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NM_000527.5(LDLR):c.*1356C>T AND Hypercholesterolemia, familial, 1

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Nov 2, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000311857.7

Allele description [Variation Report for NM_000527.5(LDLR):c.*1356C>T]

NM_000527.5(LDLR):c.*1356C>T

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.*1356C>T
HGVS:
  • NC_000019.10:g.11132672C>T
  • NG_009060.1:g.48292C>T
  • NM_000527.5:c.*1356C>TMANE SELECT
  • NM_001195798.2:c.*1356C>T
  • NM_001195799.2:c.*1356C>T
  • NM_001195800.2:c.*1356C>T
  • NM_001195803.2:c.*1356C>T
  • LRG_274t1:c.*1356C>T
  • LRG_274:g.48292C>T
  • NC_000019.9:g.11243348C>T
  • NM_000527.4:c.*1356C>T
Links:
dbSNP: rs886054173
NCBI 1000 Genomes Browser:
rs886054173
Molecular consequence:
  • NM_000527.5:c.*1356C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001195798.2:c.*1356C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001195799.2:c.*1356C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001195800.2:c.*1356C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001195803.2:c.*1356C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
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
SCV000410589Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Uncertain significance
(Jan 12, 2018) 		germlineclinical testing

Citation Link,

SCV002764414New York Genome Center
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Nov 2, 2021) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000410589.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From New York Genome Center, SCV002764414.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The c.*1356C>T variant identified in the LDLR gene substitutes a poorly conserved Cystine for Thymine in the 3’ Untranslated Region (3’UTR). Thisvariant is found with low frequency in gnomAD(v3.1.1) (12 out 150528 heterozygous alleles, 0 homozygotes; allele frequency: 0.00007972) suggesting it is not acommon benign variant in the populations represented in that database. This variant is reported as a Variant of Uncertain Significance in ClinVar (VarID: 328098) and has been reported in an individual with familial hypercholesterolemia in the literature [PMID: 30827231]. Given the lack of compelling evidence for its pathogenicity, the c.*1356C>T variant identified in the LDLR gene is reported as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Jun 23, 2024