Atlas of Genetics and Cytogenetics in Oncology and Haematology

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LDLR (low density lipoprotein receptor)

Identity

Alias_symbol (synonym)LDLCQ2
Other aliasFH
FHC
FHCL1
HGNC (Hugo) LDLR
LocusID (NCBI) 3949
Atlas_Id 50170
Location 19p13.2  [Link to chromosome band 19p13]
Location_base_pair Starts at 11089362 and ends at 11133829 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
EXOSC6 (16q22.1) / LDLR (19p13.2)LDLR (19p13.2) / ABAT (16p13.2)LDLR (19p13.2) / ANKRD11 (16q24.3)
LDLR (19p13.2) / BRK1 (3p25.3)LDLR (19p13.2) / C19orf38 (19p13.2)LDLR (19p13.2) / DNM2 (19p13.2)
LDLR (19p13.2) / LDLR (19p13.2)LDLR (19p13.2) / TNPO2 (19p13.2)PKN1 (19p13.12) / LDLR (19p13.2)
LDLR 19p13.2 / C19orf38 19p13.2LDLR 19p13.2 / DNM2 19p13.2LDLR 19p13.2 / TNPO2 19p13.2
PKN1 19p13.12 / LDLR 19p13.2

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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 6 ]
  LDLR/C19orf38 (19p13)
LDLR/DNM2 (19p13)
LDLR/TNPO2 (19p13)
LDLR/ZGLP1 (19p13)
PKN1/LDLR (19p13)
ZGLP1/LDLR (19p13)

