NM_000527.5(LDLR):c.1792A>C (p.Ile598Leu) AND Hypercholesterolemia, familial, 1

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Apr 28, 2023
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV000237670.3

Allele description [Variation Report for NM_000527.5(LDLR):c.1792A>C (p.Ile598Leu)]

NM_000527.5(LDLR):c.1792A>C (p.Ile598Leu)

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.1792A>C (p.Ile598Leu)

Other names:

NM_000527.5(LDLR):c.1792A>C; p.Ile598Leu

HGVS:

NC_000019.10:g.11116945A>C
NG_009060.1:g.32565A>C
NM_000527.5:c.1792A>CMANE SELECT
NM_001195798.2:c.1792A>C
NM_001195799.2:c.1669A>C
NM_001195800.2:c.1288A>C
NM_001195803.2:c.1411A>C
NP_000518.1:p.Ile598Leu
NP_000518.1:p.Ile598Leu
NP_001182727.1:p.Ile598Leu
NP_001182728.1:p.Ile557Leu
NP_001182729.1:p.Ile430Leu
NP_001182732.1:p.Ile471Leu
LRG_274t1:c.1792A>C
LRG_274:g.32565A>C
LRG_274p1:p.Ile598Leu
NC_000019.9:g.11227621A>C
NM_000527.4:c.1792A>C
c.1792A>C

Protein change:

I430L

Links:

LDLR-LOVD, British Heart Foundation: LDLR_000480; dbSNP: rs879255023

NCBI 1000 Genomes Browser:

rs879255023

Molecular consequence:

NM_000527.5:c.1792A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001195798.2:c.1792A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001195799.2:c.1669A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001195800.2:c.1288A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001195803.2:c.1411A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hypercholesterolemia, familial, 1
Synonyms:: LDL RECEPTOR DISORDER; Hyperlipoproteinemia Type IIa; HYPER-LOW-DENSITY-LIPOPROTEINEMIA; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007750; MedGen: C0745103; Orphanet: 391665; OMIM: 143890

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000295659	LDLR-LOVD, British Heart Foundation	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Mar 25, 2016)	germline	literature only	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV000606516	Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum	no assertion criteria provided	Pathogenic	germline	research
SCV004022462	ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel	reviewed by expert panel (ClinGen FH ACMG Specifications v1-2)	Uncertain significance (Apr 28, 2023)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000295659

LDLR-LOVD, British Heart Foundation

criteria provided, single submitter

(ACGS Guidelines, 2013)

Likely benign
(Mar 25, 2016)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV000606516

Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum

no assertion criteria provided

Pathogenic

germline

research

SCV004022462

ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel

reviewed by expert panel

(ClinGen FH ACMG Specifications v1-2)

Uncertain significance
(Apr 28, 2023)

germline

curation

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	1	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	research, curation

Citations

PubMed

The molecular basis of familial hypercholesterolemia in The Netherlands.

Fouchier SW, Defesche JC, Umans-Eckenhausen MW, Kastelein JP.

Hum Genet. 2001 Dec;109(6):602-15. Epub 2001 Nov 9.

PubMed [citation]

PMID:: 11810272

Details of each submission

From LDLR-LOVD, British Heart Foundation, SCV000295659.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	literature only	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

From Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum, SCV000606516.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	not provided

#	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

From ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel, SCV004022462.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

Description

The NM_000527.5(LDLR):c.1792A>C (p.Ile598Leu) variant is classified as Uncertain significance - insufficient evidence for Familial Hypercholesterolemia by applying evidence codes (PM2, PP4 and BP4) as defined by the ClinGen Familial Hypercholesterolemia Expert Panel LDLR-specific variant curation guidelines (https://doi.org/10.1016/j.gim.2021.09.012). The supporting evidence is as follows: PM2 - This variant is absent from gnomAD (gnomAD v2.1.1). PP4 - Variant meet PM2. PMID: 11810272 (Fouchier et al., 2001), Netherlands - et least 1 case who fulfills validated clinical criteria for FH. BP4 - REVEL: 0.487, it is below 0.50, splicing evaluation required. Functional data on splicing not available. Scenario A, Acceptor site: The variant is not located at -20 to +3 bases of canonical acceptor splicing site of any exons. Scenario A, Donor site: The variant is not located at -3 to +6 bases of canonical splicing site of any exons. Scenario B, Acceptor site: The variant is located within the range but does not create de novo AG site. Scenario B, Donor site: The variant is located within range but does not create de novo GT site. Scenario C, Acceptor site: The variant is located at -20 to +3 bases of intraexonic AG but AG is not within the range. Scenario C, Donor site: The variant is not located at -3 to +6 bases of intraexonic GT Interpretation: The variant does not affect splicing.

#	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: Aug 13, 2023

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