Human Gene LDLR (uc010xlo.2) Description and Page Index
  Description: Homo sapiens low density lipoprotein receptor (LDLR), transcript variant 4, mRNA.
RefSeq Summary (NM_001195800): The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. Low density lipoprotein (LDL) is normally bound at the cell membrane and taken into the cell ending up in lysosomes where the protein is degraded and the cholesterol is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis. At the same time, a reciprocal stimulation of cholesterol ester synthesis takes place. Mutations in this gene cause the autosomal dominant disorder, familial hypercholesterolemia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Sep 2010].
Transcript (Including UTRs)
   Position: hg19 chr19:11,200,038-11,244,505 Size: 44,468 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr19:11,200,225-11,241,992 Size: 41,768 Coding Exon Count: 16 

Page IndexSequence and LinksGenetic AssociationsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:11,200,038-11,244,505)mRNA (may differ from genome)Protein (692 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHuman Cortex Gene ExpressionLynxMGIOMIM
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LDLR
CDC HuGE Published Literature: LDLR
Positive Disease Associations: 1-Alkyl-2-acetylglycerophosphocholine Esterase , Achilles tendon xanthomas , Alzheimer's Disease , Atherosclerosis , carotid artery intima-media thickness , cholesterol , cholesterol, HDL cholesterol, LDL , cholesterol, LDL , Cholesterol, total , cirrhosis hepatitis C, chronic , Coronary Artery Disease , diabetes mellitus , differential plasma lipoprotein response to simvastatin , familial hypercholesterolemia. , hepatitis C , hypercholesterolemia of hypothyroidism , hyperlipidemia , hypertension , LDL cholesterol , Lipoproteins, LDL , mild familial hypercholesterolaemia , mild familial hypercholesterolemia , myocardial infarction (early onset) , normal serum cholesterol levels , obesity , plasma lipid and apolipoprotein levels
Related Studies:
  1. 1-Alkyl-2-acetylglycerophosphocholine Esterase
    Harald Grallert et al. European heart journal 2012, Eight genetic loci associated with variation in lipoprotein-associated phospholipase A2 mass and activity and coronary heart disease: meta-analysis of genome-wide association studies from five community-based studies., European heart journal. [PubMed 22003152]
    Levels of Lp-PLA2 mass and activity were associated with PLA2G7, the gene coding for this protein. Lipoprotein-associated phospholipase A2 activity was also strongly associated with genetic variants related to low-density lipoprotein cholesterol levels.
  2. Achilles tendon xanthomas
    Yamakawa K et al. 1991, Family studies of the LDL receptor gene of relatively severe hereditary hypercholesterolemia associated with Achilles tendon xanthomas., Human genetics. 1991 Mar;86(5):445-9. [PubMed 1673111]
  3. Alzheimer's Disease
    Bi, S. et al. 2001, Association between low-density lipoprotein receptor-related protein gene, butyrylcholinesterase gene and Alzheimer' s disease in Chinese., Chinese medical sciences journal. 2001 Jun;16(2):71-5. [PubMed 12901493]
    A positive correlation was found between LRP gene polymorphism and AD, but not between BchE gene polymorphism and AD in Chinese AD cases.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: LDLR
Diseases sorted by gene-association score: hypercholesterolemia, familial* (1260), homozygous familial hypercholesterolemia* (369), hypercholesterolemia, familial, 3* (283), ldlr-related familial hypercholesterolemia, autosomal dominant* (100), stomatitis (35), familial hyperlipidemia (17), aortic atherosclerosis (16), hypercholesterolemia, due to ligand-defective apo b (15), hypercholesterolemia, familial, autosomal recessive (15), atherosclerosis (15), xanthomatosis (14), defective apolipoprotein b-100 (13), hepatitis c (13), osteoporosis-pseudoglioma syndrome (10), hypobetalipoproteinemia (10), hyperlipoproteinemia, type iii (10), pinguecula (9), skin lipoma (7), hyperalphalipoproteinemia (7), common cold (7), lipoprotein glomerulopathy (7), smith-lemli-opitz syndrome (7), coronary artery disease (7), hepatitis (7), craniodiaphyseal dysplasia (6), arcus senilis (5), hypoalphalipoproteinemia (4), charcot-marie-tooth disease, type 4d (4), norum disease (3), lipid metabolism disorder (3), hepatitis c virus (3), cerebrovascular disease (3), vascular disease (2), artery disease (2), myocardial infarction (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 28.19 RPKM in Adrenal Gland
Total median expression: 314.14 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -68.22187-0.365 Picture PostScript Text
3' UTR -915.802513-0.364 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  Pfam Domains:
PF00057 - Low-density lipoprotein receptor domain class A
PF00058 - Low-density lipoprotein receptor repeat class B
PF07645 - Calcium-binding EGF domain
PF12661 - Human growth factor-like EGF
PF12662 - Complement Clr-like EGF-like
PF14670 - Coagulation Factor Xa inhibitory site

SCOP Domains:
50952 - Soluble quinoprotein glucose dehydrogenase
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
101898 - NHL repeat
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
57424 - LDL receptor-like module
57567 - Serine proterase inhibitors
57196 - EGF/Laminin
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on P01130-3
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  CS329402 - Sequence 3 from Patent WO2006004660.
