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    LRP3 LDL receptor related protein 3 [ Homo sapiens (human) ]

    Gene ID: 4037, updated on 3-Apr-2024

    Summary

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    Official Symbol
    LRP3provided by HGNC
    Official Full Name
    LDL receptor related protein 3provided by HGNC
    Primary source
    HGNC:HGNC:6695
    See related
    Ensembl:ENSG00000130881 MIM:603159; AllianceGenome:HGNC:6695
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Involved in negative regulation of fat cell differentiation; positive regulation of osteoblast differentiation; and regulation of gene expression. Predicted to be located in clathrin-coated pit. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in ovary (RPKM 23.4), fat (RPKM 17.1) and 24 other tissues See more
    Orthologs
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    Genomic context

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    Location:
    19q13.11
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (33194330..33208864)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (35712967..35727506)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (33685236..33699770)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene WD repeat domain 88 Neighboring gene uncharacterized LOC124904691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14440 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33666856-33667620 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14442 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14443 Neighboring gene tRNA-Thr (anticodon AGT) 1-3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14444 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51179 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51187 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33698023-33698524 Neighboring gene solute carrier family 7 member 10 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:33723689-33723856 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_51216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33739547-33740048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10494 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33741253-33742136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33742137-33743019 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33764565-33765125 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33765149-33765716 Neighboring gene HNF1 motif-containing MPRA enhancer 13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33769447-33770004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33777434-33778421 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:33782467-33783050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:33784308-33785258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10495 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10496 Neighboring gene CEBPA divergent transcript Neighboring gene CCAAT enhancer binding protein alpha

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. The apolipoprotein receptor LRP3 compromises APP levels. Cuchillo-Ibañez I, et al. Alzheimers Res Ther, 2021 Nov 2. PMID 34727970, Free PMC Article
    2. cDNA cloning of a new low-density lipoprotein receptor-related protein and mapping of its gene (LRP3) to chromosome bands 19q12-q13. 2. Ishii H, et al. Genomics, 1998 Jul 1. PMID 9693042
    3. MicroRNA-4739 regulates osteogenic and adipocytic differentiation of immortalized human bone marrow stromal cells via targeting LRP3. Elsafadi M, et al. Stem Cell Res, 2017 Apr. PMID 28340487
    4. Chromosomal localization of human genes for the LDL receptor family member glycoprotein 330 (LRP2) and its associated protein RAP (LRPAP1). Korenberg JR, et al. Genomics, 1994 Jul 1. PMID 7959795
    5. Golgi-localizing, gamma-adaptin ear homology domain, ADP-ribosylation factor-binding (GGA) proteins interact with acidic dileucine sequences within the cytoplasmic domains of sorting receptors through their Vps27p/Hrs/STAM (VHS) domains. Takatsu H, et al. J Biol Chem, 2001 Jul 27. PMID 11390366

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The apolipoprotein receptor LRP3 compromises APP levels.
      Title: The apolipoprotein receptor LRP3 compromises APP levels.
    2. Low-density lipoprotein receptor-related protein 3 (-deficient cells showed impaired osteoblastic and enhanced adipocytic differentiation.
      Title: MicroRNA-4739 regulates osteogenic and adipocytic differentiation of immortalized human bone marrow stromal cells via targeting LRP3.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in negative regulation of fat cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of osteoblast differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in receptor-mediated endocytosis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in clathrin-coated pit IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    low-density lipoprotein receptor-related protein 3
    Names
    105 kDa low-density lipoprotein receptor-related protein
    CTD-2540B15.13
    LRP-3
    hLRp105

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_002333.4 → NP_002324.2  low-density lipoprotein receptor-related protein 3 precursor

      See identical proteins and their annotated locations for NP_002324.2

      Status: VALIDATED

      Source sequence(s)
      AB009462, AC008738, AK126750, BC007408, DA496540
      Consensus CDS
      CCDS12430.1
      UniProtKB/Swiss-Prot
      B3KQD6, B4DKF2, O75074
      UniProtKB/TrEMBL
      B7ZAJ9
      Related
      ENSP00000253193.6, ENST00000253193.9
      Conserved Domains (2) summary
      cd00041
      Location:43 → 156
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      cd00112
      Location:455 → 489
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      33194330..33208864
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005258945.2 → XP_005259002.1  low-density lipoprotein receptor-related protein 3 isoform X1

      UniProtKB/TrEMBL
      B7ZAJ9
      Conserved Domains (2) summary
      cd00041
      Location:43 → 156
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      cd00112
      Location:455 → 489
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      35712967..35727506
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054321029.1 → XP_054177004.1  low-density lipoprotein receptor-related protein 3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75074.2 GenPept UniProtKB/Swiss-Prot:O75074

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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