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    LRP1B LDL receptor related protein 1B [ Homo sapiens (human) ]

    Gene ID: 53353, updated on 27-Nov-2024

    Summary

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    Official Symbol
    LRP1Bprovided by HGNC
    Official Full Name
    LDL receptor related protein 1Bprovided by HGNC
    Primary source
    HGNC:HGNC:6693
    See related
    Ensembl:ENSG00000168702 MIM:608766; AllianceGenome:HGNC:6693
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LRP-1B; LRPDIT; LRP-DIT
    Summary
    This gene encodes a member of the low density lipoprotein (LDL) receptor family. These receptors play a wide variety of roles in normal cell function and development due to their interactions with multiple ligands. Disruption of this gene has been reported in several types of cancer. [provided by RefSeq, Jun 2016]
    Expression
    Biased expression in brain (RPKM 3.0), thyroid (RPKM 1.8) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRP1B in Genome Data Viewer
    Location:
    2q22.1-q22.2
    Exon count:
    92
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (140231423..142131016, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (140677183..142576386, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (140988992..142888585, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene MT-ND1 pseudogene 27 Neighboring gene MT-ND2 pseudogene 19 Neighboring gene NANOG hESC enhancer GRCh37_chr2:141183814-141184333 Neighboring gene NANOG hESC enhancer GRCh37_chr2:141187724-141188253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11988 Neighboring gene microRNA 7157 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:141554981-141556180 Neighboring gene COPRS pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr2:141650697-141651249 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:141651395-141652594 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:141662649-141663385 Neighboring gene NANOG hESC enhancer GRCh37_chr2:141685795-141686296 Neighboring gene MPRA-validated peak3885 silencer Neighboring gene LRRC57 pseudogene 1 Neighboring gene MPRA-validated peak3886 silencer Neighboring gene MPRA-validated peak3887 silencer Neighboring gene RNA, U6 small nuclear 904, pseudogene Neighboring gene ribosomal protein S16 pseudogene 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:142213461-142214002 Neighboring gene uncharacterized LOC105373649 Neighboring gene uncharacterized LOC124906079 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:142327748-142328386 Neighboring gene uncharacterized LOC107985779 Neighboring gene uncharacterized LOC105373648 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:142888453-142889652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16597 Neighboring gene uncharacterized LOC105373651 Neighboring gene UBE2V1 pseudogene 14

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Antitumor immunity and prognosis value elicited by FAT3 and LRP1B co-mutation in endometrial cancer.
      Title: Antitumor immunity and prognosis value elicited by FAT3 and LRP1B co-mutation in endometrial cancer.
    2. LDL Receptor-Related Protein 1B Polymorphisms Associated with Increased Risk of Lymph Node Metastasis in Oral Cancer Group with Diabetes Mellitus.
      Title: LDL Receptor-Related Protein 1B Polymorphisms Associated with Increased Risk of Lymph Node Metastasis in Oral Cancer Group with Diabetes Mellitus.
    3. LRP1B-a prognostic marker in tubo-ovarian high-grade serous carcinoma.
      Title: LRP1B-a prognostic marker in tubo-ovarian high-grade serous carcinoma.
    4. Loss of LRP1B expression drives acquired chemo and radio-resistance in HPV-positive head and neck cancer.
      Title: Loss of LRP1B expression drives acquired chemo and radio-resistance in HPV-positive head and neck cancer.
    5. MicroRNA-196a-5p targeting LRP1B modulates phenotype of thyroid carcinoma cells.
      Title: MicroRNA-196a-5p targeting LRP1B modulates phenotype of thyroid carcinoma cells.
    6. Association between the LRP1B and APOE loci and the development of Parkinson's disease dementia.
      Title: Association between the LRP1B and APOE loci and the development of Parkinson's disease dementia.
    7. Integrative analysis of the proteome and transcriptome in gastric cancer identified LRP1B as a potential biomarker.
      Title: Integrative analysis of the proteome and transcriptome in gastric cancer identified LRP1B as a potential biomarker.
    8. Analysis of copy number alterations in bladder cancer stem cells revealed a prognostic role of LRP1B.
      Title: Analysis of copy number alterations in bladder cancer stem cells revealed a prognostic role of LRP1B.
    9. LRP1B mutation associates with increased tumor mutation burden and inferior prognosis in liver hepatocellular carcinoma.
      Title: LRP1B mutation associates with increased tumor mutation burden and inferior prognosis in liver hepatocellular carcinoma.
    10. Downregulation of Low-density lipoprotein receptor-related protein 1B (LRP1B) inhibits the progression of hepatocellular carcinoma cells by activating the endoplasmic reticulum stress signaling pathway.
      Title: Downregulation of Low-density lipoprotein receptor-related protein 1B (LRP1B) inhibits the progression of hepatocellular carcinoma cells by activating the endoplasmic reticulum stress signaling pathway.
    Submit: New GeneRIF Correction See all GeneRIFs (45)

