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] See more...

Aliases for LRP12 Gene

Aliases for LRP12 Gene

  • LDL Receptor Related Protein 12 2 3 5
  • ST7 2 3 4
  • Low-Density Lipoprotein Receptor-Related Protein 12 3 4
  • Suppressor Of Tumorigenicity 7 Protein 3 4
  • LDLR-Related Protein 12 3 4
  • Low Density Lipoprotein Receptor-Related Protein 12 2
  • FLJ12929 2
  • MIG13A 3
  • LRP-12 4
  • LRP12 5

External Ids for LRP12 Gene

Previous GeneCards Identifiers for LRP12 Gene

  • GC00U916985
  • GC08M105570
  • GC08M100702
  • GC08M105501

Summaries for LRP12 Gene

Entrez Gene Summary for LRP12 Gene

  • 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]

GeneCards Summary for LRP12 Gene

LRP12 (LDL Receptor Related Protein 12) is a Protein Coding gene. Diseases associated with LRP12 include Oculopharyngodistal Myopathy 1 and Neuronal Intranuclear Inclusion Disease. Among its related pathways are Signaling by GPCR and Metabolism of fat-soluble vitamins. Gene Ontology (GO) annotations related to this gene include low-density lipoprotein particle receptor activity. An important paralog of this gene is LRP3.

UniProtKB/Swiss-Prot Summary for LRP12 Gene

  • Probable receptor, which may be involved in the internalization of lipophilic molecules and/or signal transduction. May act as a tumor suppressor.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LRP12 Gene

Genomics for LRP12 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LRP12 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J104585 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 609.4 +1.0 993 4.7 SP1 CREB1 GATAD2A HNRNPL PRDM10 TFE3 IKZF1 BACH1 TARDBP JUND LRP12 lnc-DPYS-4 DCSTAMP lnc-ZFPM2-2 DPYS
GH08J104621 Enhancer 1.3 Ensembl ENCODE dbSUPER 21.9 -33.5 -33477 3.4 ZNF512 LEF1 IKZF1 BACH1 JUND DDX20 MTA2 PKNOX1 ZNF24 POLR2A LRP12 piR-43166-020 piR-53063-254 ZFPM2
GH08J104642 Enhancer 1.2 FANTOM5 Ensembl ENCODE dbSUPER 20.6 -54.1 -54076 4.6 JUND ATF7 CBX3 EGR1 ZNF316 FOS FOSL1 NFIC ZNF592 ATF3 LRP12 DCSTAMP piR-53063-254 ZFPM2 ENSG00000283157
GH08J104616 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 14.1 -29.5 -29519 4.1 LEF1 IKZF1 BACH1 JUND DDX20 MTA2 PKNOX1 ZNF24 MTA1 NR2C1 LRP12 DCSTAMP piR-43166-020 piR-53063-254 ZFPM2
GH08J104664 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 14 -76.7 -76694 2.5 SP1 CREB1 PRDM10 ZNF629 LEF1 IKZF1 BACH1 JUND STAT3 MTA2 DCSTAMP LRP12 piR-53063-254 ENSG00000283157 ZFPM2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LRP12 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LRP12

Top Transcription factor binding sites by QIAGEN in the LRP12 gene promoter:
  • CUTL1
  • Hlf
  • HNF-3beta
  • POU2F1
  • POU2F1a
  • STAT1
  • STAT1alpha
  • STAT1beta
  • STAT2
  • STAT3

Genomic Locations for LRP12 Gene

Genomic Locations for LRP12 Gene
chr8:104,489,231-104,589,024
(GRCh38/hg38)
Size:
99,794 bases
Orientation:
Minus strand
chr8:105,501,459-105,601,252
(GRCh37/hg19)
Size:
99,794 bases
Orientation:
Minus strand

Genomic View for LRP12 Gene

Genes around LRP12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LRP12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LRP12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LRP12 Gene

Proteins for LRP12 Gene

  • Protein details for LRP12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y561-LRP12_HUMAN
    Recommended name:
    Low-density lipoprotein receptor-related protein 12
    Protein Accession:
    Q9Y561
    Secondary Accessions:
    • A8K137
    • B4DRQ2

    Protein attributes for LRP12 Gene

    Size:
    859 amino acids
    Molecular mass:
    94984 Da
    Quaternary structure:
    • May interact with RACK1, ZFYVE9 and NMRK2.

