NM_000527.5(LDLR):c.2399T>A (p.Val800Asp) AND Hypercholesterolemia, familial, 1

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Mar 25, 2016
Review status:: criteria provided, conflicting classifications

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:: RCV000237819.3

Allele description [Variation Report for NM_000527.5(LDLR):c.2399T>A (p.Val800Asp)]

NM_000527.5(LDLR):c.2399T>A (p.Val800Asp)

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.2399T>A (p.Val800Asp)

HGVS:

NC_000019.10:g.11129522T>A
NG_009060.1:g.45142T>A
NM_000527.5:c.2399T>AMANE SELECT
NM_001195798.2:c.2399T>A
NM_001195799.2:c.2276T>A
NM_001195800.2:c.1895T>A
NM_001195803.2:c.1865T>A
NP_000518.1:p.Val800Asp
NP_000518.1:p.Val800Asp
NP_001182727.1:p.Val800Asp
NP_001182728.1:p.Val759Asp
NP_001182729.1:p.Val632Asp
NP_001182732.1:p.Val622Asp
LRG_274t1:c.2399T>A
LRG_274:g.45142T>A
LRG_274p1:p.Val800Asp
NC_000019.9:g.11240198T>A
NM_000527.4:c.2399T>A
c.2399T>A

Protein change:

V622D

Links:

LDLR-LOVD, British Heart Foundation: LDLR_000759; dbSNP: rs879255199

NCBI 1000 Genomes Browser:

rs879255199

Molecular consequence:

NM_000527.5:c.2399T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195798.2:c.2399T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195799.2:c.2276T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195800.2:c.1895T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195803.2:c.1865T>A - 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

Recent activity

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RING/U-box superfamily protein [Arabidopsis thaliana]
RING/U-box superfamily protein [Arabidopsis thaliana]
gi|145360522|ref|NP_180737.3|

Protein
SLC5A2 solute carrier family 5 member 2 [Homo sapiens]
SLC5A2 solute carrier family 5 member 2 [Homo sapiens]
Gene ID:6524

Gene
6524[uid] AND (alive[prop]) (1)
Gene
Prenatal Diagnosis
Prenatal Diagnosis
Determination of the nature of a pathological condition or disease in the postimplantation EMBRYO; FETUS; or pregnant female before birth.<br/>Year introduced: 1973

MeSH
Or4f56 olfactory receptor family 4 subfamily F member 56 [Mus musculus]
Or4f56 olfactory receptor family 4 subfamily F member 56 [Mus musculus]
Gene ID:258396

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000295994	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,
SCV000599416	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 1, 2016)	germline, not applicable	curation, literature only	PubMed (2) [See all records that cite these PMIDs] 25741868, 26220972

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000295994

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,

SCV000599416

Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 1, 2016)

germline, not applicable

curation, literature only

PubMed (2)
[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	yes	1	not provided	not provided	1	not provided	literature only
not provided	not applicable	not applicable	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Multiplex ARMS analysis to detect 13 common mutations in familial hypercholesterolaemia.

Taylor A, Tabrah S, Wang D, Sozen M, Duxbury N, Whittall R, Humphries SE, Norbury G.

Clin Genet. 2007 Jun;71(6):561-8.

PubMed [citation]

PMID:: 17539906

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

See all PubMed Citations (3)

Details of each submission

From LDLR-LOVD, British Heart Foundation, SCV000295994.2

#	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 Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge, SCV000599416.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (2)
2	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

"Assay Description:Heterologous cells (HepG2), WB and imunoprecipitation assays"

PubMed [ID: 26220972]

#	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
2	not applicable	not applicable	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 4, 2024

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