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Aliases for SCARF2 Gene

Aliases for SCARF2 Gene

  • Scavenger Receptor Class F Member 2 2 3 5
  • Scavenger Receptor Expressed By Endothelial Cells 2 Protein 3 4
  • SRECRP-1 3 4
  • SREC-II 3 4
  • SREC2 3 4
  • Scavenger Receptor Class F, Member 2 2
  • SREPCR 4
  • VDEGS 3
  • NSR1 3

External Ids for SCARF2 Gene

Previous GeneCards Identifiers for SCARF2 Gene

  • GC22M017481
  • GC22M019103
  • GC22M020778
  • GC22M004042

Summaries for SCARF2 Gene

Entrez Gene Summary for SCARF2 Gene

  • 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]

GeneCards Summary for SCARF2 Gene

SCARF2 (Scavenger Receptor Class F Member 2) is a Protein Coding gene. Diseases associated with SCARF2 include Van Den Ende-Gupta Syndrome and Marden Walker Like Syndrome. GO annotations related to this gene include scavenger receptor activity. An important paralog of this gene is SCARF1.

UniProtKB/Swiss-Prot for SCARF2 Gene

  • Probable adhesion protein, which mediates homophilic and heterophilic interactions. In contrast to SCARF1, it poorly mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL) (By similarity).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCARF2 Gene

Genomics for SCARF2 Gene

Regulatory Elements for SCARF2 Gene

Enhancers for SCARF2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22F020562 1.8 FANTOM5 Ensembl ENCODE 43.6 -129.6 -129579 9.2 CREB3L1 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC ZNF610 SCARF2 MED15 RPL7AP70 THAP7-AS1 DGCR8 LOC105372938 THAP7 SERPIND1 LOC100420177 RPL8P5
GH22F020548 1.7 FANTOM5 Ensembl ENCODE 32.3 -115.8 -115831 11.0 HDGF PKNOX1 ARNT CREB3L1 MLX SIN3A ARID4B FEZF1 YBX1 YY1 THAP7-AS1 SCARF2 MED15 LOC100420177 THAP7 PI4KA LOC105372938 ABHD17AP4 KLHL22 DGCR8
GH22F020543 1.3 Ensembl ENCODE 31.4 -107.7 -107703 3.6 HDGF ATF1 PKNOX1 ARNT ELK1 GATA2 KLF13 MCM3 CREB3 NFIL3 SCARF2 MED15 ABHD17AP4 KLHL22 THAP7-AS1 RNU6-225P THAP7 SERPIND1 ZNF74 LOC105372938
GH22F020506 1.5 FANTOM5 ENCODE 24.6 -71.6 -71644 5.8 HDGF WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF207 ZNF143 SCARF2 TBX1 MED15 ABHD17AP4 THAP7-AS1 THAP7 RPL7AP70 LOC100420177 ZNF74 LOC105372938
GH22F020420 1.9 VISTA Ensembl ENCODE 12.7 +14.9 14878 4.4 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 YBX1 YY1 SLC30A9 FOS SCARF2 ABHD17AP4 THAP7-AS1 THAP7 RPL7AP70 MED15 CRKL ZNF74 GC22M020421
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SCARF2 on UCSC Golden Path with GeneCards custom track

Promoters for SCARF2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000169471 459 2401 ATF1 MLX ARID4B YY1 ZNF121 GLIS2 KDM4B ZNF263 SP5 MCM5

Genomic Location for SCARF2 Gene

Chromosome:
22
Start:
20,424,584 bp from pter
End:
20,437,859 bp from pter
Size:
13,276 bases
Orientation:
Minus strand

Genomic View for SCARF2 Gene

Genes around SCARF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCARF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCARF2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCARF2 Gene

Proteins for SCARF2 Gene

  • Protein details for SCARF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96GP6-SREC2_HUMAN
    Recommended name:
    Scavenger receptor class F member 2
    Protein Accession:
    Q96GP6
    Secondary Accessions:
    • E5RFB8
    • Q58A83
    • Q8IXF3
    • Q9BW74

    Protein attributes for SCARF2 Gene

    Size:
    870 amino acids
    Molecular mass:
    92479 Da
    Quaternary structure:
    • Homophilic and heterophilic interaction via its extracellular domain. Interacts with SCARF1. The heterophilic interaction with SCARF1, which is stronger than the homophilic interaction with itself, is suppressed by the presence of SCARF1 ligand such as Ac-LDL (By similarity).

