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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. Gene Ontology (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).

Additional gene information for SCARF2 Gene

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

Genomics for SCARF2 Gene

GeneHancer (GH) Regulatory Elements for SCARF2 Gene

Promoters and enhancers for SCARF2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22I020434 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 562 +0.8 811 4.2 ATF1 ARNT ZNF121 GLIS2 ATF7 ZNF263 MCM3 MCM5 ZNF184 GLIS1 SCARF2 RPL7AP70 MED15 DGCR8 TBX1 ABHD17AP4 THAP7 UFD1 ZNF74 ENSG00000277971
GH22I020494 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 24.2 -58.0 -57984 2.7 CLOCK FEZF1 YBX1 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 MED15 KLHL22 LOC101928824 LZTR1 DGCR8 RPL7AP70 TRMT2A RPL8P5 LOC100420177 THAP7
GH22I020114 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 13.6 +320.6 320613 4.6 CLOCK MLX ZFP64 FEZF1 DMAP1 SLC30A9 E2F8 ZNF143 ZNF263 SP3 TRMT2A RANBP1 MED15 RPL7AP70 LZTR1 ZDHHC8 UFD1 DGCR8 SCARF2 THAP7
GH22I020506 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.7 -71.6 -71643 5.8 HDGF HNRNPUL1 CLOCK SMAD1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 MED15 LZTR1 LOC100420177 DGCR8 TRMT2A RPL7AP70 RPL8P5 ZNF74 KLHL22 ABHD17AP4
GH22I019753 Promoter/Enhancer 1.9 VISTA EPDnew Ensembl ENCODE 11.2 +681.1 681104 6.6 HDGF PKNOX1 ARNT ARID4B ZNF2 CBX5 ZNF143 ZNF548 ZNF263 MCM3 TBX1 DGCR8 RPL7AP70 MED15 LINC01311 LOC100420177 TRMT2A ZDHHC8 UFD1 ABHD17AP4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCARF2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCARF2 gene promoter:

Genomic Locations for SCARF2 Gene

Genomic Locations for SCARF2 Gene
chr22:20,424,584-20,437,859
(GRCh38/hg38)
Size:
13,276 bases
Orientation:
Minus strand
chr22:20,778,874-20,792,146
(GRCh37/hg19)

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 posLast=8383, isoforms=2310, isoforms=2365, and isoforms=2403

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

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for SCARF2 Gene

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for SCARF2 Gene

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

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCARF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005925 focal adhesion IDA,HDA 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

Drugs & Compounds for SCARF2 Gene

No Compound Related Data Available

Transcripts for SCARF2 Gene

Unigene Clusters for SCARF2 Gene

Scavenger receptor class F, member 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA 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 CGAP 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.

Evidence on tissue expression from TISSUES for SCARF2 Gene

  • Nervous system(4.2)
  • Liver(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SCARF2 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeleton
Regions:
Head and neck:
  • cheek
  • ear
  • epiglottis
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • tooth
  • vocal cord
Thorax:
  • bronchus
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
  • trachea
Pelvis:
  • pelvis
  • uterus
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • skin
  • spinal column
  • vertebrae
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 33 34
  • 97.78 (n)
cow
(Bos Taurus)
Mammalia SCARF2 33 34
  • 87.37 (n)
rat
(Rattus norvegicus)
Mammalia Scarf2 33
  • 83.84 (n)
dog
(Canis familiaris)
Mammalia SCARF2 33 34
  • 83.61 (n)
mouse
(Mus musculus)
Mammalia Scarf2 33 16 34
  • 83.45 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SCARF2 34
  • 72 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 19 (a)
ManyToMany
chicken
(Gallus gallus)
Aves SCARF2 33 34
  • 68.44 (n)
lizard
(Anolis carolinensis)
Reptilia SCARF2 34
  • 58 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100485666 33
  • 56.76 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100329632 33
  • 56.03 (n)
SCARF2 34
  • 51 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta nimA 34
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 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 Variation AA Info Type
rs387907086 pathogenic, Marden Walker like syndrome 20,431,099(-) C/T coding_sequence_variant, missense_variant
rs537247534 uncertain-significance, not specified, not provided 20,425,454(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs587776902 pathogenic, Marden Walker like syndrome, not provided 20,429,631(-) CAC/C coding_sequence_variant, frameshift
rs587777657 pathogenic, Marden Walker like syndrome 20,431,972(-) A/G coding_sequence_variant, missense_variant
rs587777658 pathogenic, Marden Walker like syndrome 20,425,445(-) T/ coding_sequence_variant, frameshift, genic_downstream_transcript_variant

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)

Additional Variant Information 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

(6) MalaCards diseases for SCARF2 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
van den ende-gupta syndrome
  • vdegs
marden walker like syndrome
  • vdegs
sclerocornea
  • isolated congenital sclerocornea
eyelid disease
  • abnormality of the eyelid
blepharophimosis
- 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.

Additional Disease Information for SCARF2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 (The Journal of biological chemistry 2002) 2 3 4 58
  2. Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome. (PMID: 20887961) Anastasio N … Jerome-Majewska LA (American journal of human genetics 2010) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y … Zou H (Journal of proteomics 2014) 4 58

Products for SCARF2 Gene

Sources for SCARF2 Gene

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