Human Gene LRP12 (uc003yma.3) Description and Page Index
  Description: Homo sapiens low density lipoprotein receptor-related protein 12 (LRP12), transcript variant 1, mRNA.
RefSeq Summary (NM_013437): This gene encodes a member of the low-density lipoprotein receptor related protein family. The product of this gene is a transmembrane protein that is differentially expressed in many cancer cells. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2010].
Transcript (Including UTRs)
   Position: hg19 chr8:105,501,459-105,601,252 Size: 99,794 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr8:105,502,901-105,601,125 Size: 98,225 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:105,501,459-105,601,252)mRNA (may differ from genome)Protein (859 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: LRP12_HUMAN
DESCRIPTION: RecName: Full=Low-density lipoprotein receptor-related protein 12; Short=LRP-12; AltName: Full=Suppressor of tumorigenicity 7 protein; Flags: Precursor;
FUNCTION: Probable receptor, which may be involved in the internalization of lipophilic molecules and/or signal transduction. May act as a tumor suppressor.
SUBUNIT: May interact with GNB2L1, ZFYVE9 and NMRK2.
INTERACTION: P63244:GNB2L1; NbExp=2; IntAct=EBI-296693, EBI-296739; Q9NPI5:NMRK2; NbExp=2; IntAct=EBI-296693, EBI-514059; O95405:ZFYVE9; NbExp=2; IntAct=EBI-296693, EBI-296817;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein. Membrane, coated pit.
TISSUE SPECIFICITY: Widely expressed in heart, skeletal muscle, brain, lung, placenta and pancreas, but not in tissues consisting of a large number of epithelial cells, such as liver and kidney. Expressed at very low levels in a number of tumor-derived cell lines.
SIMILARITY: Belongs to the LDLR family.
SIMILARITY: Contains 2 CUB domains.
SIMILARITY: Contains 5 LDL-receptor class A domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LRP12
CDC HuGE Published Literature: LRP12
Positive Disease Associations: Benzodiazepines , Blood Coagulation Factors , Body Weight , C-Reactive Protein , Death, Sudden, Cardiac , Glaucoma , Hip , Intercellular Adhesion Molecule-1 , Myocardial Infarction , Waist-Hip Ratio
Related Studies:
  1. Benzodiazepines
    D E Adkins et al. Molecular psychiatry 2011, Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs., Molecular psychiatry. [PubMed 20195266]
  2. Blood Coagulation Factors
    Qiong Yang et al. BMC medical genetics 2007, Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903294]
    Using genome-wide association methodology, we have successfully identified a SNP in complete LD with a sequence variant previously shown to be strongly associated with factor VII, providing proof of principle for this approach. Further study of additional strongly associated SNPs and linked regions may identify novel variants that influence the inter-individual variability in hemostatic factors and hematological phenotypes.
  3. Body Weight
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
           more ... click here to view the complete list

-  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: 7.93 RPKM in Cells - Transformed fibroblasts
Total median expression: 135.36 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -49.00127-0.386 Picture PostScript Text
3' UTR -308.391442-0.214 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
  InterPro Domains: Graphical view of domain structure
IPR000859 - CUB
IPR023415 - LDLR_class-A_CS
IPR002172 - LDrepeatLR_classA_rpt

Pfam Domains:
PF00057 - Low-density lipoprotein receptor domain class A
PF00431 - CUB domain

SCOP Domains:
49854 - Spermadhesin, CUB domain
57424 - LDL receptor-like module

ModBase Predicted Comparative 3D Structure on Q9Y561
FrontTopSide
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 orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005041 low-density lipoprotein receptor activity
GO:0005515 protein binding

Biological Process:
GO:0001764 neuron migration
GO:0006897 endocytosis
GO:0006898 receptor-mediated endocytosis
GO:0007165 signal transduction
GO:0031175 neuron projection development
GO:0040008 regulation of growth

Cellular Component:
GO:0005887 integral component of plasma membrane
GO:0005905 clathrin-coated pit
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  LP896525 - Sequence 1389 from Patent EP3253886.
AB208957 - Homo sapiens mRNA for suppression of tumorigenicity variant protein.
BC032109 - Homo sapiens low density lipoprotein-related protein 12, mRNA (cDNA clone MGC:22991 IMAGE:4842797), complete cds.
AF166350 - Homo sapiens ST7 protein (ST7) mRNA, complete cds.
AK299374 - Homo sapiens cDNA FLJ55619 complete cds, highly similar to Low-density lipoprotein receptor-related protein 12 precursor.
AK289752 - Homo sapiens cDNA FLJ76215 complete cds, highly similar to Homo sapiens low density lipoprotein-related protein 12 (LRP12), mRNA.
DQ892323 - Synthetic construct clone IMAGE:100004953; FLH185255.01X; RZPDo839H01146D low density lipoprotein-related protein 12 (LRP12) gene, encodes complete protein.
DQ895525 - Synthetic construct Homo sapiens clone IMAGE:100009985; FLH185253.01L; RZPDo839H01145D low density lipoprotein-related protein 12 (LRP12) gene, encodes complete protein.
AF064841 - Homo sapiens map 13p13; 44cR from WI-8572 repeat region, complete sequence.
CU689274 - Synthetic construct Homo sapiens gateway clone IMAGE:100021977 5' read LRP12 mRNA.
BC017381 - Homo sapiens low density lipoprotein-related protein 12, mRNA (cDNA clone IMAGE:4070101).
AK126348 - Homo sapiens cDNA FLJ44376 fis, clone TRACH3034903, highly similar to Low-density lipoprotein receptor-related protein 12 precursor.
AK022991 - Homo sapiens cDNA FLJ12929 fis, clone NT2RP2004775.
JD284800 - Sequence 265824 from Patent EP1572962.
KJ902521 - Synthetic construct Homo sapiens clone ccsbBroadEn_11915 LRP12 gene, encodes complete protein.
JD093832 - Sequence 74856 from Patent EP1572962.
JD534694 - Sequence 515718 from Patent EP1572962.
JD292505 - Sequence 273529 from Patent EP1572962.
JD486221 - Sequence 467245 from Patent EP1572962.
JD557087 - Sequence 538111 from Patent EP1572962.
JD322667 - Sequence 303691 from Patent EP1572962.
JD250697 - Sequence 231721 from Patent EP1572962.
CR749434 - Homo sapiens mRNA; cDNA DKFZp781F1053 (from clone DKFZp781F1053).

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y561 (Reactome details) participates in the following event(s):

R-HSA-2404131 LRPs transport extracellular CR:atREs:HSPG:apoE to cytosol
R-HSA-975634 Retinoid metabolism and transport
R-HSA-2187338 Visual phototransduction
R-HSA-6806667 Metabolism of fat-soluble vitamins
R-HSA-418594 G alpha (i) signalling events
R-HSA-196854 Metabolism of vitamins and cofactors
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: A8K137, B4DRQ2, LRP12_HUMAN, NM_013437, NP_038465, Q9Y561, ST7
UCSC ID: uc003yma.3
RefSeq Accession: NM_013437
Protein: Q9Y561 (aka LRP12_HUMAN or LR12_HUMAN)
CCDS: CCDS6303.1, CCDS47907.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_013437.4
exon count: 7CDS single in 3' UTR: no RNA size: 4149
ORF size: 2580CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5360.00frame shift in genome: no % Coverage: 100.00
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.