NM_000527.5(LDLR):c.168TGA[1] (p.Asp57del) AND Familial hypercholesterolemia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 3, 2018
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:: RCV002229685.6

Allele description [Variation Report for NM_000527.5(LDLR):c.168TGA[1] (p.Asp57del)]

NM_000527.5(LDLR):c.168TGA[1] (p.Asp57del)

Gene:

LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_000527.5(LDLR):c.168TGA[1] (p.Asp57del)

HGVS:

NC_000019.10:g.11100323TGA[1]
NC_000019.9:g.11210999_11211001del
NG_009060.1:g.15943TGA[1]
NM_000527.4:c.171_173del
NM_000527.5:c.168TGA[1]MANE SELECT
NM_001195798.2:c.168TGA[1]
NM_001195799.2:c.168TGA[1]
NM_001195800.2:c.168TGA[1]
NM_001195803.2:c.168TGA[1]
NP_000518.1:p.Asp57del
NP_001182727.1:p.Asp57del
NP_001182728.1:p.Asp57del
NP_001182729.1:p.Asp57del
NP_001182732.1:p.Asp57del
LRG_274t1:c.171_173del
LRG_274:g.15943TGA[1]
NC_000019.9:g.11210999TGA[1]
NC_000019.9:g.11210999_11211001del
NC_000019.9:g.11211002_11211004delTGA
NM_000527.4:c.171_173delTGA
NP_000518.1:p.D57del
c.171_173delTGA

Protein change:

D57del

Links:

LDLR-LOVD, British Heart Foundation: LDLR_000921; dbSNP: rs879254421

NCBI 1000 Genomes Browser:

rs879254421

Molecular consequence:

NM_000527.5:c.168TGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001195798.2:c.168TGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001195799.2:c.168TGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001195800.2:c.168TGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001195803.2:c.168TGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000826713	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 3, 2018)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11668627, 16389549, 21520333, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000826713

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 3, 2018)

germline

clinical testing

PubMed (4)
[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

Low density lipoprotein receptor (LDLR) gene mutations in Canadian subjects with familial hypercholesterolemia, but not of French descent.

Wang J, Huff E, Janecka L, Hegele RA.

Hum Mutat. 2001 Oct;18(4):359.

PubMed [citation]

PMID:: 11668627

Mutational analysis in UK patients with a clinical diagnosis of familial hypercholesterolaemia: relationship with plasma lipid traits, heart disease risk and utility in relative tracing.

Humphries SE, Cranston T, Allen M, Middleton-Price H, Fernandez MC, Senior V, Hawe E, Iversen A, Wray R, Crook MA, Wierzbicki AS.

J Mol Med (Berl). 2006 Mar;84(3):203-14. Epub 2005 Dec 31.

PubMed [citation]

PMID:: 16389549

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000826713.4

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

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. This variant, c.171_173delTGA, results in the deletion of 1 amino acid(s) of the LDLR protein (p.Asp57del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (ExAC no frequency). This variant has been reported in several individuals affected with familial hypercholesterolemia (PMID: 11668627, 16389549). This variant is also known as D36del in the literature. It has been reported in an individual in the Leiden Open-source Variation Database (PMID: 21520333). ClinVar contains an entry for this variant (Variation ID: 251041). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acid is currently unknown.

#	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 29, 2024

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