    Alternative splice isoforms for SCARF2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCARF2 Gene

Post-translational modifications for SCARF2 Gene

  • Glycosylation at Asn 83, Asn 310, Asn 365, and Asn 403
  • Modification sites at PhosphoSitePlus

Other Protein References for SCARF2 Gene

No data available for DME Specific Peptides for SCARF2 Gene

Domains & Families for SCARF2 Gene

Gene Families for SCARF2 Gene

Suggested Antigen Peptide Sequences for SCARF2 Gene

Graphical View of Domain Structure for InterPro Entry

Q96GP6

UniProtKB/Swiss-Prot:

SREC2_HUMAN :
  • Contains 7 EGF-like domains.
Domain:
  • Contains 7 EGF-like domains.
genes like me logo Genes that share domains with SCARF2: view

Function for SCARF2 Gene

Molecular function for SCARF2 Gene

UniProtKB/Swiss-Prot Function:
Probable adhesion protein, which mediates homophilic and heterophilic interactions. In contrast to SCARF1, it poorly mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL) (By similarity).

Gene Ontology (GO) - Molecular Function for SCARF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17474147
genes like me logo Genes that share ontologies with SCARF2: view
genes like me logo Genes that share phenotypes with SCARF2: view

Human Phenotype Ontology for SCARF2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SCARF2 Gene

MGI Knock Outs for SCARF2:

Animal Model Products

  • Taconic Biosciences Mouse Models for SCARF2

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SCARF2 Gene

Localization for SCARF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCARF2 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCARF2 gene
Compartment Confidence
plasma membrane 3
nucleus 3
cytosol 2
endoplasmic reticulum 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SCARF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005925 focal adhesion IDA 21423176
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SCARF2: view

Pathways & Interactions for SCARF2 Gene

SuperPathways for SCARF2 Gene

No Data Available

Interacting Proteins for SCARF2 Gene

Gene Ontology (GO) - Biological Process for SCARF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006898 receptor-mediated endocytosis IEA --
GO:0007155 cell adhesion IEA --
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IEA --
genes like me logo Genes that share ontologies with SCARF2: view

No data available for Pathways by source and SIGNOR curated interactions for SCARF2 Gene

Transcripts for SCARF2 Gene

Unigene Clusters for SCARF2 Gene

Scavenger receptor class F, member 2:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCARF2 Gene

No ASD Table

Relevant External Links for SCARF2 Gene

GeneLoc Exon Structure for
SCARF2
ECgene alternative splicing isoforms for
SCARF2

Expression for SCARF2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCARF2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCARF2 Gene

This gene is overexpressed in Artery - Aorta (x4.3).

Protein differential expression in normal tissues from HIPED for SCARF2 Gene

This gene is overexpressed in Heart (35.6), Platelet (14.1), and Monocytes (8.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SCARF2 Gene



Protein tissue co-expression partners for SCARF2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SCARF2 Gene:

SCARF2

SOURCE GeneReport for Unigene cluster for SCARF2 Gene:

Hs.474251

mRNA Expression by UniProt/SwissProt for SCARF2 Gene:

Q96GP6-SREC2_HUMAN
Tissue specificity: Predominantly expressed in endothelial cells. Expressed in heart, placenta, lung, kidney, spleen, small intestine and ovary.
genes like me logo Genes that share expression patterns with SCARF2: view

Primer Products

Orthologs for SCARF2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SCARF2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCARF2 34 35
  • 97.78 (n)
cow
(Bos Taurus)
Mammalia SCARF2 34 35
  • 87.37 (n)
rat
(Rattus norvegicus)
Mammalia Scarf2 34
  • 83.84 (n)
dog
(Canis familiaris)
Mammalia SCARF2 34 35
  • 83.61 (n)
mouse
(Mus musculus)
Mammalia Scarf2 34 16 35
  • 83.45 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SCARF2 35
  • 72 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 19 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SCARF2 34 35
  • 68.44 (n)
lizard
(Anolis carolinensis)
Reptilia SCARF2 35
  • 58 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100485666 34
  • 56.76 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100329632 34
  • 56.03 (n)
SCARF2 35
  • 51 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta nimA 35
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 19 (a)
OneToMany
Species where no ortholog for SCARF2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCARF2 Gene

