NM_000527.5(LDLR):c.2323G>A (p.Val775Ile) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 17, 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:: RCV003478469.1

Allele description [Variation Report for NM_000527.5(LDLR):c.2323G>A (p.Val775Ile)]

NM_000527.5(LDLR):c.2323G>A (p.Val775Ile)

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.2323G>A (p.Val775Ile)

HGVS:

NC_000019.10:g.11128019G>A
NG_009060.1:g.43639G>A
NM_000527.5:c.2323G>AMANE SELECT
NM_001195798.2:c.2323G>A
NM_001195799.2:c.2200G>A
NM_001195800.2:c.1819G>A
NM_001195803.2:c.1789G>A
NP_000518.1:p.Val775Ile
NP_000518.1:p.Val775Ile
NP_001182727.1:p.Val775Ile
NP_001182728.1:p.Val734Ile
NP_001182729.1:p.Val607Ile
NP_001182732.1:p.Val597Ile
LRG_274t1:c.2323G>A
LRG_274:g.43639G>A
LRG_274p1:p.Val775Ile
NC_000019.9:g.11238695G>A
NM_000527.4:c.2323G>A

Protein change:

V597I

Links:

dbSNP: rs199766976

NCBI 1000 Genomes Browser:

rs199766976

Molecular consequence:

NM_000527.5:c.2323G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195798.2:c.2323G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195799.2:c.2200G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195800.2:c.1819G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001195803.2:c.1789G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004219976	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Apr 17, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25487149, 29192238, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004219976

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Apr 17, 2023)

unknown

clinical testing

PubMed (3)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction.

Do R, Stitziel NO, Won HH, Jørgensen AB, Duga S, Angelica Merlini P, Kiezun A, Farrall M, Goel A, Zuk O, Guella I, Asselta R, Lange LA, Peloso GM, Auer PL; NHLBI Exome Sequencing Project., Girelli D, Martinelli N, Farlow DN, DePristo MA, Roberts R, Stewart AF, et al.

Nature. 2015 Feb 5;518(7537):102-6. doi: 10.1038/nature13917. Epub 2014 Dec 10.

PubMed [citation]

PMID:: 25487149
PMCID:: PMC4319990

Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2049 individuals.

Yamaguchi-Kabata Y, Yasuda J, Tanabe O, Suzuki Y, Kawame H, Fuse N, Nagasaki M, Kawai Y, Kojima K, Katsuoka F, Saito S, Danjoh I, Motoike IN, Yamashita R, Koshiba S, Saigusa D, Tamiya G, Kure S, Yaegashi N, Kawaguchi Y, Nagami F, Kuriyama S, et al.

J Hum Genet. 2018 Feb;63(2):213-230. doi: 10.1038/s10038-017-0347-1. Epub 2017 Dec 1.

PubMed [citation]

PMID:: 29192238

See all PubMed Citations (3)

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004219976.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The frequency of this variant in the general population, 0.000098 (3/30616 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in an individual with myocardial infraction (PMID: 25487149 (2019)), as well as an unaffected individual (PMID: 29192238 (2017)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant. Testing affected family members could help clarify the clinical significance of this variant

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

Last Updated: Sep 1, 2024

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