NM_000527.5(LDLR):c.1750T>C (p.Ser584Pro) AND Hypercholesterolemia, familial, 1

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Mar 25, 2016
Review status:: criteria provided, conflicting classifications

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:: RCV000238337.3

Allele description [Variation Report for NM_000527.5(LDLR):c.1750T>C (p.Ser584Pro)]

NM_000527.5(LDLR):c.1750T>C (p.Ser584Pro)

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.1750T>C (p.Ser584Pro)

HGVS:

NC_000019.10:g.11116903T>C
NG_009060.1:g.32523T>C
NM_000527.5:c.1750T>CMANE SELECT
NM_001195798.2:c.1750T>C
NM_001195799.2:c.1627T>C
NM_001195800.2:c.1246T>C
NM_001195803.2:c.1369T>C
NP_000518.1:p.Ser584Pro
NP_000518.1:p.Ser584Pro
NP_001182727.1:p.Ser584Pro
NP_001182728.1:p.Ser543Pro
NP_001182729.1:p.Ser416Pro
NP_001182732.1:p.Ser457Pro
LRG_274t1:c.1750T>C
LRG_274:g.32523T>C
LRG_274p1:p.Ser584Pro
NC_000019.9:g.11227579T>C
NM_000527.4:c.1750T>C
c.1750T>C

Protein change:

S416P

Links:

LDLR-LOVD, British Heart Foundation: LDLR_001519; dbSNP: rs879255010

NCBI 1000 Genomes Browser:

rs879255010

Molecular consequence:

NM_000527.5:c.1750T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001195798.2:c.1750T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001195799.2:c.1627T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001195800.2:c.1246T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001195803.2:c.1369T>C - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

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HPODL_03182 [Ogataea parapolymorpha DL-1]
HPODL_03182 [Ogataea parapolymorpha DL-1]
Gene ID:25772626

Gene
Hyperacanthus amoenus chloroplast tRNA-Leu gene, trnT-trnL intergenic spacer and...
Hyperacanthus amoenus chloroplast tRNA-Leu gene, trnT-trnL intergenic spacer and trnL-trnF intergenic spacer, specimen voucher Bremer et al. 4286 (UPS)
gi|211575968|emb|AM117364.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000295637	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,
SCV000607635	Fundacion Hipercolesterolemia Familiar - SAFEHEART	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 1, 2016)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000295637

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,

SCV000607635

Fundacion Hipercolesterolemia Familiar - SAFEHEART

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 1, 2016)

germline

research

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	research
not provided	germline	yes	1	not provided	not provided	1	not provided	literature only

Citations

PubMed

Genetic diagnosis of familial hypercholesterolemia using a DNA-array based platform.

Alonso R, Defesche JC, Tejedor D, Castillo S, Stef M, Mata N, Gomez-Enterria P, Martinez-Faedo C, Forga L, Mata P.

Clin Biochem. 2009 Jun;42(9):899-903. doi: 10.1016/j.clinbiochem.2009.01.017. Epub 2009 Feb 6.

PubMed [citation]

PMID:: 19318025

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 LDLR-LOVD, British Heart Foundation, SCV000295637.2

#	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 Fundacion Hipercolesterolemia Familiar - SAFEHEART, SCV000607635.1

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

#	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

Last Updated: Sep 1, 2024

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