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NM_000527.5(LDLR):c.1706-1G>T AND Familial hypercholesterolemia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 6, 2018
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:
RCV000791379.8

Allele description [Variation Report for NM_000527.5(LDLR):c.1706-1G>T]

NM_000527.5(LDLR):c.1706-1G>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.1706-1G>T
HGVS:
  • NC_000019.10:g.11116858G>T
  • NG_009060.1:g.32478G>T
  • NM_000527.5:c.1706-1G>TMANE SELECT
  • NM_001195798.2:c.1706-1G>T
  • NM_001195799.2:c.1583-1G>T
  • NM_001195800.2:c.1202-1G>T
  • NM_001195803.2:c.1325-1G>T
  • LRG_274t1:c.1706-1G>T
  • LRG_274:g.32478G>T
  • NC_000019.9:g.11227534G>T
  • NM_000527.4:c.1706-1G>T
  • c.1706-1G>T
Links:
LDLR-LOVD, British Heart Foundation: LDLR_000656; dbSNP: rs879254996
NCBI 1000 Genomes Browser:
rs879254996
Molecular consequence:
  • NM_000527.5:c.1706-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001195798.2:c.1706-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001195799.2:c.1583-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001195800.2:c.1202-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001195803.2:c.1325-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000814532Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 6, 2018) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Molecular spectrum of autosomal dominant hypercholesterolemia in France.

Marduel M, Carrié A, Sassolas A, Devillers M, Carreau V, Di Filippo M, Erlich D, Abifadel M, Marques-Pinheiro A, Munnich A, Junien C; French ADH Research Network., Boileau C, Varret M, Rabès JP.

Hum Mutat. 2010 Nov;31(11):E1811-24. doi: 10.1002/humu.21348.

PubMed [citation]
PMID:
20809525
PMCID:
PMC3152176
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000814532.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in LDLR are known to be pathogenic (PMID: 20809525). A different variant affecting this nucleotide (c.1706-1G>A) has been determined to be pathogenic (PMID: 16159606). This suggests that this nucleotide is important for normal RNA splicing, and that other variants at this position may also be pathogenic. This variant has been observed in individuals affected with familial hypercholesterolemia (PMID: 9763532, 23680767). ClinVar contains an entry for this variant (Variation ID: 251993). This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in intron 11 of the LDLR gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

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

Last Updated: Sep 29, 2024