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

Gene ID: 950, updated on 3-Jan-2019

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

Genomic context

See SCARB2 in Genome Data Viewer
Location:
4q21.1
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (76158737..76213899, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (77079890..77135052, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ADP-ribosyltransferase 3 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 FunctionsWhat's a GeneRIF?

Phenotypes

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

NHGRI GWAS Catalog

Description
Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease.
NHGRI GWA Catalog
Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease.
NHGRI GWA Catalog

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

Pathways from BioSystems

  • Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Cargo recognition for clathrin-mediated endocytosis, organism-specific biosystemRecruitment of plasma membrane-localized cargo into clathrin-coated endocytic vesicles is mediated by interaction with a variety of clathrin-interacting proteins collectively called CLASPs (clathrin-...
  • Clathrin-mediated endocytosis, organism-specific biosystem (from REACTOME)
    Clathrin-mediated endocytosis, organism-specific biosystemClathrin-mediated endocytosis (CME) is one of a number of process that control the uptake of material from the plasma membrane, and leads to the formation of clathrin-coated vesicles (Pearse et al, 1...
  • Lysosome, organism-specific biosystem (from KEGG)
    Lysosome, organism-specific biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Lysosome, conserved biosystem (from KEGG)
    Lysosome, conserved biosystemLysosomes are membrane-delimited organelles in animal cells serving as the cell's main digestive compartment to which all sorts of macromolecules are delivered for degradation. They contain more than...
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystem (from WikiPathways)
    Primary Focal Segmental Glomerulosclerosis FSGS, organism-specific biosystemPrimary or idiopathic focal segmental glomerulosclerosis (FSGS) a cause of nephrotic syndrome in children and adolescents, as well as an important cause of end stage renal disease in adults. FSGS is ...
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

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
    4984..60146
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001204255.1NP_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, ENST00000264896.7
    Conserved Domains (1) summary
    pfam01130
    Location:28455
    CD36; CD36 family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    76158737..76213899 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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