CS329403 - Sequence 4 from Patent WO2006004660.
AK299038 - Homo sapiens cDNA FLJ50622 complete cds, highly similar to Low-density lipoprotein receptor precursor.
AK300313 - Homo sapiens cDNA FLJ50672 complete cds, highly similar to Low-density lipoprotein receptor precursor.
AK296312 - Homo sapiens cDNA FLJ50552 complete cds, highly similar to Low-density lipoprotein receptor precursor.
AK295612 - Homo sapiens cDNA FLJ54620 complete cds, highly similar to Low-density lipoprotein receptor precursor.
AB209409 - Homo sapiens mRNA for low density lipoprotein receptor precursor variant protein.
BC014514 - Homo sapiens low density lipoprotein receptor, mRNA (cDNA clone MGC:654 IMAGE:3542845), complete cds.
JD297445 - Sequence 278469 from Patent EP1572962.
JD554167 - Sequence 535191 from Patent EP1572962.
JD214881 - Sequence 195905 from Patent EP1572962.
AY114155 - Homo sapiens low density lipoprotein receptor (LDLR) mRNA, complete cds.
AB384938 - Synthetic construct DNA, clone: pF1KB4387, Homo sapiens LDLR gene for low-density lipoprotein receptor precursor, complete cds, without stop codon, in Flexi system.
DQ893879 - Synthetic construct Homo sapiens clone IMAGE:100008339; FLH165214.01L; RZPDo839H05157D low density lipoprotein receptor (familial hypercholesterolemia) (LDLR) gene, encodes complete protein.
BT007361 - Homo sapiens low density lipoprotein receptor (familial hypercholesterolemia) mRNA, complete cds.
BX648281 - Homo sapiens mRNA; cDNA DKFZp686J1411 (from clone DKFZp686J1411).
FW340025 - Screening.
CS329401 - Sequence 2 from Patent WO2006004660.
S40543 - low density lipoprotein receptor {exon 6} [human, mRNA Partial Mutant, 177 nt].
HM369522 - Homo sapiens mutant low density lipoprotein (LDLR) mRNA, partial sequence.
M28219 - Homo sapiens low density lipoprotein receptor (FH 10 mutant causing familial hypercholesterolemia) mRNA, 3' end.
S70123 - Homo sapiens low density lipoprotein receptor mRNA, partial cds.
JD264032 - Sequence 245056 from Patent EP1572962.
JD537121 - Sequence 518145 from Patent EP1572962.
JD399489 - Sequence 380513 from Patent EP1572962.
JD403606 - Sequence 384630 from Patent EP1572962.
JD244551 - Sequence 225575 from Patent EP1572962.
JD553924 - Sequence 534948 from Patent EP1572962.
JD244611 - Sequence 225635 from Patent EP1572962.
JD319854 - Sequence 300878 from Patent EP1572962.
JD118583 - Sequence 99607 from Patent EP1572962.