    Alternative splice isoforms for LRP12 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LRP12 Gene

Post-translational modifications for LRP12 Gene

  • Glycosylation at Asn75, Asn146, Asn284, Asn366, Asn409, and Asn441
  • Ubiquitination at Lys160 and Lys678
  • Modification sites at PhosphoSitePlus

Other Protein References for LRP12 Gene

No data available for DME Specific Peptides for LRP12 Gene

Domains & Families for LRP12 Gene

Gene Families for LRP12 Gene

Protein Domains for LRP12 Gene

InterPro:
Blocks:
  • CUB domain
  • Low density lipoprotein-receptor, class A
ProtoNet:

Suggested Antigen Peptide Sequences for LRP12 Gene

GenScript: Design optimal peptide antigens:
  • Suppressor of tumorigenicity 7 protein (LRP12_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y561

UniProtKB/Swiss-Prot:

LRP12_HUMAN :
  • Belongs to the LDLR family.
Family:
  • Belongs to the LDLR family.
genes like me logo Genes that share domains with LRP12: view

Function for LRP12 Gene

Molecular function for LRP12 Gene

UniProtKB/Swiss-Prot Function:
Probable receptor, which may be involved in the internalization of lipophilic molecules and/or signal transduction. May act as a tumor suppressor.

Phenotypes From GWAS Catalog for LRP12 Gene

Gene Ontology (GO) - Molecular Function for LRP12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005041 low-density lipoprotein particle receptor activity NAS 12809483
GO:0005515 protein binding IEA,IPI 12809483
genes like me logo Genes that share ontologies with LRP12: view
genes like me logo Genes that share phenotypes with LRP12: view

Human Phenotype Ontology for LRP12 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRP12

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for LRP12 Gene

Localization for LRP12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LRP12 Gene

Membrane. Single-pass type I membrane protein. Membrane, coated pit.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LRP12 gene
Compartment Confidence
plasma membrane 5
extracellular 2
mitochondrion 2
nucleus 2
cytoskeleton 1
endoplasmic reticulum 1
endosome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (2)
  • Nucleoli fibrillar center (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LRP12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005887 integral component of plasma membrane IDA 12809483
GO:0005905 clathrin-coated pit IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,NAS 9927190
genes like me logo Genes that share ontologies with LRP12: view

Pathways & Interactions for LRP12 Gene

genes like me logo Genes that share pathways with LRP12: view

Gene Ontology (GO) - Biological Process for LRP12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001764 neuron migration IDA 26639854
GO:0006897 endocytosis NAS 12809483
GO:0007165 signal transduction NAS 12809483
GO:0031175 neuron projection development IEA,IDA 26639854
GO:0040008 regulation of growth NAS 9927190
genes like me logo Genes that share ontologies with LRP12: view

No data available for SIGNOR curated interactions for LRP12 Gene

Drugs & Compounds for LRP12 Gene

No Compound Related Data Available

Transcripts for LRP12 Gene

mRNA/cDNA for LRP12 Gene

2 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LRP12

Alternative Splicing Database (ASD) splice patterns (SP) for LRP12 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b
SP1: - -
SP2: -
SP3: - -
SP4:

Relevant External Links for LRP12 Gene

GeneLoc Exon Structure for
LRP12

Expression for LRP12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LRP12 Gene

Protein differential expression in normal tissues from HIPED for LRP12 Gene

This gene is overexpressed in Liver (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LRP12 Gene



Protein tissue co-expression partners for LRP12 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LRP12

SOURCE GeneReport for Unigene cluster for LRP12 Gene:

Hs.600630

mRNA Expression by UniProt/SwissProt for LRP12 Gene:

Q9Y561-LRP12_HUMAN
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.

