathway.

Zhou XP, Waite KA, Pilarski R, Hampel H, Fernandez MJ, Bos C, Dasouki M, Feldman GL, Greenberg LA, Ivanovich J, Matloff E, Patterson A, Pierpont ME, Russo D, Nassif NT, Eng C.

Am J Hum Genet. 2003 Aug;73(2):404-11. Epub 2003 Jul 3.

PubMed [citation]

PMID:: 12844284
PMCID:: PMC1180378

Details of each submission

From Ambry Genetics, SCV000216993.7

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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

Last Updated: Sep 16, 2024

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