Atlas of Genetics and Cytogenetics in Oncology and Haematology

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LDLR (low density lipoprotein receptor)

Identity

Other namesFH
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 (Hinxton)ENSG00000130164 [Gene_View]  chr19:11200038-11244505 [Contig_View]  LDLR [Vega]
ICGC DataPortalENSG00000130164
cBioPortalLDLR
AceView (NCBI)LDLR
Genatlas (Paris)LDLR
WikiGenes3949
SOURCE (Princeton)NM_000527 NM_001195798 NM_001195799 NM_001195800 NM_001195802 NM_001195803
Genomic and cartography
GoldenPath (UCSC)LDLR  -  19p13.2   chr19:11200038-11244505 +  19p13.2   [Description]    (hg19-Feb_2009)
EnsemblLDLR - 19p13.2 [CytoView]
Mapping of homologs : NCBILDLR [Mapview]
OMIM143890   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 : UnigeneHs.713981 [ NCBI ]
CGAP (NCI)Hs.713981
Alternative Splicing : Fast-db (Paris)GSHG0014582
Alternative Splicing GalleryENSG00000130164
Gene ExpressionLDLR [ NCBI-GEO ]     LDLR [ SEEK ]   LDLR [ MEM ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP01130 (Uniprot)
NextProtP01130  [Medical]
With graphics : InterProP01130
Splice isoforms : SwissVarP01130 (Swissvar)
Domaine pattern : Prosite (Expaxy)ASX_HYDROXYL (PS00010)    EGF_1 (PS00022)    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 [organisation]   cEGF [organisation]   EG-like_dom [organisation]   EGF-like_Ca-bd_dom [organisation]   EGF-like_CS [organisation]   EGF-type_Asp/Asn_hydroxyl_site [organisation]   EGF_Ca-bd_CS [organisation]   Growth_fac_rcpt_N_dom [organisation]   LDLR_class-A_CS [organisation]   LDLR_classB_rpt [organisation]   LDrepeatLR_classA_rpt [organisation]  
Related proteins : CluSTrP01130
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 mutations3949
Blocks (Seattle)P01130
PDB (SRS)1AJJ    1D2J    1F5Y    1F8Z    1HJ7    1HZ8    1I0U    1IJQ    1LDL    1LDR    1LRX    1N7D    1XFE    2FCW    2KRI    2LGP    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    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    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    2W2M    2W2N    2W2O    2W2P    2W2Q    3BPS    3GCW    3GCX    3M0C    3P5B    3P5C    3SO6   
Human Protein AtlasENSG00000130164 [gene] [tissue] [antibody] [cell] [cancer]
Peptide AtlasP01130
HPRD06091
IPIIPI00000070   IPI00815700   IPI00983312   IPI00983910   IPI00908663   IPI00982869   IPI00980161   
Protein Interaction databases
DIP (DOE-UCLA)P01130
IntAct (EBI)P01130
FunCoupENSG00000130164
BioGRIDLDLR
InParanoidP01130
Interologous Interaction database P01130
IntegromeDBLDLR
STRING (EMBL)LDLR
Ontologies - Pathways
Ontology : AmiGOretinoid metabolic process  glycoprotein binding  low-density lipoprotein receptor activity  calcium ion binding  protein binding  lysosome  early endosome  late endosome  Golgi apparatus  plasma membrane  integral to 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  modulation by virus of host morphology or physiology  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  small molecule metabolic process  cholesterol import  
Ontology : EGO-EBIretinoid metabolic process  glycoprotein binding  low-density lipoprotein receptor activity  calcium ion binding  protein binding  lysosome  early endosome  late endosome  Golgi apparatus  plasma membrane  integral to 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  modulation by virus of host morphology or physiology  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  small molecule metabolic process  cholesterol import  
Pathways : BIOCARTAFXR and LXR Regulation of Cholesterol Metabolism [Genes]    SREBP control of lipid synthesis [Genes]    Low-density lipoprotein (LDL) pathway during atherogenesis [Genes]   
Pathways : KEGGEndocytosis    Ovarian steroidogenesis    Bile secretion    Toxoplasmosis    Hepatitis C   
Protein Interaction DatabaseLDLR
Wikipedia pathwaysLDLR
Gene fusion - rearrangments
Polymorphisms : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)LDLR
snp3D : Map Gene to Disease3949
SNP (GeneSNP Utah)LDLR
SNP : HGBaseLDLR
Genetic variants : HAPMAPLDLR
Exome VariantLDLR
1000_GenomesLDLR 
ICGC programENSG00000130164 
Somatic Mutations in Cancer : COSMICLDLR 
CONAN: Copy Number AnalysisLDLR 
Mutations and Diseases : HGMDLDLR
Genomic VariantsLDLR  LDLR [DGVbeta]
dbVarLDLR
ClinVarLDLR
Pred. of missensesPolyPhen-2  SIFT(SG)  SIFT(JCVI)  Align-GVGD  MutAssessor  Mutanalyser  
Pred. splicesGeneSplicer  Human Splicing Finder  MaxEntScan  
Diseases
OMIM143890    606945   
MedgenLDLR
GENETestsLDLR
Disease Genetic AssociationLDLR
Huge Navigator LDLR [HugePedia]  LDLR [HugeCancerGEM]
General knowledge
Homologs : HomoloGeneLDLR
Homology/Alignments : Family Browser (UCSC)LDLR
Phylogenetic Trees/Animal Genes : TreeFamLDLR
Chemical/Protein Interactions : CTD3949
Chemical/Pharm GKB GenePA227
Clinical trialLDLR
Cancer Resource (Charite)ENSG00000130164
Other databases
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
CoreMineLDLR
iHOPLDLR
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated12-2013Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri Jul 11 17:02:44 CEST 2014
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