Evidence on tissue expression from TISSUES for LRP12 Gene

  • Nervous system(4.5)
  • Eye(4.1)
genes like me logo Genes that share expression patterns with LRP12: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for LRP12 Gene

Orthologs for LRP12 Gene

This gene was present in the common ancestor of animals.

Orthologs for LRP12 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LRP12 30 31
  • 99.69 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia LRP12 31
  • 93 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia LRP12 31
  • 92 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LRP12 30 31
  • 91.09 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LRP12 30 31
  • 90.22 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Lrp12 30 17 31
  • 86.32 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Lrp12 30
  • 85.31 (n)
Chicken
(Gallus gallus)
Aves LRP12 30 31
  • 82.77 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia LRP12 31
  • 85 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lrp12 30
  • 72.49 (n)
Zebrafish
(Danio rerio)
Actinopterygii lrp12 30 31
  • 68.43 (n)
OneToOne
wufc44e04 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG6553 31
  • 27 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea M03E7.4 31
  • 17 (a)
OneToMany
Species where no ortholog for LRP12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for LRP12 Gene

ENSEMBL:
Gene Tree for LRP12 (if available)
TreeFam:
Gene Tree for LRP12 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LRP12: view image

Paralogs for LRP12 Gene

Paralogs for LRP12 Gene

(3) SIMAP similar genes for LRP12 Gene using alignment to 2 proteins:

  • LRP12_HUMAN
  • E5RIW8_HUMAN
genes like me logo Genes that share paralogs with LRP12: view

Variants for LRP12 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LRP12 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
rs16871494 - p.Ser694Gly

Additional dbSNP identifiers (rs#s) for LRP12 Gene

Structural Variations from Database of Genomic Variants (DGV) for LRP12 Gene

Variant ID Type Subtype PubMed ID
esv2422460 CNV duplication 17116639
esv2445240 CNV deletion 19546169
nsv1115119 CNV deletion 24896259
nsv1132162 CNV deletion 24896259
nsv508522 CNV deletion 20534489
nsv831417 CNV loss 17160897

Variation tolerance for LRP12 Gene

Residual Variation Intolerance Score: 7.26% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.35; 53.75% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LRP12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LRP12

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LRP12 Gene

Disorders for LRP12 Gene

MalaCards: The human disease database

(5) MalaCards diseases for LRP12 Gene - From: OMIM, ClinVar, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
oculopharyngodistal myopathy 1
  • opdm1
neuronal intranuclear inclusion disease
  • niid
myopathy
  • muscular diseases
familial adult myoclonic epilepsy
  • adcme
ptosis
  • blepharoptosis
- elite association - COSMIC cancer census association via MalaCards
Search LRP12 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

LRP12_HUMAN
  • Oculopharyngodistal myopathy 1 (OPDM1) [MIM:164310]: A disease characterized by ptosis, external ophthalmoplegia and weakness of the masseter, facial, pharyngeal and distal limb muscles. OPDM1 inheritance can be autosomal dominant or autosomal recessive. {ECO:0000269 PubMed:31332380}. Note=The disease is caused by mutations affecting the gene represented in this entry. The causative mutation is a heterozygous trinucleotide repeat expansion (CGG) in the 5-prime untranslated region of the gene. {ECO:0000269 PubMed:31332380}.

Additional Disease Information for LRP12

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with LRP12: view

No data available for Genatlas for LRP12 Gene

Publications for LRP12 Gene

  1. ST7 is a novel low-density lipoprotein receptor-related protein (LRP) with a cytoplasmic tail that interacts with proteins related to signal transduction pathways. (PMID: 12809483) Battle MA … McCormick JJ (Biochemistry 2003) 2 3 4
  2. Cloning and characterization of a novel gene encoding a putative transmembrane protein with altered expression in some human transformed and tumor-derived cell lines. (PMID: 9927190) Qing J … McCormick JJ (Oncogene 1999) 3 4 23
  3. Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease. (PMID: 31332380) Ishiura H … Tsuji S (Nature genetics 2019) 3 4
  4. Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. (PMID: 22570617) Wiggs JL … Haines JL (PLoS genetics 2012) 3 41
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

Products for LRP12 Gene

Sources for LRP12 Gene