NM_000527.5(LDLR):c.1575T>A (p.Asp525Glu) AND Hypercholesterolemia, familial, 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 18, 2023
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:: RCV004008839.2

Allele description [Variation Report for NM_000527.5(LDLR):c.1575T>A (p.Asp525Glu)]

NM_000527.5(LDLR):c.1575T>A (p.Asp525Glu)

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.1575T>A (p.Asp525Glu)

HGVS:

NC_000019.10:g.11113751T>A
NG_009060.1:g.29371T>A
NM_000527.5:c.1575T>AMANE SELECT
NM_001195798.2:c.1575T>A
NM_001195799.2:c.1452T>A
NM_001195800.2:c.1071T>A
NM_001195803.2:c.1194T>A
NP_000518.1:p.Asp525Glu
NP_001182727.1:p.Asp525Glu
NP_001182728.1:p.Asp484Glu
NP_001182729.1:p.Asp357Glu
NP_001182732.1:p.Asp398Glu
LRG_274t1:c.1575T>A
LRG_274:g.29371T>A
NC_000019.9:g.11224427T>A
NM_000527.4:c.1575T>A

Protein change:

D357E

Links:

dbSNP: rs763884010

NCBI 1000 Genomes Browser:

rs763884010

Molecular consequence:

NM_000527.5:c.1575T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195798.2:c.1575T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195799.2:c.1452T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195800.2:c.1071T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195803.2:c.1194T>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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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heavy metal atpase 3 [Arabidopsis thaliana]
heavy metal atpase 3 [Arabidopsis thaliana]
gi|22329026|ref|NP_194741.2|

Protein
Cation transporter/ E1-E2 ATPase family protein [Arabidopsis thaliana]
Cation transporter/ E1-E2 ATPase family protein [Arabidopsis thaliana]
gi|15234277|ref|NP_192910.1|

Protein
Homo sapiens LYR motif containing 7 (LYRM7), transcript variant 1, mRNA
Homo sapiens LYR motif containing 7 (LYRM7), transcript variant 1, mRNA
gi|1519243513|ref|NM_181705.4|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004822478	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Dec 18, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004822478

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Dec 18, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

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

Details of each submission

From All of Us Research Program, National Institutes of Health, SCV004822478.1

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

Description

This missense variant replaces aspartic acid with glutamic acid at codon 525 of the LDLR protein. This variant is also known as p.Asp504Glu in the mature protein. This variant alters a conserved aspartic acid residue in the LDLR type B repeat 3 of the LDLR protein (a.a. 486 - 528), where pathogenic missense variants are found enriched (ClinVar-LDLR). Computational prediction tools indicate that this variant has a deleterious impact on protein structure and function. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with LDLR-related disorders in the literature. This variant has been identified in 1/251302 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 1, 2024

ClinVar

Relating variation to medicine