LDLR (low density lipoprotein receptor)

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LDLR (low density lipoprotein receptor)

Identity

Alias_symbol (synonym)	LDLCQ2
Other alias	FH
	FHC
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 19p13.2	LDLR 19p13.2 / DNM2 19p13.2	LDLR 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
Aliases	FH; FHC; 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 DataPortal	ENSG00000130164
TCGA cBioPortal	LDLR
AceView (NCBI)	LDLR
Genatlas (Paris)	LDLR
WikiGenes	3949
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)
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)
Consensus coding sequences : CCDS (NCBI)	LDLR
Cluster EST : Unigene	Hs.713981 [ NCBI ]
CGAP (NCI)	Hs.713981
Alternative Splicing Gallery	ENSG00000130164
Gene Expression	LDLR [ 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]
Genevestigator	Expression in : [tissues] [cell-lines] [cancer] [perturbations]
BioGPS (Tissue expression)	3949
GTEX Portal (Tissue expression)	LDLR
Human Protein Atlas	ENSG00000130164-LDLR [pathology] [cell] [tissue]
	Protein : pattern, domain, 3D structure
UniProt/SwissProt	P01130 [function] [subcellular_location] [family_and_domains] [pathology_and_biotech] [ptm_processing] [expression] [interaction]
NextProt	P01130 [Sequence] [Exons] [Medical] [Publications]
With graphics : InterPro	P01130
Splice isoforms : SwissVar	P01130
PhosPhoSitePlus	P01130
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 mutations	3949
Blocks (Seattle)	LDLR
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 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
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
Structural Biology KnowledgeBase	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
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
Superfamily	P01130
Human Protein Atlas [tissue]	ENSG00000130164-LDLR [tissue]
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
STRING (EMBL)	LDLR
ZODIAC	LDLR
	Ontologies - Pathways
QuickGO	P01130
Ontology : AmiGO	amyloid-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 intracellular lysosome early endosome late endosome Golgi apparatus plasma membrane integral component of plasma membrane clathrin-coated pit lipid metabolic process endocytosis receptor-mediated endocytosis 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 positive regulation of lipoprotein particle clearance 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 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 positive regulation of endocytosis viral entry into host cell 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 positive regulation of amyloid-beta clearance negative regulation of microglial cell activation positive regulation of lysosomal protein catabolic process negative regulation of amyloid fibril formation PCSK9-LDLR complex
Ontology : EGO-EBI	amyloid-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 intracellular lysosome early endosome late endosome Golgi apparatus plasma membrane integral component of plasma membrane clathrin-coated pit lipid metabolic process endocytosis receptor-mediated endocytosis 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 positive regulation of lipoprotein particle clearance 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 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 positive regulation of endocytosis viral entry into host cell 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 positive regulation of amyloid-beta clearance negative regulation of microglial cell activation positive regulation of lysosomal protein catabolic process negative regulation of amyloid fibril formation PCSK9-LDLR complex
Pathways : KEGG	Endocytosis Ovarian steroidogenesis Bile secretion Toxoplasmosis Hepatitis C
NDEx Network	LDLR
Atlas of Cancer Signalling Network	LDLR
Wikipedia pathways	LDLR
	Orthology - Evolution
OrthoDB	3949
GeneTree (enSembl)	ENSG00000130164
Phylogenetic Trees/Animal Genes : TreeFam	LDLR
HOVERGEN	P01130
HOGENOM	P01130
Homologs : HomoloGene	LDLR
Homology/Alignments : Family Browser (UCSC)	LDLR
	Gene fusions - Rearrangements
Fusion : Mitelman	LDLR/C19orf38 [19p13.2/19p13.2]
Fusion : Mitelman	LDLR/DNM2 [19p13.2/19p13.2] [t(19;19)(p13;p13)]
Fusion : Mitelman	LDLR/TNPO2 [19p13.2/19p13.2] [t(19;19)(p13;p13)]
Fusion : Mitelman	PKN1/LDLR [19p13.12/19p13.2] [t(19;19)(p13;p13)]
Fusion Portal	LDLR 19p13.2 C19orf38 19p13.2 LUAD
Fusion Portal	LDLR 19p13.2 DNM2 19p13.2 HNSC
Fusion Portal	LDLR 19p13.2 TNPO2 19p13.2 BRCA
Fusion Portal	PKN1 19p13.12 LDLR 19p13.2 BRCA
Fusion : Quiver	LDLR
	Polymorphisms : SNP and Copy number variants
NCBI Variation Viewer	LDLR [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)	LDLR
dbVar	LDLR
ClinVar	LDLR
1000_Genomes	LDLR
Exome Variant Server	LDLR
ExAC (Exome Aggregation Consortium)	ENSG00000130164
GNOMAD Browser	ENSG00000130164
Varsome Browser	LDLR
Genetic variants : HAPMAP	3949
Genomic Variants (DGV)	LDLR [DGVbeta]
DECIPHER	LDLR [patients] [syndromes] [variants] [genes]
CONAN: Copy Number Analysis	LDLR
	Mutations
ICGC Data Portal	LDLR
TCGA Data Portal	LDLR
Broad Tumor Portal	LDLR
OASIS Portal	LDLR [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMIC	LDLR [overview] [genome browser] [tissue] [distribution]
Mutations and Diseases : HGMD	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
BioMuta	search 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)
intoGen	LDLR
Cancer3D	LDLR(select the gene name)
Impact of mutations	[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
	Diseases
OMIM	143890 606945
Orphanet	22639
DisGeNET	LDLR
Medgen	LDLR
Genetic Testing Registry	LDLR
NextProt	P01130 [Medical]
TSGene	3949
GENETests	LDLR
Target Validation	LDLR
Huge Navigator	LDLR [HugePedia]
snp3D : Map Gene to Disease	3949
BioCentury BCIQ	LDLR
ClinGen	LDLR (curated)
	Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD	3949
Chemical/Pharm GKB Gene	PA227
Clinical trial	LDLR
	Miscellaneous
canSAR (ICR)	LDLR (select the gene name)
	Probes
	Litterature
PubMed	499 Pubmed reference(s) in Entrez
GeneRIFs	Gene References Into Functions (Entrez)
CoreMine	LDLR
EVEX	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

indexed on : Tue Nov 6 11:16:08 CET 2018

Home Genes Leukemias Solid Tumors Cancer-Prone Deep Insight Case Reports Journals Portal Teaching

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.

Atlas of Genetics and Cytogenetics in Oncology and Haematology

LDLR (low density lipoprotein receptor)

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

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