LDLR (low density lipoprotein receptor)

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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
Donations are also welcome

LDLR (low density lipoprotein receptor)

Identity

Other names	FH
	FHC
	LDLCQ2
HGNC (Hugo)	LDLR
LocusID (NCBI)	3949
Location	19p13.2
Location_base_pair	Starts at 11200038 and ends at 11244505 bp from pter ( according to hg19-Feb_2009)
Note	Non-annotated gene. Preliminary data : if you are an author who wish to write a full paper/card on this gene, go to How to contribute

DNA/RNA

External links

	Nomenclature
HGNC (Hugo)	LDLR 6547
	Cards
Entrez_Gene (NCBI)	LDLR 3949 low density lipoprotein receptor
GeneCards (Weizmann)	LDLR
Ensembl hg19 (Hinxton)	ENSG00000130164 [Gene_View] chr19:11200038-11244505 [Contig_View] LDLR [Vega]
Ensembl hg38 (Hinxton)	ENSG00000130164 [Gene_View] chr19:11200038-11244505 [Contig_View] LDLR [Vega]
ICGC DataPortal	ENSG00000130164
cBioPortal	LDLR
AceView (NCBI)	LDLR
Genatlas (Paris)	LDLR
WikiGenes	3949
SOURCE (Princeton)	LDLR
	Genomic and cartography
GoldenPath hg19 (UCSC)	LDLR - chr19:11200038-11244505 + 19p13.2 [Description] (hg19-Feb_2009)
GoldenPath hg38 (UCSC)	LDLR - 19p13.2 [Description] (hg38-Dec_2013)
Ensembl	LDLR - 19p13.2 [CytoView hg19] LDLR - 19p13.2 [CytoView hg38]
Mapping of homologs : NCBI	LDLR [Mapview hg19] LDLR [Mapview hg38]
OMIM	143890 606945
	Gene and transcription
Genbank (Entrez)	AA292214 AB209409 AK295612 AK296312 AK299038
RefSeq transcript (Entrez)	NM_000527 NM_001195798 NM_001195799 NM_001195800 NM_001195802 NM_001195803
RefSeq genomic (Entrez)	AC_000151 NC_000019 NC_018930 NG_009060 NT_011295 NW_001838483 NW_004929414
Consensus coding sequences : CCDS (NCBI)	LDLR
Cluster EST : Unigene	Hs.713981 [ NCBI ]
CGAP (NCI)	Hs.713981
Alternative Splicing : Fast-db (Paris)	GSHG0014582
Alternative Splicing Gallery	ENSG00000130164
Gene Expression	LDLR [ NCBI-GEO ] LDLR [ SEEK ] LDLR [ MEM ]
SOURCE (Princeton)	Expression in : [Normal Tissue Atlas] [carcinoma Classsification] [NCI60]
	Protein : pattern, domain, 3D structure
UniProt/SwissProt	P01130 (Uniprot)
NextProt	P01130 [Medical]
With graphics : InterPro	P01130
Splice isoforms : SwissVar	P01130 (Swissvar)
Domaine pattern : Prosite (Expaxy)	ASX_HYDROXYL (PS00010) EGF_2 (PS01186) EGF_3 (PS50026) EGF_CA (PS01187) LDLRA_1 (PS01209) LDLRA_2 (PS50068) LDLRB (PS51120)
Domains : Interpro (EBI)	6-blade_b-propeller_TolB-like cEGF EG-like_dom EGF-like_Ca-bd_dom EGF-like_CS EGF-type_Asp/Asn_hydroxyl_site EGF_Ca-bd_CS Growth_fac_rcpt_N_dom LDLR_class-A_CS LDLR_classB_rpt LDrepeatLR_classA_rpt
Related proteins : CluSTr	P01130
Domain families : Pfam (Sanger)	cEGF (PF12662) Ldl_recept_a (PF00057) Ldl_recept_b (PF00058)
Domain families : Pfam (NCBI)	pfam12662 pfam00057 pfam00058
Domain families : Smart (EMBL)	EGF (SM00181) EGF_CA (SM00179) LDLa (SM00192) LY (SM00135)
DMDM Disease mutations	3949
Blocks (Seattle)	P01130
PDB (SRS)	1AJJ 1D2J 1F5Y 1F8Z 1HJ7 1HZ8 1I0U 1IJQ 1LDL 1LDR 1LRX 1N7D 1XFE 2FCW 2KRI 2LGP 2M7P 2MG9 2W2M 2W2N 2W2O 2W2P 2W2Q 3BPS 3GCW 3GCX 3M0C 3P5B 3P5C 3SO6
PDB (PDBSum)	1AJJ 1D2J 1F5Y 1F8Z 1HJ7 1HZ8 1I0U 1IJQ 1LDL 1LDR 1LRX 1N7D 1XFE 2FCW 2KRI 2LGP 2M7P 2MG9 2W2M 2W2N 2W2O 2W2P 2W2Q 3BPS 3GCW 3GCX 3M0C 3P5B 3P5C 3SO6
PDB (IMB)	1AJJ 1D2J 1F5Y 1F8Z 1HJ7 1HZ8 1I0U 1IJQ 1LDL 1LDR 1LRX 1N7D 1XFE 2FCW 2KRI 2LGP 2M7P 2MG9 2W2M 2W2N 2W2O 2W2P 2W2Q 3BPS 3GCW 3GCX 3M0C 3P5B 3P5C 3SO6
PDB (RSDB)	1AJJ 1D2J 1F5Y 1F8Z 1HJ7 1HZ8 1I0U 1IJQ 1LDL 1LDR 1LRX 1N7D 1XFE 2FCW 2KRI 2LGP 2M7P 2MG9 2W2M 2W2N 2W2O 2W2P 2W2Q 3BPS 3GCW 3GCX 3M0C 3P5B 3P5C 3SO6
Human Protein Atlas	ENSG00000130164
Peptide Atlas	P01130
HPRD	06091
IPI	IPI00000070 IPI00815700 IPI00983312 IPI00983910 IPI00908663 IPI00982869 IPI00980161
	Protein Interaction databases
DIP (DOE-UCLA)	P01130
IntAct (EBI)	P01130
FunCoup	ENSG00000130164
BioGRID	LDLR
IntegromeDB	LDLR
STRING (EMBL)	LDLR
	Ontologies - Pathways
QuickGO	P01130
