NC_000019.10:g.11089411del AND Familial hypercholesterolemia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 22, 2023
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:: RCV002512730.11

Allele description [Variation Report for NC_000019.10:g.11089411del]

NC_000019.10:g.11089411del

Genes:

LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
LDLR-AS1:LDLR antisense RNA 1 [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NC_000019.10:g.11089411del

Other names:

FH Pyrgos

HGVS:

NC_000019.10:g.11089411del
NG_009060.1:g.5031del
NM_001195798.1:c.-138delT
NM_001195799.1:c.-138delT
NM_001195800.1:c.-138delT
NM_001195803.1:c.-138delT
LRG_274t1:c.-138del
LRG_274:g.5031del
NC_000019.9:g.11200087del
NC_000019.9:g.11200087delT
NM_000527.4:c.-138del
NM_000527.4:c.-138delT
NR_163945.1:n.249del
c.-138delT

Nucleotide change:

-45T DEL

Links:

LDLR-LOVD, British Heart Foundation: LDLR_000959; OMIM: 606945.0064; dbSNP: rs387906307

NCBI 1000 Genomes Browser:

rs387906307

Molecular consequence:

NR_163945.1:n.249del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Familial hypercholesterolemia
Identifiers:: MONDO: MONDO:0005439; MedGen: C0020445; OMIM: PS143890

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003472875	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 22, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17625505, 14616764, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003472875

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 22, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

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

A functional mutation in the LDLR promoter (-139C>G) in a patient with familial hypercholesterolemia.

Smith AJ, Ahmed F, Nair D, Whittall R, Wang D, Taylor A, Norbury G, Humphries SE.

Eur J Hum Genet. 2007 Nov;15(11):1186-9. Epub 2007 Jul 11.

PubMed [citation]

PMID:: 17625505

FH-Pyrgos: a novel mutation in the promoter (-45delT) of the low-density lipoprotein receptor gene associated with familial hypercholesterolemia.

Dedoussis GV, Pitsavos C, Kelberman D, Skoumas J, Prassa ME, Choumerianou DM, Stefanadis C, Humphries SE, Toutouzas P.

Clin Genet. 2003 Nov;64(5):414-9.

PubMed [citation]

PMID:: 14616764

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003472875.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Studies have shown that this variant alters LDLR gene expression (PMID: 14616764, 17625505). ClinVar contains an entry for this variant (Variation ID: 3745). This variant is also known as c.-45del. This variant has been observed in individual(s) with familial hypercholesterolemia (PMID: 14616764). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This variant occurs in a non-coding region of the LDLR gene. It does not change the encoded amino acid sequence of the LDLR protein.

#	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: Apr 20, 2025

ClinVar

Relating variation to medicine