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

Gene ID: 53353, updated on 2-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
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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 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)

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

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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