Ontology : AmiGO	retinoid metabolic process glycoprotein binding low-density lipoprotein receptor activity calcium ion binding protein binding lysosome early endosome late endosome Golgi apparatus plasma membrane integral component of plasma membrane coated pit lipid metabolic process endocytosis receptor-mediated endocytosis phototransduction, visible light cholesterol metabolic process external side of plasma membrane cell surface endosome membrane positive regulation of triglyceride biosynthetic process regulation of phosphatidylcholine catabolic process phospholipid transport membrane viral process low-density lipoprotein particle binding very-low-density lipoprotein particle receptor activity intestinal cholesterol absorption cholesterol transport clathrin-coated endocytic vesicle membrane low-density lipoprotein particle low-density lipoprotein particle clearance lipoprotein metabolic process lipoprotein catabolic process cholesterol homeostasis receptor complex small molecule metabolic process cholesterol import
Ontology : EGO-EBI	retinoid metabolic process glycoprotein binding low-density lipoprotein receptor activity calcium ion binding protein binding lysosome early endosome late endosome Golgi apparatus plasma membrane integral component of plasma membrane coated pit lipid metabolic process endocytosis receptor-mediated endocytosis phototransduction, visible light cholesterol metabolic process external side of plasma membrane cell surface endosome membrane positive regulation of triglyceride biosynthetic process regulation of phosphatidylcholine catabolic process phospholipid transport membrane viral process low-density lipoprotein particle binding very-low-density lipoprotein particle receptor activity intestinal cholesterol absorption cholesterol transport clathrin-coated endocytic vesicle membrane low-density lipoprotein particle low-density lipoprotein particle clearance lipoprotein metabolic process lipoprotein catabolic process cholesterol homeostasis receptor complex small molecule metabolic process cholesterol import
Pathways : BIOCARTA	FXR and LXR Regulation of Cholesterol Metabolism [Genes] SREBP control of lipid synthesis [Genes] Low-density lipoprotein (LDL) pathway during atherogenesis [Genes]
Pathways : KEGG	Endocytosis Ovarian steroidogenesis Bile secretion Toxoplasmosis Hepatitis C
Protein Interaction Database	LDLR
DoCM (Curated mutations)	LDLR
Wikipedia pathways	LDLR
	Gene fusion - rearrangements
	Polymorphisms : SNP, variants
NCBI Variation Viewer	LDLR [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)	LDLR
dbVar	LDLR
ClinVar	LDLR
1000_Genomes	LDLR
Exome Variant Server	LDLR
SNP (GeneSNP Utah)	LDLR
SNP : HGBase	LDLR
Genetic variants : HAPMAP	LDLR
Genomic Variants (DGV)	LDLR [DGVbeta]
	Mutations
ICGC Data Portal	ENSG00000130164
Somatic Mutations in Cancer : COSMIC	LDLR
CONAN: Copy Number Analysis	LDLR
LOVD (Leiden Open Variation Database)	Whole genome datasets
LOVD (Leiden Open Variation Database)	LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)	LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)	MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
LOVD (Leiden Open Variation Database)	FH UCL BHF
Impact of mutations	[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor]
	Diseases
DECIPHER (Syndromes)	19:11200038-11244505
Mutations and Diseases : HGMD	LDLR
OMIM	143890 606945
Medgen	LDLR
NextProt	P01130 [Medical]
GENETests	LDLR
Disease Genetic Association	LDLR
Huge Navigator	LDLR [HugePedia] LDLR [HugeCancerGEM]
snp3D : Map Gene to Disease	3949
DGIdb (Drug Gene Interaction db)	LDLR
	General knowledge
Homologs : HomoloGene	LDLR
Homology/Alignments : Family Browser (UCSC)	LDLR
Phylogenetic Trees/Animal Genes : TreeFam	LDLR
Chemical/Protein Interactions : CTD	3949
Chemical/Pharm GKB Gene	PA227
Clinical trial	LDLR
Cancer Resource (Charite)	ENSG00000130164
	Other databases
	Probes
	Litterature
PubMed	499 Pubmed reference(s) in Entrez
CoreMine	LDLR
GoPubMed	LDLR
iHOP	LDLR

Genes in title	automatic search in PubMed
REVIEW articles	automatic search in PubMed
Last year publications	automatic search in PubMed

Search in all EBI NCBI

Contributor(s)

Written	09-2002	Dessen P, Le Minor S

Updated	12-2014	Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology

indexed on : Sat Feb 14 16:34:03 CET 2015

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jlhuret@AtlasGeneticsOncology.org.