NM_000527.5(LDLR):c.557del (p.Gly186fs) AND Familial hypercholesterolemia

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 28, 2024
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:: RCV002518479.3

Allele description [Variation Report for NM_000527.5(LDLR):c.557del (p.Gly186fs)]

NM_000527.5(LDLR):c.557del (p.Gly186fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

19p13.2

Genomic location:

Preferred name:

NM_000527.5(LDLR):c.557del (p.Gly186fs)

HGVS:

NC_000019.10:g.11105463del
NC_000019.9:g.11216136del
NG_009060.1:g.21083del
NM_000527.5:c.557delMANE SELECT
NM_001195798.2:c.557del
NM_001195799.2:c.434del
NM_001195800.2:c.314-1929del
NM_001195803.2:c.314-1102del
NP_000518.1:p.Gly186fs
NP_001182727.1:p.Gly186fs
NP_001182728.1:p.Gly145fs
LRG_274t1:c.557del
LRG_274:g.21083del
NC_000019.10:g.11105463delG
NC_000019.9:g.11216136del
NC_000019.9:g.11216139del
NC_000019.9:g.11216139delG
NM_000527.4:c.554delG
NM_000527.4:c.557delG
c.557delG

Protein change:

G145fs

Links:

LDLR-LOVD, British Heart Foundation: LDLR_000649; dbSNP: rs879254573

NCBI 1000 Genomes Browser:

rs879254573

Molecular consequence:

NM_000527.5:c.557del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001195798.2:c.557del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001195799.2:c.434del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001195800.2:c.314-1929del - intron variant - [Sequence Ontology: SO:0001627]
NM_001195803.2:c.314-1102del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

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

Recent activity

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Scalesia crockeri voucher Rivas-Torres 336 (QUSF) internal transcribed spacer 1,...
Scalesia crockeri voucher Rivas-Torres 336 (QUSF) internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
gi|1808499270|gb|MT044173.1|

Nucleotide
HS2ST1 [Protobothrops mucrosquamatus]
HS2ST1 [Protobothrops mucrosquamatus]
Gene ID:107290888

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003442666	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 28, 2024)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20809525, 28645073, 8882879, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003442666

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 28, 2024)

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

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 (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003442666.2

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

Description

This sequence change creates a premature translational stop signal (p.Gly186Valfs*20) in the LDLR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LDLR are known to be pathogenic (PMID: 20809525, 28645073). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with familial hypercholesterolemia (PMID: 8882879). This variant is also known as del165. ClinVar contains an entry for this variant (Variation ID: 251295). For these reasons, this variant has been classified as Pathogenic.

#	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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