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NM_000527.5(LDLR):c.1794_1795del (p.Leu599fs) AND Hypercholesterolemia, familial, 1

Germline classification:
Likely pathogenic (1 submission)
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:
RCV003128550.2

Allele description [Variation Report for NM_000527.5(LDLR):c.1794_1795del (p.Leu599fs)]

NM_000527.5(LDLR):c.1794_1795del (p.Leu599fs)

Gene:
LDLR:low density lipoprotein receptor [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_000527.5(LDLR):c.1794_1795del (p.Leu599fs)
HGVS:
  • NC_000019.10:g.11116947_11116948del
  • NG_009060.1:g.32567_32568del
  • NM_000527.5:c.1794_1795delMANE SELECT
  • NM_001195798.2:c.1794_1795del
  • NM_001195799.2:c.1671_1672del
  • NM_001195800.2:c.1290_1291del
  • NM_001195803.2:c.1413_1414del
  • NP_000518.1:p.Leu599Glyfs
  • NP_000518.1:p.Leu599fs
  • NP_001182727.1:p.Leu599fs
  • NP_001182728.1:p.Leu558fs
  • NP_001182729.1:p.Leu431fs
  • NP_001182732.1:p.Leu472fs
  • LRG_274t1:c.1794_1795del
  • LRG_274:g.32567_32568del
  • LRG_274p1:p.Leu599Glyfs
  • NC_000019.9:g.11227623_11227624del
  • NM_000527.4:c.1794_1795delCT
Protein change:
L431fs
Molecular consequence:
  • NM_000527.5:c.1794_1795del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001195798.2:c.1794_1795del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001195799.2:c.1671_1672del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001195800.2:c.1290_1291del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001195803.2:c.1413_1414del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003804592Interventional Cardiology Department, Nhan Dan Gia Dinh Hospital

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Kinhgermlineyes21not providednot providednot providedclinical 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 Interventional Cardiology Department, Nhan Dan Gia Dinh Hospital, SCV003804592.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Kinh2not providednot providedclinical testing PubMed (1)

Description

The 42-year-old male patient was admitted to the Interventional Cardiology Department, Nhan Dan Gia Dinh hospital, Vietnam with the diagnosis of Stable Angina (CCS III) and Triple Vessel Coronary Disease on Coronary CT. He was implanted with 2 DES/LAD and 1 DES/RCA. He was reported with a history of hypercholesterolemia and a paternal history of myocardial infarction. His laboratory test showed an increase in serum cholesterol, which was consistent with his medical history and clinical symptom of xanthomas on his knees, elbows, and the Achilles tendons. Based on the Dutch Lipid Clinic Network Score (DLCNS), he was scored 12 and definitely diagnosed with Familial Hypercholesterolemia (FH). According to the current ClinVar database, his genetic testing of LDLR, APOB, and PCSK9 genes was reported with no significant mutation related to FH disorder. However, there was an identified heterozygous variant of the LDLR gene (c.1794_1795del [p.Leu599GlyfsTer3]), which is classified as “Likely Pathogenic” for FH by applying evidence codes (PVS1_very strong, PM2_supporting) as defined by the ACMG guidelines. His younger brother was also diagnosed with FH and found with the exact same heterozygous variant of LDLR gene (c.1794_1795del). This novel variant is the first time to be described in ClinVar.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not provided1not provided

Last Updated: Jun 23, 2024