External links

Nomenclature
HGNC (Hugo)LDLR   6547
LRG (Locus Reference Genomic)LRG_274
Cards
Entrez_Gene (NCBI)LDLR  3949  low density lipoprotein receptor
AliasesFH; FHC; FHCL1; LDLCQ2
GeneCards (Weizmann)LDLR
Ensembl hg19 (Hinxton)ENSG00000130164 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000130164 [Gene_View]  ENSG00000130164 [Sequence]  chr19:11089362-11133829 [Contig_View]  LDLR [Vega]
ICGC DataPortalENSG00000130164
TCGA cBioPortalLDLR
AceView (NCBI)LDLR
Genatlas (Paris)LDLR
WikiGenes3949
SOURCE (Princeton)LDLR
Genetics Home Reference (NIH)LDLR
Genomic and cartography
GoldenPath hg38 (UCSC)LDLR  -     chr19:11089362-11133829 +  19p13.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LDLR  -     19p13.2   [Description]    (hg19-Feb_2009)
GoldenPathLDLR - 19p13.2 [CytoView hg19]  LDLR - 19p13.2 [CytoView hg38]
ImmunoBaseENSG00000130164
Mapping of homologs : NCBILDLR [Mapview hg19]  LDLR [Mapview hg38]
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)
Consensus coding sequences : CCDS (NCBI)LDLR
Cluster EST : UnigeneHs.713981 [ NCBI ]
CGAP (NCI)Hs.713981
Alternative Splicing GalleryENSG00000130164
Gene ExpressionLDLR [ NCBI-GEO ]   LDLR [ EBI - ARRAY_EXPRESS ]   LDLR [ SEEK ]   LDLR [ MEM ]
Gene Expression Viewer (FireBrowse)LDLR [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3949
GTEX Portal (Tissue expression)LDLR
Human Protein AtlasENSG00000130164-LDLR [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP01130   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP01130  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP01130
Splice isoforms : SwissVarP01130
PhosPhoSitePlusP01130
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    EGF-like_Ca-bd_dom    EGF-like_CS    EGF-like_dom    EGF-type_Asp/Asn_hydroxyl_site    EGF_Ca-bd_CS    Growth_fac_rcpt_cys_sf    LDL_receptor-like_sf    LDLR_class-A_CS    LDLR_classB_rpt    LDrepeatLR_classA_rpt   
Domain families : Pfam (Sanger)EGF_CA (PF07645)    Ldl_recept_a (PF00057)    Ldl_recept_b (PF00058)   
Domain families : Pfam (NCBI)pfam07645    pfam00057    pfam00058   
Domain families : Smart (EMBL)EGF (SM00181)  EGF_CA (SM00179)  LDLa (SM00192)  LY (SM00135)  
Conserved Domain (NCBI)LDLR
DMDM Disease mutations3949
Blocks (Seattle)LDLR
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    4NE9   
PDB Europe1AJJ    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    4NE9   
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    4NE9   
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    4NE9   
Structural Biology KnowledgeBase1AJJ    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    4NE9   
SCOP (Structural Classification of Proteins)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    4NE9   
CATH (Classification of proteins structures)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    4NE9   
SuperfamilyP01130
Human Protein Atlas [tissue]ENSG00000130164-LDLR [tissue]
Peptide AtlasP01130
HPRD06091
IPIIPI00000070   IPI00815700   IPI00983312   IPI00983910   IPI00908663   IPI00982869   IPI00980161   
Protein Interaction databases
DIP (DOE-UCLA)P01130
IntAct (EBI)P01130
FunCoupENSG00000130164
BioGRIDLDLR
STRING (EMBL)LDLR
ZODIACLDLR
Ontologies - Pathways
QuickGOP01130
Ontology : AmiGOamyloid-beta binding  virus receptor activity  protease binding  low-density lipoprotein particle receptor activity  low-density lipoprotein particle receptor activity  low-density lipoprotein particle receptor activity  low-density lipoprotein particle receptor activity  calcium ion binding  protein binding  cell  lysosome  early endosome  late endosome  Golgi apparatus  plasma membrane  integral component of plasma membrane  clathrin-coated pit  lipid metabolic process  endocytosis  receptor-mediated endocytosis  receptor-mediated endocytosis  phagocytosis  long-term memory  cholesterol metabolic process  external side of plasma membrane  cell surface  cell surface  endosome membrane  positive regulation of gene expression  negative regulation of gene expression  positive regulation of triglyceride biosynthetic process  regulation of phosphatidylcholine catabolic process  phospholipid transport  membrane  basolateral plasma membrane  low-density lipoprotein particle binding  very-low-density lipoprotein particle receptor activity  intestinal cholesterol absorption  cholesterol transport  cholesterol transport  clathrin-coated endocytic vesicle membrane  clathrin heavy chain binding  low-density lipoprotein particle  plasma lipoprotein particle clearance  plasma lipoprotein particle clearance  chylomicron remnant clearance  low-density lipoprotein particle clearance  low-density lipoprotein particle clearance  high-density lipoprotein particle clearance  endolysosome membrane  somatodendritic compartment  lipoprotein catabolic process  cholesterol homeostasis  cholesterol homeostasis  cholesterol homeostasis  identical protein binding  receptor complex  apical part of cell  viral entry into host cell  artery morphogenesis  positive regulation of inflammatory response  regulation of protein metabolic process  negative regulation of protein metabolic process  membrane organization  response to caloric restriction  negative regulation of astrocyte activation  cholesterol import  cholesterol import  cellular response to fatty acid  cellular response to low-density lipoprotein particle stimulus  receptor-mediated endocytosis involved in cholesterol transport  regulation of cholesterol metabolic process  amyloid-beta clearance  sorting endosome  amyloid-beta clearance by cellular catabolic process  negative regulation of microglial cell activation  positive regulation of lysosomal protein catabolic process  negative regulation of amyloid fibril formation  PCSK9-LDLR complex  
