NM_000527.5(LDLR):c.1891_2311+1062del AND Hypercholesterolemia, familial, 1

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Mar 25, 2016
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:: RCV000003922.14

Allele description

NM_000527.5(LDLR):c.1891_2311+1062del

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.1891_2311+1062del

Other names:

FH Potenza

HGVS:

NC_000019.10:g.11120137_11124406del
NG_009060.1:g.35757_40026del
NM_000527.5:c.1891_2311+1062delMANE SELECT
NM_001195798.2:c.1891_2311+1062del
NM_001195799.2:c.1768_2188+1062del
NM_001195800.2:c.1387_1807+1062del
NM_001195803.2:c.1510_1777+1062del
NP_000518.1:p.(?)
NP_000518.1:p.(?)
LRG_274t1:c.1891_2311+1062del
LRG_274:g.35757_40026del
LRG_274p1:p.(?)
NC_000019.9:g.11230813_11235082del
NM_000527.4:c.1891_2311+1062del
c.1891_2311+1062del

Note:

Deletion from LDLR resulting in loss of part of exon 13, plus exons 14 and 15.

Nucleotide change:

EX13-15DEL

Links:

LDLR-LOVD, British Heart Foundation: LDLR_001543; dbVar: nssv3761595; dbVar: nsv1067859; OMIM: 606945.0042

Molecular consequence:

NM_000527.5:c.1891_2311+1062del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001195798.2:c.1891_2311+1062del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001195799.2:c.1768_2188+1062del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001195800.2:c.1387_1807+1062del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001195803.2:c.1510_1777+1062del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_000527.5:c.1891_2311+1062del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001195798.2:c.1891_2311+1062del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001195799.2:c.1768_2188+1062del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001195800.2:c.1387_1807+1062del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001195803.2:c.1510_1777+1062del - splice donor variant - [Sequence Ontology: SO:0001575]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000024087	OMIM	no assertion criteria provided	Pathogenic (Jun 1, 1986)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000295743	LDLR-LOVD, British Heart Foundation	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely pathogenic (Mar 25, 2016)	germline	literature only	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV000599398	Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 1, 2016)	germline, not applicable	curation, literature only	PubMed (2) [See all records that cite these PMIDs] 25741868, 3012527

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000024087

OMIM

no assertion criteria provided

Pathogenic
(Jun 1, 1986)

germline

literature only

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

SCV000295743

LDLR-LOVD, British Heart Foundation

criteria provided, single submitter

(ACGS Guidelines, 2013)

Likely pathogenic
(Mar 25, 2016)

germline

literature only

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

Citation Link,

SCV000599398

Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Mar 1, 2016)

germline, not applicable

curation, literature only

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	yes	1	not provided	not provided	1	not provided	literature only
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	curation
not provided	not applicable	not applicable	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

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

Exon-Alu recombination deletes 5 kilobases from the low density lipoprotein receptor gene, producing a null phenotype in familial hypercholesterolemia.

Lehrman MA, Russell DW, Goldstein JL, Brown MS.

Proc Natl Acad Sci U S A. 1986 Jun;83(11):3679-83.

PubMed [citation]

PMID:: 3012527
PMCID:: PMC323586

Details of each submission

From OMIM, SCV000024087.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In an Italian patient with FH (FHCL1; 143890), Lehrman et al. (1986) found deletion of exons 14 and 15 and part of 13.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From LDLR-LOVD, British Heart Foundation, SCV000295743.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	literature only	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	1	not provided	not provided		1	not provided	not provided	not provided

From Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge, SCV000599398.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (2)
2	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

"Assay Description:Htz patients' fibroblasts, RNA assays"

PubMed [ID: 3012527]

#	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
2	not applicable	not applicable	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 30, 2023

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