JD149610 - Sequence 130634 from Patent EP1572962.
JD062374 - Sequence 43398 from Patent EP1572962.
JD246085 - Sequence 227109 from Patent EP1572962.
JD470528 - Sequence 451552 from Patent EP1572962.
JD391024 - Sequence 372048 from Patent EP1572962.
JD231616 - Sequence 212640 from Patent EP1572962.
JD381808 - Sequence 362832 from Patent EP1572962.
JD372649 - Sequence 353673 from Patent EP1572962.
JD469883 - Sequence 450907 from Patent EP1572962.
JD071223 - Sequence 52247 from Patent EP1572962.
JD230361 - Sequence 211385 from Patent EP1572962.
JD411508 - Sequence 392532 from Patent EP1572962.
JD554955 - Sequence 535979 from Patent EP1572962.
JD396896 - Sequence 377920 from Patent EP1572962.
JD516030 - Sequence 497054 from Patent EP1572962.
JD287718 - Sequence 268742 from Patent EP1572962.
JD388592 - Sequence 369616 from Patent EP1572962.
JD075505 - Sequence 56529 from Patent EP1572962.
JD171896 - Sequence 152920 from Patent EP1572962.
JD440922 - Sequence 421946 from Patent EP1572962.
JD529352 - Sequence 510376 from Patent EP1572962.
JD169571 - Sequence 150595 from Patent EP1572962.
JD169572 - Sequence 150596 from Patent EP1572962.
JD306258 - Sequence 287282 from Patent EP1572962.
JD055135 - Sequence 36159 from Patent EP1572962.
JD125514 - Sequence 106538 from Patent EP1572962.
JD125515 - Sequence 106539 from Patent EP1572962.
JD395299 - Sequence 376323 from Patent EP1572962.
JD138436 - Sequence 119460 from Patent EP1572962.
JD138438 - Sequence 119462 from Patent EP1572962.
JD176482 - Sequence 157506 from Patent EP1572962.
JD066684 - Sequence 47708 from Patent EP1572962.
JD183978 - Sequence 165002 from Patent EP1572962.
JD092341 - Sequence 73365 from Patent EP1572962.
JD558978 - Sequence 540002 from Patent EP1572962.
JD404816 - Sequence 385840 from Patent EP1572962.
JD455354 - Sequence 436378 from Patent EP1572962.
JD266518 - Sequence 247542 from Patent EP1572962.
JD207409 - Sequence 188433 from Patent EP1572962.
JD445279 - Sequence 426303 from Patent EP1572962.
JD143828 - Sequence 124852 from Patent EP1572962.
JD510958 - Sequence 491982 from Patent EP1572962.
JD088815 - Sequence 69839 from Patent EP1572962.
JD268260 - Sequence 249284 from Patent EP1572962.
JD183418 - Sequence 164442 from Patent EP1572962.
JD357275 - Sequence 338299 from Patent EP1572962.
JD553156 - Sequence 534180 from Patent EP1572962.
JD511086 - Sequence 492110 from Patent EP1572962.
JD354072 - Sequence 335096 from Patent EP1572962.
JD269721 - Sequence 250745 from Patent EP1572962.
JD273802 - Sequence 254826 from Patent EP1572962.
JD166791 - Sequence 147815 from Patent EP1572962.
JD043147 - Sequence 24171 from Patent EP1572962.
JD117105 - Sequence 98129 from Patent EP1572962.
JD277616 - Sequence 258640 from Patent EP1572962.
JD103041 - Sequence 84065 from Patent EP1572962.
JD098671 - Sequence 79695 from Patent EP1572962.
JD318571 - Sequence 299595 from Patent EP1572962.
JD444542 - Sequence 425566 from Patent EP1572962.
JD444543 - Sequence 425567 from Patent EP1572962.
JD182725 - Sequence 163749 from Patent EP1572962.
JD531907 - Sequence 512931 from Patent EP1572962.
JD259010 - Sequence 240034 from Patent EP1572962.
JD274940 - Sequence 255964 from Patent EP1572962.
JD474058 - Sequence 455082 from Patent EP1572962.
