NM_000527.5(LDLR):c.1867A>T (p.Ile623Phe) AND Familial hypercholesterolemia

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 10, 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:: RCV003740886.2

Allele description [Variation Report for NM_000527.5(LDLR):c.1867A>T (p.Ile623Phe)]

NM_000527.5(LDLR):c.1867A>T (p.Ile623Phe)

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.1867A>T (p.Ile623Phe)

HGVS:

NC_000019.10:g.11120113A>T
NG_009060.1:g.35733A>T
NM_000527.5:c.1867A>TMANE SELECT
NM_001195798.2:c.1867A>T
NM_001195799.2:c.1744A>T
NM_001195800.2:c.1363A>T
NM_001195803.2:c.1486A>T
NP_000518.1:p.Ile623Phe
NP_000518.1:p.Ile623Phe
NP_001182727.1:p.Ile623Phe
NP_001182728.1:p.Ile582Phe
NP_001182729.1:p.Ile455Phe
NP_001182732.1:p.Ile496Phe
LRG_274t1:c.1867A>T
LRG_274:g.35733A>T
LRG_274p1:p.Ile623Phe
NC_000019.9:g.11230789A>T
NM_000527.4:c.1867A>T

Protein change:

I455F

Molecular consequence:

NM_000527.5:c.1867A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195798.2:c.1867A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195799.2:c.1744A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195800.2:c.1363A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001195803.2:c.1486A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Familial hypercholesterolemia
Identifiers:: MONDO: MONDO:0005439; MedGen: C0020445; OMIM: PS143890

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Nerita polita isolate Reu.2 cytochrome c oxidase subunit I gene, partial cds; mitochondrial
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004535476	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 10, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30971288, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004535476

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 10, 2023)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Effects of familial hypercholesterolemia-associated genes on the phenotype of premature myocardial infarction.

Lee C, Cui Y, Song J, Li S, Zhang F, Wu M, Li L, Hu D, Chen H.

Lipids Health Dis. 2019 Apr 11;18(1):95. doi: 10.1186/s12944-019-1042-3.

PubMed [citation]

PMID:: 30971288
PMCID:: PMC6458678

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004535476.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on LDLR protein function. This missense change has been observed in individuals with clinical features of familial hypercholesterolemia (PMID: 30971288; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 623 of the LDLR protein (p.Ile623Phe).

#	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: Sep 29, 2024

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