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    SCARB2 scavenger receptor class B member 2 [ Homo sapiens (human) ]

    Gene ID: 950, updated on 8-Jul-2021

    Summary

    Official Symbol
    SCARB2provided by HGNC
    Official Full Name
    scavenger receptor class B member 2provided by HGNC
    Primary source
    HGNC:HGNC:1665
    See related
    Ensembl:ENSG00000138760 MIM:602257
    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
    AMRF; EPM4; LGP85; CD36L2; HLGP85; LIMP-2; LIMPII; SR-BII
    Summary
    The protein encoded by this gene is a type III glycoprotein that is located primarily in limiting membranes of lysosomes and endosomes. Earlier studies in mice and rat suggested that this protein may participate in membrane transportation and the reorganization of endosomal/lysosomal compartment. The protein deficiency in mice was reported to impair cell membrane transport processes and cause pelvic junction obstruction, deafness, and peripheral neuropathy. Further studies in human showed that this protein is a ubiquitously expressed protein and that it is involved in the pathogenesis of HFMD (hand, foot, and mouth disease) caused by enterovirus-71 and possibly by coxsackievirus A16. Mutations in this gene caused an autosomal recessive progressive myoclonic epilepsy-4 (EPM4), also known as action myoclonus-renal failure syndrome (AMRF). Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2011]
    Expression
    Ubiquitous expression in brain (RPKM 74.6), prostate (RPKM 71.6) and 25 other tissues See more
    Orthologs
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    Genomic context

    See SCARB2 in Genome Data Viewer
    Location:
    4q21.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (76158737..76213824, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (77079890..77134977, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ADP-ribosyltransferase 3 (inactive) Neighboring gene ribosomal protein L36 pseudogene 8 Neighboring gene nucleoporin 54 Neighboring gene uncharacterized LOC105377286 Neighboring gene family with sequence similarity 47 member E Neighboring gene FAM47E-STBD1 readthrough Neighboring gene NFE2L2 motif-containing MPRA enhancer 290

    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?

    Phenotypes

    Associated conditions

    Description Tests
    Epilepsy, progressive myoclonic 4, with or without renal failure Compare labs
    Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease.
    GeneReviews: Not available
    Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease.
    GeneReviews: Not available

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-07-06)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-07-06)

    ClinGen Genome Curation Page

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Vpr vpr A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of scavenger receptor class B, member 2 (SCARB2) expression by HIV-1 Vpr in Vpr transduced macrophages PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cargo receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables chaperone binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables cholesterol binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables phosphatidylcholine binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables phosphatidylserine binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables scavenger receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables scavenger receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables scavenger receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables transmembrane signaling receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables virus receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in aminophospholipid transport ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein targeting to lysosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in protein targeting to lysosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein targeting to lysosome NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in receptor-mediated endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in receptor-mediated endocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in regulation of cellular carbohydrate catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of endosome organization TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in regulation of glucosylceramidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of lysosome organization TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in sensory perception of sound IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in viral entry into host cell IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in clathrin-coated endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in endocytic vesicle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in focal adhesion HDA PubMed 
    located_in integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in late endosome membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in lysosomal lumen ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in lysosomal membrane HDA PubMed 
    located_in lysosomal membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in membrane HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    lysosome membrane protein 2
    Names
    85 kDa lysosomal membrane sialoglycoprotein
    85 kDa lysosomal sialoglycoprotein scavenger receptor class B, member 2
    CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2 (lysosomal integral membrane protein II)
    CD36 antigen-like 2
    LIMP II
    lysosome membrane protein II

    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.

    Genomic

    1. NG_012054.1 RefSeqGene

      Range
      5059..60146
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001204255.2NP_001191184.1  lysosome membrane protein 2 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks three consecutive exons in the CDS, as compared to variant 1. The reading frame is not affected and the resulting isoform (2) lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      AC034139, AC110795, AK296519, AK313016
      Consensus CDS
      CCDS56335.1
      UniProtKB/Swiss-Prot
      Q14108
      Related
      ENSP00000399154.2, ENST00000452464.6
      Conserved Domains (1) summary
      pfam01130
      Location:28312
      CD36; CD36 family
    2. NM_005506.4NP_005497.1  lysosome membrane protein 2 isoform 1 precursor

      See identical proteins and their annotated locations for NP_005497.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC034139, AC110795, AK313016, BC035111
      Consensus CDS
      CCDS3577.1
      UniProtKB/Swiss-Prot
      Q14108
      UniProtKB/TrEMBL
      A0A024RDG6
      Related
      ENSP00000264896.2, ENST00000264896.8
      Conserved Domains (1) summary
      pfam01130
      Location:28455
      CD36; CD36 family

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

      Range
      76158737..76213824 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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