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    SCARF2 scavenger receptor class F member 2 [ Homo sapiens (human) ]

    Gene ID: 91179, updated on 11-Apr-2024

    Summary

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    Official Symbol
    SCARF2provided by HGNC
    Official Full Name
    scavenger receptor class F member 2provided by HGNC
    Primary source
    HGNC:HGNC:19869
    See related
    Ensembl:ENSG00000244486 MIM:613619; AllianceGenome:HGNC:19869
    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
    NSR1; SREC2; VDEGS; SREC-II; SRECRP-1
    Summary
    The protein encoded by this gene is similar to SCARF1/SREC-I, a scavenger receptor protein that mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). This protein has only little activity of internalizing modified low density lipoproteins (LDL), but it can interact with SCARF1 through its extracellular domain. The association of this protein with SCARF1 is suppressed by the presence of scavenger ligands. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in fat (RPKM 3.8), prostate (RPKM 3.4) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    22q11.21
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (20424584..20437825, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (20828870..20842097, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (20778874..20792112, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20747551-20748540 Neighboring gene zinc finger protein 74 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62654 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62657 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:20764690-20764912 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62670 Neighboring gene VISTA enhancer hs1620 Neighboring gene RNA, U6 small nuclear 225, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr22:20783264-20783430 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20784487-20785326 Neighboring gene uncharacterized LOC107985588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20795983-20796484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20796485-20796984 Neighboring gene kelch like family member 22 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62725 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62734 Neighboring gene KLHL12 pseudogene 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
    • 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. Two novel variants in SCARF2 gene underlie van den Ende-Gupta syndrome. Karaer D, et al. Am J Med Genet A, 2022 Jun. PMID 35224863
    2. Sclerocornea in a patient with van den Ende-Gupta syndrome homozygous for a SCARF2 microdeletion. Migliavacca MP, et al. Am J Med Genet A, 2014 May. PMID 24478002, Free PMC Article
    3. Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome. Anastasio N, et al. Am J Hum Genet, 2010 Oct 8. PMID 20887961, Free PMC Article
    4. Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome. Hildebrandt CC, et al. Am J Med Genet A, 2021 Jul. PMID 33783941
    5. SREC-II, a new member of the scavenger receptor type F family, trans-interacts with SREC-I through its extracellular domain. Ishii J, et al. J Biol Chem, 2002 Oct 18. PMID 12154095

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Two novel variants in SCARF2 gene underlie van den Ende-Gupta syndrome.
      Title: Two novel variants in SCARF2 gene underlie van den Ende-Gupta syndrome.
    2. Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome.
      Title: Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome.
    3. the full VDEGS phenotype may include sclerocornea resulting from homozygosity or compound heterozygosity for loss of function variants in SCARF2.
      Title: Sclerocornea in a patient with van den Ende-Gupta syndrome homozygous for a SCARF2 microdeletion.
    4. Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome.
      Title: Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome.
    5. SRECII binds to SRECI and has a similar tissue distribution pattern
      Title: SREC-II, a new member of the scavenger receptor type F family, trans-interacts with SREC-I through its extracellular domain.
    Submit: New GeneRIF Correction

    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
    Van den Ende-Gupta syndrome
    MedGen: C1833136 OMIM: 600920 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables scavenger receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in focal adhesion HDA PubMed 
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    scavenger receptor class F member 2
    Names
    scavenger receptor expressed by endothelial cells 2 protein

    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_031868.2 RefSeqGene

      Range
      5035..18276
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_153334.7 → NP_699165.3  scavenger receptor class F member 2 isoform 1 precursor

      See identical proteins and their annotated locations for NP_699165.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AF522196, BC009326
      Consensus CDS
      CCDS13779.2
      UniProtKB/Swiss-Prot
      E5RFB8, Q58A83, Q8IXF3, Q96GP6, Q9BW74
      Related
      ENSP00000485276.1, ENST00000623402.1
      Conserved Domains (1) summary
      PHA03247
      Location:534 → 871
      PHA03247; large tegument protein UL36; Provisional

    2. NM_182895.5 → NP_878315.2  scavenger receptor class F member 2 isoform 2 precursor

      See identical proteins and their annotated locations for NP_878315.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment within the coding region, as compared to variant 1. The resulting isoform (2) lacks an internal region, as compared to isoform 1.
      Source sequence(s)
      AB024433, BC009326
      Consensus CDS
      CCDS46666.1
      UniProtKB/Swiss-Prot
      Q96GP6
      Related
      ENSP00000477564.2, ENST00000622235.5
      Conserved Domains (1) summary
      PHA03247
      Location:529 → 866
      PHA03247; large tegument protein UL36; Provisional

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      20424584..20437825 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017029065.3 → XP_016884554.1  scavenger receptor class F member 2 isoform X2

    2. XM_047441585.1 → XP_047297541.1  scavenger receptor class F member 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      20828870..20842097 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054326108.1 → XP_054182083.1  scavenger receptor class F member 2 isoform X2

    2. XM_054326107.1 → XP_054182082.1  scavenger receptor class F member 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96GP6.5 GenPept UniProtKB/Swiss-Prot:Q96GP6

    Gene LinkOut

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

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