ENSEMBL:
Gene Tree for SCARF2 (if available)
TreeFam:
Gene Tree for SCARF2 (if available)

Paralogs for SCARF2 Gene

Paralogs for SCARF2 Gene

(1) SIMAP similar genes for SCARF2 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SCARF2: view

Variants for SCARF2 Gene

Sequence variations from dbSNP and Humsavar for SCARF2 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
VAR_035837 A breast cancer sample
VAR_065302 Van den Ende-Gupta syndrome (VDEGS) [MIM:600920]
rs387907086 Pathogenic 20,431,099(-) CACGT(A/G)TGCCT reference, missense
rs587776902 Pathogenic 20,429,631(+) CCCAT(-/CA)CGCCC reference, frameshift-variant
rs587777657 Pathogenic 20,431,972(+) GCAGC(A/G)CGTGG reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SCARF2 Gene

Variant ID Type Subtype PubMed ID
nsv953032 CNV deletion 24416366
nsv834138 CNV loss 17160897
nsv834136 CNV loss 17160897
nsv834135 CNV gain 17160897
nsv828955 CNV gain 20364138
nsv828954 CNV gain 20364138
nsv588293 CNV gain 21841781
nsv523162 CNV loss 19592680
nsv519901 CNV gain 19592680
nsv509809 CNV insertion 20534489
nsv436864 CNV insertion 17901297
nsv1056614 CNV loss 25217958
esv3893438 CNV gain 25118596
esv3647293 CNV gain 21293372
esv3647292 CNV gain 21293372
esv3575430 CNV gain 25503493
dgv7993n54 CNV gain 21841781
dgv4483n100 CNV gain 25217958

Variation tolerance for SCARF2 Gene

Gene Damage Index Score: 12.49; 94.36% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SCARF2 Gene

Human Gene Mutation Database (HGMD)
SCARF2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCARF2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCARF2 Gene

Disorders for SCARF2 Gene

MalaCards: The human disease database

(7) MalaCards diseases for SCARF2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
van den ende-gupta syndrome
  • marden walker like syndrome
marden walker like syndrome
  • blepharophimosis, arachnodactyly, and congenital contractures
van den ende-gupta sndrome
  • blepharophimosis, arachnodactyly, and congenital contractures
sclerocornea
  • isolated congenital sclerocornea
eyelid disease
  • eyelid disorders
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SREC2_HUMAN
  • Van den Ende-Gupta syndrome (VDEGS) [MIM:600920]: A syndrome characterized by craniofacial and skeletal abnormalities that include blepharophimosis, a flat and wide nasal bridge, narrow and beaked nose, hypoplastic maxilla with or without cleft palate and everted lower lip, prominent ears, down-slanting eyes, arachnodactyly, and camptodactyly. Patients present congenital joint contractures that improve without intervention, and normal growth and development. Intelligence is normal. Rarely, enlarged cerebella can be present. Some patients experience respiratory problems due to laryngeal abnormalities. {ECO:0000269 PubMed:20887961}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SCARF2

Genetic Association Database (GAD)
SCARF2
Human Genome Epidemiology (HuGE) Navigator
SCARF2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SCARF2
genes like me logo Genes that share disorders with SCARF2: view

No data available for Genatlas for SCARF2 Gene

Publications for SCARF2 Gene

  1. SREC-II, a new member of the scavenger receptor type F family, trans- interacts with SREC-I through its extracellular domain. (PMID: 12154095) Ishii J. … Arai H. (J. Biol. Chem. 2002) 2 3 4 64
  2. Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome. (PMID: 20887961) Anastasio N. … Jerome-Majewska L.A. (Am. J. Hum. Genet. 2010) 3 4 64
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  4. Sclerocornea in a patient with van den Ende-Gupta syndrome homozygous for a SCARF2 microdeletion. (PMID: 24478002) Migliavacca M.P. … Perez A.B. (Am. J. Med. Genet. A 2014) 3 64
  5. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y. … Zou H. (J. Proteomics 2014) 4 64

Products for SCARF2 Gene

Sources for SCARF2 Gene

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