JD058317 - Sequence 39341 from Patent EP1572962.
JD081452 - Sequence 62476 from Patent EP1572962.
JD196479 - Sequence 177503 from Patent EP1572962.
JD144149 - Sequence 125173 from Patent EP1572962.
JD195068 - Sequence 176092 from Patent EP1572962.
JD195069 - Sequence 176093 from Patent EP1572962.
JD472482 - Sequence 453506 from Patent EP1572962.
JD533106 - Sequence 514130 from Patent EP1572962.
JD178669 - Sequence 159693 from Patent EP1572962.
JD447054 - Sequence 428078 from Patent EP1572962.
JD292798 - Sequence 273822 from Patent EP1572962.
JD442741 - Sequence 423765 from Patent EP1572962.
JD377639 - Sequence 358663 from Patent EP1572962.
JD366411 - Sequence 347435 from Patent EP1572962.
JD168230 - Sequence 149254 from Patent EP1572962.
JD556890 - Sequence 537914 from Patent EP1572962.
JD183453 - Sequence 164477 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04144 - Endocytosis

BioCarta from NCI Cancer Genome Anatomy Project
h_fxrPathway - FXR and LXR Regulation of Cholesterol Metabolism
h_s1pPathway - SREBP control of lipid synthesis
h_LDLpathway - Low-density lipoprotein (LDL) pathway during atherogenesis

Reactome (by CSHL, EBI, and GO)

Protein P01130 (Reactome details) participates in the following event(s):

R-HSA-171122 LDL + LDLR => LDL:LDLR complex
R-HSA-174657 chylomicron remnant:apoE complex + LDLR => chylomicron remnant:apoE:LDLR complex
R-HSA-6784734 PCSK9 binds LDLR
R-HSA-171087 LDLR [endosome membrane] => LDLR [plasma membrane]
R-HSA-171106 LDLR:LDL complex => LDLR + LDL
R-HSA-174624 chylomicron remnant:apoE:LDLR complex => chylomicron remnant:apoE + LDLR
R-HSA-171141 LDL:LDLR complex [plasma membrane] => LDL:LDLR complex [clathrin-coated vesicle] (LDLRAP1-independent)
R-HSA-8863471 LDLR is bound by DAB2 and ARH
R-HSA-174706 chylomicron remnant:apoE:LDLR complex [plasma membrane] => chylomicron remnant:apoE:LDLR complex [clathrin-coated vesicle] (LDLRAP1-dependent)
R-HSA-6784735 PCSK9:LDLR bind to Clathrin
R-HSA-2424254 LDLR transports extracellular CR:atREs to cytosol
R-HSA-171059 LDLR:LDL complex [coated vesicle membrane] => LDLR:LDL complex [endosome membrane]
R-HSA-174808 chylomicron remnant:apoE:LDLR complex [coated vesicle membrane] => chylomicron remnant:apoE:LDLR complex [endosome membrane]
R-HSA-6784729 PCSK9:LDLR:Clathrin-coated vesicle transport from plasma membrane to endolysosome
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-8964038 LDL clearance
R-HSA-8964026 Chylomicron clearance
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-8964043 Plasma lipoprotein clearance
R-HSA-975634 Retinoid metabolism and transport
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-174824 Plasma lipoprotein assembly, remodeling, and clearance
R-HSA-2187338 Visual phototransduction
R-HSA-6806667 Metabolism of fat-soluble vitamins
R-HSA-199991 Membrane Trafficking
R-HSA-382551 Transport of small molecules
R-HSA-418594 G alpha (i) signalling events
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-5653656 Vesicle-mediated transport
R-HSA-388396 GPCR downstream signalling
R-HSA-1430728 Metabolism
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001195800, NP_001182729, P01130-3
UCSC ID: uc010xlo.2
RefSeq Accession: NM_001195800
Protein: P01130-3 CCDS: CCDS56084.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene LDLR:
hyperchol (Familial Hypercholesterolemia)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001195800.1
exon count: 16CDS single in 3' UTR: no RNA size: 4788
ORF size: 2079CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4174.00frame shift in genome: no % Coverage: 99.81
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.