    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

    EBI GWAS Catalog

    Description
    A genome screen of successful aging without cognitive decline identifies LRP1B by haplotype analysis.
    EBI GWAS Catalog
    Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
    EBI GWAS Catalog
    Gene-Smoking Interactions Identify Several Novel Blood Pressure Loci in the Framingham Heart Study.
    EBI GWAS Catalog
    Genome-wide association identifies ATOH7 as a major gene determining human optic disc size.
    EBI GWAS Catalog
    Genome-wide association study of chronic periodontitis in a general German population.
    EBI GWAS Catalog
    Genome-wide association study on dimethylarginines reveals novel AGXT2 variants associated with heart rate variability but not with overall mortality.
    EBI GWAS Catalog
    Genome-wide association study to identify single nucleotide polymorphisms (SNPs) associated with the development of erectile dysfunction in African-American men after radiotherapy for prostate cancer.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog
    Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables low-density lipoprotein particle receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in receptor-mediated endocytosis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of receptor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    low-density lipoprotein receptor-related protein 1B
    Names
    LRP-deleted in tumors
    low density lipoprotein receptor related protein-deleted in tumor
    low density lipoprotein receptor-related protein 1B
    low density lipoprotein-related protein 1B (deleted in tumors)

    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.

    Genomic

    1. NG_051023.1 RefSeqGene

      Range
      6448..1906041
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018557.3 → NP_061027.2  low-density lipoprotein receptor-related protein 1B precursor

      See identical proteins and their annotated locations for NP_061027.2

      Status: REVIEWED

      Source sequence(s)
      AC010740, AC012353, AC068195, AC068287, AC073319, AC087056, AC092156, AC092575, AC093039, AC108036, AC110087, AC117947
      Consensus CDS
      CCDS2182.1
      UniProtKB/Swiss-Prot
      Q8WY29, Q8WY30, Q8WY31, Q9NZR2
      Related
      ENSP00000374135.3, ENST00000389484.8
      Conserved Domains (9) summary
      smart00192
      Location:926 → 958
      LDLa; Low-density lipoprotein receptor domain class A
      smart00135
      Location:1947 → 1987
      LY; Low-density lipoprotein-receptor YWTD domain
      smart00179
      Location:2968 → 2998
      EGF_CA; Calcium-binding EGF-like domain
      cd00112
      Location:3476 → 3510
      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 ...
      cd05819
      Location:285 → 321
      NHL; NHL repeat [structural motif]
      pfam00058
      Location:2008 → 2048
      Ldl_recept_b; Low-density lipoprotein receptor repeat class B
      pfam12662
      Location:2948 → 2971
      cEGF; Complement Clr-like EGF-like
      pfam14670
      Location:3277 → 3313
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl18310
      Location:282 → 459
      NHL; NHL repeat unit of beta-propeller proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      140231423..142131016 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004341.2 → XP_016859830.1  low-density lipoprotein receptor-related protein 1B isoform X1

    2. XM_017004342.1 → XP_016859831.1  low-density lipoprotein receptor-related protein 1B isoform X3

    3. XM_047444771.1 → XP_047300727.1  low-density lipoprotein receptor-related protein 1B isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      140677183..142576386 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054342572.1 → XP_054198547.1  low-density lipoprotein receptor-related protein 1B isoform X1

    2. XM_054342574.1 → XP_054198549.1  low-density lipoprotein receptor-related protein 1B isoform X3

    3. XM_054342573.1 → XP_054198548.1  low-density lipoprotein receptor-related protein 1B isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NZR2.2 GenPept UniProtKB/Swiss-Prot:Q9NZR2

    Gene LinkOut

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

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