NM_000527.5(LDLR):c.1469G>A (p.Trp490Ter) AND Familial hypercholesterolemia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 30, 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:: RCV001389977.7

Allele description [Variation Report for NM_000527.5(LDLR):c.1469G>A (p.Trp490Ter)]

NM_000527.5(LDLR):c.1469G>A (p.Trp490Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_000527.5(LDLR):c.1469G>A (p.Trp490Ter)

HGVS:

NC_000019.10:g.11113645G>A
NG_009060.1:g.29265G>A
NM_000527.5:c.1469G>AMANE SELECT
NM_001195798.2:c.1469G>A
NM_001195799.2:c.1346G>A
NM_001195800.2:c.965G>A
NM_001195803.2:c.1088G>A
NP_000518.1:p.Trp490Ter
NP_000518.1:p.Trp490Ter
NP_001182727.1:p.Trp490Ter
NP_001182728.1:p.Trp449Ter
NP_001182729.1:p.Trp322Ter
NP_001182732.1:p.Trp363Ter
LRG_274t1:c.1469G>A
LRG_274:g.29265G>A
LRG_274p1:p.Trp490Ter
NC_000019.9:g.11224321G>A
NM_000527.4:c.1469G>A
c.1469G>A

Protein change:

W322*

Links:

LDLR-LOVD, British Heart Foundation: LDLR_000203; dbSNP: rs875989922

NCBI 1000 Genomes Browser:

rs875989922

Molecular consequence:

NM_000527.5:c.1469G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001195798.2:c.1469G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001195799.2:c.1346G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001195800.2:c.965G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001195803.2:c.1088G>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001591539	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 30, 2020)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 20809525, 28645073, 1301956, 31491741, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001591539

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 30, 2020)

germline

clinical testing

PubMed (5)
[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

Molecular spectrum of autosomal dominant hypercholesterolemia in France.

Marduel M, Carrié A, Sassolas A, Devillers M, Carreau V, Di Filippo M, Erlich D, Abifadel M, Marques-Pinheiro A, Munnich A, Junien C; French ADH Research Network., Boileau C, Varret M, Rabès JP.

Hum Mutat. 2010 Nov;31(11):E1811-24. doi: 10.1002/humu.21348.

PubMed [citation]

PMID:: 20809525
PMCID:: PMC3152176

Analysis of LDLR variants from homozygous FH patients carrying multiple mutations in the LDLR gene.

Jiang L, Benito-Vicente A, Tang L, Etxebarria A, Cui W, Uribe KB, Pan XD, Ostolaza H, Yang SW, Zhou YJ, Martin C, Wang LY.

Atherosclerosis. 2017 Aug;263:163-170. doi: 10.1016/j.atherosclerosis.2017.06.014. Epub 2017 Jun 8.

PubMed [citation]

PMID:: 28645073

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001591539.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in LDLR are known to be pathogenic (PMID: 20809525, 28645073). This variant has been observed in individual(s) with familial hypercholesterolemia (PMID: 1301956, 31491741). This variant is also described as W469X in the literature. ClinVar contains an entry for this variant (Variation ID: 226357). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Trp490*) in the LDLR gene. It is expected to result in an absent or disrupted protein product.

#	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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