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

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; 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

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_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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?

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.
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.
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.
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.
Knockdown LIMP2 inhibits colorectal cancer cells migration, invasion, and metastasis.
Title: Knockdown LIMP2 inhibits colorectal cancer cells migration, invasion, and metastasis.
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.
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.
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.
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.
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

Associated conditions

Description	Tests
Action myoclonus-renal failure syndrome MedGen: C0751779 OMIM: 254900 GeneReviews: SCARB2-Related Action Myoclonus - Renal Failure Syndrome	Compare labs

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 EBI GWAS CatalogPubMed
Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

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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

D4S2990 (e-PCR), detects polymorphism
- UniSTS:78887

D4S3271 (e-PCR)
- UniSTS:60714

D8S2279 (e-PCR)
- UniSTS:473907

A007G26 (e-PCR)
- UniSTS:3428

D1S1423 (e-PCR)
- UniSTS:149619

SHGC-50251 (e-PCR)
- UniSTS:76411

SHGC-86226 (e-PCR)
- UniSTS:104847

D16S325 (e-PCR)
- UniSTS:147089

SCARB2_2188 (e-PCR)
- UniSTS:280980

D4S2490E (e-PCR)
- UniSTS:150958

D4S2820 (e-PCR)
- UniSTS:6836

HSC0FA022 (e-PCR)
- UniSTS:41414

STS-D12676 (e-PCR)
- UniSTS:75474

SHGC-144424 (e-PCR)
- UniSTS:172242

SHGC-50473 (e-PCR)
- UniSTS:2034

SHGC-59239 (e-PCR)
- UniSTS:11258

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 more info	PubMed
located_in focal adhesion	HDA more info	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 more info	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 more info	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

NG_012054.2 RefSeqGene

Range

25708..80795

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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