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NM_000527.5(LDLR):c.1060+10G>A AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Feb 20, 2024
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:
RCV001576239.5

Allele description [Variation Report for NM_000527.5(LDLR):c.1060+10G>A]

NM_000527.5(LDLR):c.1060+10G>A

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.1060+10G>A
HGVS:
  • NC_000019.10:g.11110781G>A
  • NG_009060.1:g.26401G>A
  • NM_000527.5:c.1060+10G>AMANE SELECT
  • NM_001195798.2:c.1060+10G>A
  • NM_001195799.2:c.937+10G>A
  • NM_001195800.2:c.556+10G>A
  • NM_001195803.2:c.679+10G>A
  • LRG_274t1:c.1060+10G>A
  • LRG_274:g.26401G>A
  • NC_000019.9:g.11221457G>A
  • NM_000527.4(LDLR):c.1060+10G>A
  • NM_000527.4:c.1060+10G>A
  • c.1060+10G>A
  • p.(Asp354Glyfs*20)
Links:
LDLR-LOVD, British Heart Foundation: LDLR_000880;
Molecular consequence:
  • NM_000527.5:c.1060+10G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195798.2:c.1060+10G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195799.2:c.937+10G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195800.2:c.556+10G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001195803.2:c.679+10G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001803385GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Feb 20, 2024)
germlineclinical testing

Citation Link,

SCV004219935Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)
Uncertain significance
(Jan 9, 2023)
unknownclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Spectrum of mutations and phenotypic expression in patients with autosomal dominant hypercholesterolemia identified in Italy.

Bertolini S, Pisciotta L, Rabacchi C, Cefalù AB, Noto D, Fasano T, Signori A, Fresa R, Averna M, Calandra S.

Atherosclerosis. 2013 Apr;227(2):342-8. doi: 10.1016/j.atherosclerosis.2013.01.007. Epub 2013 Jan 19.

PubMed [citation]
PMID:
23375686

The relationship of molecular genetic to clinical diagnosis of familial hypercholesterolemia in a Danish population.

Damgaard D, Larsen ML, Nissen PH, Jensen JM, Jensen HK, Soerensen VR, Jensen LG, Faergeman O.

Atherosclerosis. 2005 May;180(1):155-60. Epub 2005 Jan 12.

PubMed [citation]
PMID:
15823288
See all PubMed Citations (6)

Details of each submission

From GeneDx, SCV001803385.2

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

Description

Identified in both heterozygous and homozygous states in several unrelated individuals with a clinical diagnosis of FH (PMID: 12436241, 23375686, 15823288, 34297352, 34456049, 28965616, 36991406); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 26332594, 15823288, 23375686, 28965616, 12436241, 34297352, 36991406, 34456049)

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004219935.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

The frequency of this variant in the general population, 0.000012 (3/249942 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in individuals with familial hypercholesterolemia (PMIDs: 28965616 (2017), 23375686 (2013), 15823288 (2005), 12436241 (2002)). Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on LDLR mRNA splicing yielded predictions that this variant may result in the gain of a cryptic splice site without affecting the natural splice sites . Based on the available information, we are unable to determine the clinical significance of this variant.

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

Last Updated: Sep 29, 2024