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    LAMP1 lysosomal associated membrane protein 1 [ Homo sapiens (human) ]

    Gene ID: 3916, updated on 17-Jun-2024

    Summary

    Official Symbol
    LAMP1provided by HGNC
    Official Full Name
    lysosomal associated membrane protein 1provided by HGNC
    Primary source
    HGNC:HGNC:6499
    See related
    Ensembl:ENSG00000185896 MIM:153330; AllianceGenome:HGNC:6499
    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
    LAMPA; CD107a; LGP120
    Summary
    The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may also play a role in tumor cell metastasis. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in kidney (RPKM 123.3), thyroid (RPKM 98.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See LAMP1 in Genome Data Viewer
    Location:
    13q34
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (113297239..113323672)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (112550907..112577228)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (113951554..113977987)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene cullin 4A Neighboring gene microRNA 8075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113928297-113928796 Neighboring gene Sharpr-MPRA regulatory region 2925 Neighboring gene lactate dehydrogenase B pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113945996-113946505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:113946506-113947014 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8037 Neighboring gene Sharpr-MPRA regulatory region 10208 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:113959050-113959215 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113967994-113968742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:113968743-113969490 Neighboring gene growth hormone regulated TBC protein 1 Neighboring gene MAGE-like protein 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:114003074-114003239 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114003888-114004548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:114004549-114005209 Neighboring gene GRTP1 antisense RNA 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Ab-dependent activation of NK cells to upregulate the expression of CD107a is most robust when the NK cells are stimulated with HIV-1 gp120-coated primary T cells in the presence of HIV-1 infected plasma PubMed
    env HIV-1 gp120 co-localizes with LAMP-1 in human plasmacytoid dendritic cells PubMed
    Envelope surface glycoprotein gp160, precursor env HIV-1 Env co-localizes with LAMP1 in lysosomes PubMed
    env LAMP1 localizes to endosome compartments and is incorporated into the viral envelope of macrophage-derived HIV-1 particles PubMed
    Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 mutants W614A, S615A, N616A, and S618A downregulates the cellular surface expression of CD107a on NK-cells PubMed
    Nef nef HIV-1 Nef sequesters HLA-I A2 and co-localizes with CD63 and LAMP1 markers in late endosomes and lysosomes PubMed
    nef Both HIV-1 Nef and Vpu downregulate the cell surface expression of lysosomal-associated membrane protein 1 (CD107a) PubMed
    nef The proportion of HIV-1 Nef-specific CD8+ T cells endowed with TNF-alpha+, IFN-gamma+, CD107a+, and MIP-1beta+ is significantly higher in patients with the lowest virus set point than those with the highest virus set point PubMed
    nef HIV-1 Nef co-localizes with CXCR4, AIP4, NEDD4, CD63/LAMP-1-positive vesicles, and HRS/VPS27-positive ESCRT-0 structures in HeLa cells PubMed
    Pr55(Gag) gag Co-localization of HIV-1 Gag virus-like particles in THP-1/CD169YF cells is reduced within CD81+ compartments, but enhanced within CD63+ or LAMP1+ compartments PubMed
    gag The proportion of HIV-1 Gag-specific CD8+ T cells endowed with TNF-alpha+, IFN-gamma+, CD107A+, and MIP-1beta+ is significantly higher in patients with the lowest virus set point than those with the highest virus set point PubMed
    gag LAMP-mediated upregulation of HIV-1 LAMP-Gag fusion protein expression is dependent on the LAMP luminal domain, leading to induce LAMP-Gag secretion through exosomes PubMed
    gag In human macrophages, HIV-1 Gag proteins co-localize with MHC II (HLA-DR), CD63, and Lamp1 in MHC II compartments PubMed
    gag HIV-1 Gag co-localizes with Rab7-, Rab9-, and LAMP1-containing membranes at cytoplasmic and juxtanuclear sites in Staufen1-depleted cells PubMed
    gag HIV-1 Gag and viral RNA co-localize with LAMP1 in lysosomes PubMed
    gag Gag myristoylation is important for the co-trafficking of HIV-1 RNA and Gag on LAMP-1+ membranes. Gag nucleocapsid mutations lead to a loss of colocalization between LAMP-1 and HIV-1 RNA or Gag PubMed
    gag HIV-1 RNA is distributed throughout the cytoplasm in a punctate pattern, at the plasma membrane , and partially co-localizes with both Gag and LAMP-1 in the perinuclear region PubMed
    Tat tat HIV-1 Tat upregulates LAMP1 on the surface of primary astrocytes, which is a measurement for lysosomal exocytosis PubMed
    Vpr vpr HIV-1 YU-2 or ADA Vpr inhibits LAMP1 recruitment to and maturation of phagosomes in primary human macrophages PubMed
    vpr HIV-1 Vpr abrogates co-localization of LAMP1 with HIV-1 MA (p17) (lysosomal targeting) in monocyte-derived macropaphages PubMed
    vpr HIV-1 Vpr impairs NK cell function through cytokine dysregulation, including diminshed expression of CD107a, reduced production of IFN-gamma, differential regulation of IL-12 and TGF-beta, and activation of the Smad3 signalling pathway PubMed
    Vpu vpu Both HIV-1 Nef and Vpu downregulate the cell surface expression of lysosomal-associated membrane protein 1 (CD107a) PubMed
    vpu Expression of HIV-1 Vpu induces co-localization of tetherin with early endosome protein EEA-1 or late endosome protein LAMP-1 PubMed
    capsid gag HIV-1 CA-stimulated CD8+ T cells upregulate CD107 expression compared to unstimulated cells PubMed
    gag In human macrophages, HIV-1 Capsid (p24) co-localizes with MHC II (HLA-DR), CD63, and Lamp1 in MHC II compartments PubMed
    matrix gag HIV-1 MA (p17) colocalizes with LAMP1 (lysosomal targeting) in the absense of Vpr in monocyte-derived macrophages PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ion channel inhibitor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables virus receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in autolysosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in autophagosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in azurophil granule membrane TAS
    Traceable Author Statement
    more info
     
