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

Gene ID: 950, updated on 14-Nov-2024

Summary

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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; AllianceGenome:HGNC:1665
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
mouse all
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Genomic context

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See SCARB2 in Genome Data Viewer
Location:
4q21.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (76158737..76234532, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (79499409..79554492, complement)
RS_2024_09 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 NANOG hESC enhancer GRCh37_chr4:77016693-77017194 Neighboring gene nucleoporin 54 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21626 Neighboring gene uncharacterized LOC124900718 Neighboring gene NANOG hESC enhancer GRCh37_chr4:77075501-77076330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15485 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21628 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:77134378-77134782 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:77155049-77155925 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 Neighboring gene starch binding domain 1

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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Related articles in PubMed

  1. SCARB2/LIMP-2 Regulates IFN Production of Plasmacytoid Dendritic Cells by Mediating Endosomal Translocation of TLR9 and Nuclear Translocation of IRF7. Guo H, et al. J Immunol, 2015 May 15. PMID 25862818, Free PMC Article
  2. The role of SCARB2 as susceptibility factor in Parkinson's disease. Hopfner F, et al. Mov Disord, 2013 Apr. PMID 23408458
  3. Human SCARB2 transgenic mice as an infectious animal model for enterovirus 71. Lin YW, et al. PLoS One, 2013. PMID 23451246, Free PMC Article
  4. Association study of rs6812193 polymorphism with Parkinson's disease in a Greek population. Kalinderi K, et al. Neurosci Lett, 2013 Apr 29. PMID 23473716
  5. Transgenic mouse model for the study of enterovirus 71 neuropathogenesis. Fujii K, et al. Proc Natl Acad Sci U S A, 2013 Sep 3. PMID 23959904, Free PMC Article

See all (139) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SCARB2 associates with tumor-infiltrating neutrophils and predicts poor prognosis in breast cancer.
    Title: SCARB2 associates with tumor-infiltrating neutrophils and predicts poor prognosis in breast cancer.
  2. Enterovirus A71 does not meet the uncoating receptor SCARB2 at the cell surface.
    Title: Enterovirus A71 does not meet the uncoating receptor SCARB2 at the cell surface.
  3. Lysosomal membrane proteins LAMP1 and LIMP2 are segregated in the Golgi apparatus independently of their clathrin adaptor binding motif.
    Title: Lysosomal membrane proteins LAMP1 and LIMP2 are segregated in the Golgi apparatus independently of their clathrin adaptor binding motif.
  4. SCARB2 drives hepatocellular carcinoma tumor initiating cells via enhanced MYC transcriptional activity.
    Title: SCARB2 drives hepatocellular carcinoma tumor initiating cells via enhanced MYC transcriptional activity.
  5. Knockdown LIMP2 inhibits colorectal cancer cells migration, invasion, and metastasis.
    Title: Knockdown LIMP2 inhibits colorectal cancer cells migration, invasion, and metastasis.
  6. The effects of SCARB2 and SELPLG gene polymorphisms on EV71 infection in hand, foot and mouth disease.
    Title: The effects of SCARB2 and SELPLG gene polymorphisms on EV71 infection in hand, foot and mouth disease.
  7. Human SCARB2 Acts as a Cellular Associator for Helping Coxsackieviruses A10 Infection.
    Title: Human SCARB2 Acts as a Cellular Associator for Helping Coxsackieviruses A10 Infection.
  8. LIMP-2 enhances cancer stem-like cell properties by promoting autophagy-induced GSK3beta degradation in head and neck squamous cell carcinoma.
    Title: LIMP-2 enhances cancer stem-like cell properties by promoting autophagy-induced GSK3β degradation in head and neck squamous cell carcinoma.
  9. LIMP2 gene, evolutionarily conserved regulation by TFE3, relieves lysosomal stress induced by cholesterol.
    Title: LIMP2 gene, evolutionarily conserved regulation by TFE3, relieves lysosomal stress induced by cholesterol.
  10. Relationship between polymorphism of receptor SCARB2 gene and clinical severity of enterovirus-71 associated hand-foot-mouth disease.
    Title: Relationship between polymorphism of receptor SCARB2 gene and clinical severity of enterovirus-71 associated hand-foot-mouth disease.
Submit: New GeneRIF Correction See all GeneRIFs (74)

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

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

EBI GWAS Catalog

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

HIV-1 interactions

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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 PubChem

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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 cargo receptor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 protein-folding chaperone binding IEA
Inferred from Electronic Annotation
more info
  
enables scavenger receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
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 endosome to plasma membrane protein transport 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
  
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
  
involved_in receptor-mediated endocytosis ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in regulation of 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 glucosylceramide catabolic process TAS
Traceable Author Statement
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 symbiont 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
  
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 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 
is_active_in lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
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

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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)

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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_012054.2 RefSeqGene

    Range
    25708..80795
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    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:28 → 312
    CD36; CD36 family

  2. NM_005506.4 → NP_005497.1  lysosome membrane protein 2 isoform 1

    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
    B4DKD8, E7EM68, Q14108, Q53Y63
    UniProtKB/TrEMBL
    A0A1W2PS43
    Related
    ENSP00000264896.2, ENST00000264896.8
    Conserved Domains (1) summary
    pfam01130
    Location:28 → 455
    CD36; CD36 family

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    76158737..76234532 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416429.1 → XP_047272385.1  lysosome membrane protein 2 isoform X1

    UniProtKB/TrEMBL
    A0A1W2PRF6
    Related
    ENSP00000492288.1, ENST00000638295.1

  2. XM_047416430.1 → XP_047272386.1  lysosome membrane protein 2 isoform X1

    UniProtKB/TrEMBL
    A0A1W2PRF6

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    79499409..79554492 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q14108.2 GenPept UniProtKB/Swiss-Prot:Q14108

Gene LinkOut

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

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