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NM_000527.5(LDLR):c.1478_1479del (p.Ser493fs) AND LDLR-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 14, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003401115.6

Allele description [Variation Report for NM_000527.5(LDLR):c.1478_1479del (p.Ser493fs)]

NM_000527.5(LDLR):c.1478_1479del (p.Ser493fs)

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.1478_1479del (p.Ser493fs)
Other names:
FH Frosinone-2; FH Sidney-2; FH Yrmeih
HGVS:
  • NC_000019.10:g.11113652CT[1]
  • NG_009060.1:g.29272CT[1]
  • NM_000527.5:c.1478_1479delMANE SELECT
  • NM_001195798.2:c.1478_1479del
  • NM_001195799.2:c.1355_1356del
  • NM_001195800.2:c.974_975del
  • NM_001195803.2:c.1097_1098del
  • NP_000518.1:p.Ser493fs
  • NP_001182727.1:p.Ser493fs
  • NP_001182728.1:p.Ser452fs
  • NP_001182729.1:p.Ser325fs
  • NP_001182732.1:p.Ser366fs
  • LRG_274:g.29272CT[1]
  • NC_000019.9:g.11224328CT[1]
  • NC_000019.9:g.11224328_11224329del
  • NM_000527.4:c.1478_1479delCT
  • NM_000527.5:c.1478_1479del
  • NP_000518.1:p.S493Cfs*41
  • c.1478_1479del
  • p.(Ser493Cysfs*42)
  • p.Ser493Cysfs*42
Protein change:
S325fs
Links:
LDLR-LOVD, British Heart Foundation: LDLR_000206; dbSNP: rs869025453
NCBI 1000 Genomes Browser:
rs869025453
Molecular consequence:
  • NM_000527.5:c.1478_1479del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001195798.2:c.1478_1479del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001195799.2:c.1355_1356del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001195800.2:c.974_975del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001195803.2:c.1097_1098del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
LDLR-related disorder
Synonyms:
LDLR-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004105732PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Feb 14, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004105732.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The LDLR c.1478_1479delCT variant is predicted to result in a frameshift and premature protein termination (p.Ser493Cysfs*42). This variant has been well-documented to be pathogenic for Hypercholesterolemia (Chmara et al. 2010. PubMed ID: 20145306; Bertolini et al. 2020. PubMed ID: 32977124. Table S2; Sturm et al. 2021. PubMed ID: 34037665. eTable 1). This variant is reported in 0.0065% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Frameshift variants in LDLR are expected to be pathogenic. This variant is interpreted as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024