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... See more...

Aliases for SCARF2 Gene

Aliases for SCARF2 Gene

  • Scavenger Receptor Class F Member 2 2 3 4 5
  • SREC-II 2 3 4
  • SREC2 2 3 4
  • Scavenger Receptor Expressed By Endothelial Cells 2 Protein 3 4
  • SRECRP-1 3 4
  • Scavenger Receptor Class F, Member 2 2
  • HUMZD58C02 2
  • SCARF2 5
  • 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 Sclerocornea. Gene Ontology (GO) annotations related to this gene include scavenger receptor activity. An important paralog of this gene is SCARF1.

UniProtKB/Swiss-Prot Summary 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 CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCARF2 Gene

Genomics for SCARF2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SCARF2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCARF2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCARF2

Top Transcription factor binding sites by QIAGEN in the SCARF2 gene promoter:
  • AhR
  • Arnt
  • GR
  • GR-alpha
  • GR-beta
  • Nkx2-5
  • p300
  • POU2F1
  • POU2F1a
  • Sp1

Genomic Locations for SCARF2 Gene

Latest Assembly
chr22:20,424,584-20,437,826
(GRCh38/hg38)
Size:
13,243 bases
Orientation:
Minus strand

Previous Assembly
chr22:20,778,874-20,792,112
(GRCh37/hg19 by Entrez Gene)
Size:
13,239 bases
Orientation:
Minus strand

chr22:20,778,874-20,792,146
(GRCh37/hg19 by Ensembl)
Size:
13,273 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:
    871 amino acids
    Molecular mass:
    92384 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).
    SequenceCaution:
    • Sequence=AAN45861.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for SCARF2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCARF2 Gene

Post-translational modifications for SCARF2 Gene

  • Glycosylation at Asn83, Asn310, Asn365, and Asn403
  • 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

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

Protein Domains for SCARF2 Gene

InterPro:
Blocks:
  • Laminin-type EGF-like domain
  • Type I EGF
  • EGF, extracellular
ProtoNet:

Suggested Antigen Peptide Sequences for SCARF2 Gene

GenScript: Design optimal peptide antigens:
  • Scavenger receptor class F, member 2, isoform CRA_a (Q58A83_HUMAN)
  • Scavenger receptor expressed by endothelial cells 2 protein (SREC2_HUMAN)
genes like me logo Genes that share domains with SCARF2: view

No data available for Graphical View of Domain Structure and 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).

Phenotypes From GWAS Catalog for SCARF2 Gene

Gene Ontology (GO) - Molecular Function for SCARF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005044 scavenger receptor activity IEA --
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:
  • Scarf2 Scarf2<tm1.1(KOMP)Vlcg>

Animal Models for research

  • Taconic Biosciences Mouse Models for SCARF2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCARF2

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 2
cytosol 2
extracellular 1
cytoskeleton 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (1)
  • Nuclear bodies (1)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCARF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005925 focal adhesion 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

PathCards logo

SuperPathways for SCARF2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SCARF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006897 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

mRNA/cDNA for SCARF2 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCARF2

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

No ASD Table

Relevant External Links for SCARF2 Gene

GeneLoc Exon Structure 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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(4.3)
  • Liver(4.3)

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 for research

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 30 31
  • 97.78 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SCARF2 30 31
  • 87.37 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Scarf2 30
  • 83.84 (n)
Dog
(Canis familiaris)
Mammalia SCARF2 30 31
  • 83.61 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Scarf2 30 17 31
  • 83.45 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SCARF2 31
  • 72 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 19 (a)
ManyToMany
Chicken
(Gallus gallus)
Aves SCARF2 30 31
  • 68.44 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SCARF2 31
  • 58 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100485666 30
  • 56.76 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC100329632 30
  • 56.03 (n)
SCARF2 31
  • 51 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta nimA 31
  • 17 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 19 (a)
OneToMany
Species where no ortholog for SCARF2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SCARF2: view image

Paralogs for SCARF2 Gene

Paralogs for SCARF2 Gene

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

  • SREC2_HUMAN
genes like me logo Genes that share paralogs with SCARF2: view

Variants for SCARF2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCARF2 Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
813638 Uncertain Significance: Microcephaly 20,425,946(-) G/A
NM_182895.5(SCARF2):c.2030C>T (p.Ala677Val)
MISSENSE
993021 Likely Pathogenic: Van den Ende-Gupta syndrome 20,437,729(-) GC/G
NM_182895.5(SCARF2):c.25del (p.Ala9fs)
FRAMESHIFT
rs1241075295 Likely Pathogenic: Van den Ende-Gupta syndrome 20,430,848(-) G/C
NM_182895.5(SCARF2):c.915C>G (p.Cys305Trp)
MISSENSE
rs1475035263 Uncertain Significance: not provided 20,426,096(-) G/A
NM_182895.5(SCARF2):c.1880C>T (p.Ala627Val)
MISSENSE
rs367657189 Uncertain Significance: not provided 20,425,397(-) C/T
NM_153334.7(SCARF2):c.2594G>A (p.Arg865Lys)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SCARF2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

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

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

SNP Genotyping and Copy Number Assays for research

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

Disorders for SCARF2 Gene

MalaCards: The human disease database

(8) MalaCards diseases for SCARF2 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

Disorder Aliases PubMed IDs
van den ende-gupta syndrome
  • vdegs
sclerocornea
  • isolated congenital sclerocornea
blepharophimosis
cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome
  • cednik syndrome
eyelid disease
  • abnormality of the eyelid
- 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 variants affecting the gene represented in this entry.

Additional Disease Information for SCARF2

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

No data available for Genatlas for SCARF2 Gene

Publications for SCARF2 Gene

  1. 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 74
  2. 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
  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
  4. Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane. (PMID: 32788342) Hannigan MM … Nicchitta CV (Molecular & cellular proteomics : MCP 2020) 3
  5. LMBR1L regulates lymphopoiesis through Wnt/β-catenin signaling. (PMID: 31073040) Choi JH … Beutler B (Science (New York, N.Y.) 2019) 3

Products for SCARF2 Gene

Sources for SCARF2 Gene