    located_in cytolytic granule membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in ficolin-1-rich granule membrane TAS
    Traceable Author Statement
    more info
     
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    colocalizes_with lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in melanosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane HDA PubMed 
    located_in multivesicular body IEA
    Inferred from Electronic Annotation
    more info
     
    located_in perinuclear region of cytoplasm IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in phagolysosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in sarcolemma IEA
    Inferred from Electronic Annotation
    more info
     
    located_in synaptic vesicle IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    lysosome-associated membrane glycoprotein 1
    Names
    CD107 antigen-like family member A
    LAMP-1
    lysosome-associated membrane protein 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_005561.4NP_005552.3  lysosome-associated membrane glycoprotein 1 precursor

      See identical proteins and their annotated locations for NP_005552.3

      Status: REVIEWED

      Source sequence(s)
      AL136221
      Consensus CDS
      CCDS41909.1
      UniProtKB/Swiss-Prot
      B4DWL3, P11279, Q8WU33, Q96I40, Q9BRD2, Q9NP13
      Related
      ENSP00000333298.4, ENST00000332556.5
      Conserved Domains (2) summary
      cd12087
      Location:381411
      TM_EGFR-like; Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases
      pfam01299
      Location:221365
      Lamp; Lysosome-associated membrane glycoprotein (Lamp)

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      113297239..113323672
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047430302.1XP_047286258.1  lysosome-associated membrane glycoprotein 1 isoform X2

      UniProtKB/TrEMBL
      B3KRY3
    2. XM_011537494.3XP_011535796.1  lysosome-associated membrane glycoprotein 1 isoform X1

      Conserved Domains (1) summary
      cd12087
      Location:362392
      TM_EGFR-like; Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      112550907..112577228
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374518.1XP_054230493.1  lysosome-associated membrane glycoprotein 1 isoform X1