Ontology : EGO-EBIamyloid-beta binding  virus receptor activity  protease binding  low-density lipoprotein particle receptor activity  low-density lipoprotein particle receptor activity  low-density lipoprotein particle receptor activity  low-density lipoprotein particle receptor activity  calcium ion binding  protein binding  cell  lysosome  early endosome  late endosome  Golgi apparatus  plasma membrane  integral component of plasma membrane  clathrin-coated pit  lipid metabolic process  endocytosis  receptor-mediated endocytosis  receptor-mediated endocytosis  phagocytosis  long-term memory  cholesterol metabolic process  external side of plasma membrane  cell surface  cell surface  endosome membrane  positive regulation of gene expression  negative regulation of gene expression  positive regulation of triglyceride biosynthetic process  regulation of phosphatidylcholine catabolic process  phospholipid transport  membrane  basolateral plasma membrane  low-density lipoprotein particle binding  very-low-density lipoprotein particle receptor activity  intestinal cholesterol absorption  cholesterol transport  cholesterol transport  clathrin-coated endocytic vesicle membrane  clathrin heavy chain binding  low-density lipoprotein particle  plasma lipoprotein particle clearance  plasma lipoprotein particle clearance  chylomicron remnant clearance  low-density lipoprotein particle clearance  low-density lipoprotein particle clearance  high-density lipoprotein particle clearance  endolysosome membrane  somatodendritic compartment  lipoprotein catabolic process  cholesterol homeostasis  cholesterol homeostasis  cholesterol homeostasis  identical protein binding  receptor complex  apical part of cell  viral entry into host cell  artery morphogenesis  positive regulation of inflammatory response  regulation of protein metabolic process  negative regulation of protein metabolic process  membrane organization  response to caloric restriction  negative regulation of astrocyte activation  cholesterol import  cholesterol import  cellular response to fatty acid  cellular response to low-density lipoprotein particle stimulus  receptor-mediated endocytosis involved in cholesterol transport  regulation of cholesterol metabolic process  amyloid-beta clearance  sorting endosome  amyloid-beta clearance by cellular catabolic process  negative regulation of microglial cell activation  positive regulation of lysosomal protein catabolic process  negative regulation of amyloid fibril formation  PCSK9-LDLR complex  
Pathways : KEGGEndocytosis    Ovarian steroidogenesis    Bile secretion    Toxoplasmosis    Hepatitis C   
NDEx NetworkLDLR
Atlas of Cancer Signalling NetworkLDLR
Wikipedia pathwaysLDLR
Orthology - Evolution
OrthoDB3949
GeneTree (enSembl)ENSG00000130164
Phylogenetic Trees/Animal Genes : TreeFamLDLR
HOGENOMP01130
Homologs : HomoloGeneLDLR
Homology/Alignments : Family Browser (UCSC)LDLR
Gene fusions - Rearrangements
Fusion : MitelmanLDLR/C19orf38 [19p13.2/19p13.2]  
Fusion : MitelmanLDLR/DNM2 [19p13.2/19p13.2]  [t(19;19)(p13;p13)]  
Fusion : MitelmanLDLR/TNPO2 [19p13.2/19p13.2]  [t(19;19)(p13;p13)]  
Fusion : MitelmanPKN1/LDLR [19p13.12/19p13.2]  [t(19;19)(p13;p13)]  
Fusion PortalLDLR 19p13.2 C19orf38 19p13.2 LUAD
Fusion PortalLDLR 19p13.2 DNM2 19p13.2 HNSC
Fusion PortalLDLR 19p13.2 TNPO2 19p13.2 BRCA
Fusion PortalPKN1 19p13.12 LDLR 19p13.2 BRCA
Fusion : QuiverLDLR
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLDLR [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LDLR
dbVarLDLR
ClinVarLDLR
1000_GenomesLDLR 
Exome Variant ServerLDLR
ExAC (Exome Aggregation Consortium)ENSG00000130164
GNOMAD BrowserENSG00000130164
Varsome BrowserLDLR
Genetic variants : HAPMAP3949
Genomic Variants (DGV)LDLR [DGVbeta]
DECIPHERLDLR [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLDLR 
Mutations
ICGC Data PortalLDLR 
TCGA Data PortalLDLR 
Broad Tumor PortalLDLR
OASIS PortalLDLR [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLDLR  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DLDLR
Mutations and Diseases : HGMDLDLR
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
BioMutasearch LDLR
DgiDB (Drug Gene Interaction Database)LDLR
DoCM (Curated mutations)LDLR (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LDLR (select a term)
intoGenLDLR
Cancer3DLDLR(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM143890    606945   
Orphanet22639   
DisGeNETLDLR
MedgenLDLR
Genetic Testing Registry LDLR
NextProtP01130 [Medical]
TSGene3949
GENETestsLDLR
Target ValidationLDLR
Huge Navigator LDLR [HugePedia]
snp3D : Map Gene to Disease3949
BioCentury BCIQLDLR
ClinGenLDLR (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3949
Chemical/Pharm GKB GenePA227
Clinical trialLDLR
Miscellaneous
canSAR (ICR)LDLR (select the gene name)
DataMed IndexLDLR
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLDLR
EVEXLDLR
GoPubMedLDLR
iHOPLDLR
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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