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SCYL2 Gene(Protein Coding)

SCY1 Like Pseudokinase 2

GCID:
GC12P100267
GIFtS:
44
Genes Participants
UDN Logo

Aliases for SCYL2 Gene

Aliases for SCYL2 Gene

  • SCY1 Like Pseudokinase 2 2 3 5
  • Coated Vesicle-Associated Kinase Of 104 KDa 2 3 4
  • SCY1-Like, Kinase-Like 2 2 3
  • CVAK104 3 4
  • SCY1-Like 2 (S. Cerevisiae) 2
  • SCY1-Like Protein 2 3
  • SCY1-Like 2 3
  • KIAA1360 4

External Ids for SCYL2 Gene

Previous GeneCards Identifiers for SCYL2 Gene

  • GC12P099164
  • GC12P100661
  • GC12P097722

Summaries for SCYL2 Gene

Entrez Gene Summary for SCYL2 Gene

  • The protein encoded by this gene associates with clathrin-coated complexes at the plasma membrane and with endocytic coated vesicles. The encoded protein phosphorylates the beta2 subunit of the plasma membrane adapter complex AP2 and interacts with clathrin, showing involvement in clathrin-dependent pathways between the trans-Golgi network and the endosomal system. In addition, this protein has a role in the Wnt signaling pathway by targeting frizzled 5 (Fzd5) for lysosomal degradation. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2015]

GeneCards Summary for SCYL2 Gene

SCYL2 (SCY1 Like Pseudokinase 2) is a Protein Coding gene. Diseases associated with SCYL2 include Cataract 8, Multiple Types. Gene Ontology (GO) annotations related to this gene include transferase activity, transferring phosphorus-containing groups and binding.

UniProtKB/Swiss-Prot for SCYL2 Gene

  • Component of AP2-containing clathrin coated structures at the plasma membrane or of endocytic coated vesicles. According to PubMed:15809293, probable serine/threonine-protein kinase that phosphorylates, in vitro, the beta2-subunit of the plasma membrane adapter complex AP2 and other proteins in presence of poly-L-lysine. According to PubMed:16914521, has no detectable kinase activity in vitro. May regulate clathrin-dependent trafficking between the TGN and/or the endosomal system.

Gene Wiki entry for SCYL2 Gene

Additional gene information for SCYL2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCYL2 Gene

Genomics for SCYL2 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for SCYL2 Gene

Promoters and enhancers for SCYL2 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
GH12I100266 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 564.3 +0.8 838 3.6 HDGF PKNOX1 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SCYL2 DEPDC4 ACTR6 RN7SL176P GC12M100395
GH12I100277 Promoter 0.5 EPDnew 550.4 +10.8 10831 0.1 SCYL2 SLC17A8 ACTR6 DEPDC4 GC12M100395
GH12I100198 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 23.2 -66.0 -66018 4.4 HDGF SMAD1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B E2F8 ACTR6 ENSG00000257489 SCYL2 GOLGA2P5 ANKS1B GC12M100397
GH12I100500 Promoter/Enhancer 1.4 EPDnew ENCODE dbSUPER 11.9 +236.4 236448 5.7 FOXA2 RXRA TAF1 MAX REST RAD21 FOXA1 GABPA YY1 JUND NR1H4 UTP20 SCYL2 ENSG00000271177
GH12I100228 Enhancer 0.7 ENCODE 11.8 -36.7 -36681 3.1 MEIS2 CTCF PKNOX1 DDX20 ZSCAN4 NEUROD1 CEBPG ZBTB40 RAD21 CC2D1A SCYL2 ACTR6 ANKS1B GC12P100217 GC12M100398 DEPDC4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCYL2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCYL2 gene promoter:

Genomic Locations for SCYL2 Gene

Genomic Locations for SCYL2 Gene
chr12:100,267,137-100,341,724
(GRCh38/hg38)
Size:
74,588 bases
Orientation:
Plus strand
chr12:100,660,918-100,735,502
(GRCh37/hg19)

Genomic View for SCYL2 Gene

Genes around SCYL2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCYL2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCYL2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SCYL2 Gene

Proteins for SCYL2 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for SCYL2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6P3W7-SCYL2_HUMAN
    Recommended name:
    SCY1-like protein 2
    Protein Accession:
    Q6P3W7
    Secondary Accessions:
    • A8KAB5
    • Q96EF4
    • Q96ST4
    • Q9H7V5
    • Q9NVH3
    • Q9P2I7

    Protein attributes for SCYL2 Gene

    Size:
    929 amino acids
    Molecular mass:
    103709 Da
    Quaternary structure:
    • Interacts with clathrin and AP2B1; the interaction mediates the association with the AP-2 complex.
    SequenceCaution:
    • Sequence=BAA91778.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB14869.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB55194.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for SCYL2 Gene

Protein Expression for SCYL2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SCYL2 Gene

  • According to PubMed:15809293, autophosphorylated in presence of poly-L-lysine.

Other Protein References for SCYL2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SCYL2 Gene

Domains & Families for SCYL2 Gene

Gene Families for SCYL2 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for SCYL2 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SCYL2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q6P3W7

UniProtKB/Swiss-Prot:

SCYL2_HUMAN :
  • Belongs to the protein kinase superfamily.
Family:
  • Belongs to the protein kinase superfamily.
genes like me logo Genes that share domains with SCYL2: view

Function for SCYL2 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for SCYL2 Gene

UniProtKB/Swiss-Prot Function:
Component of AP2-containing clathrin coated structures at the plasma membrane or of endocytic coated vesicles. According to PubMed:15809293, probable serine/threonine-protein kinase that phosphorylates, in vitro, the beta2-subunit of the plasma membrane adapter complex AP2 and other proteins in presence of poly-L-lysine. According to PubMed:16914521, has no detectable kinase activity in vitro. May regulate clathrin-dependent trafficking between the TGN and/or the endosomal system.

Phenotypes From GWAS Catalog for SCYL2 Gene

Gene Ontology (GO) - Molecular Function for SCYL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004672 protein kinase activity IEA --
GO:0005102 receptor binding IPI 19643732
GO:0005515 protein binding IPI 19643732
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with SCYL2: view
genes like me logo Genes that share phenotypes with SCYL2: view

Animal Models for SCYL2 Gene

MGI Knock Outs for SCYL2:

Animal Model Products

miRNA for SCYL2 Gene

miRTarBase miRNAs that target SCYL2

Clone Products

  • Addgene plasmids for SCYL2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SCYL2 Gene

Localization for SCYL2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCYL2 Gene

Cytoplasm, perinuclear region. Cytoplasmic vesicle, clathrin-coated vesicle. Golgi apparatus, trans-Golgi network membrane. Endosome membrane. Note=According to PubMed:15809293, plasma membrane-associated in clathrin-coated vesicles. According to PubMed:16914521, colocalizes to the trans-Golgi network (TGN) and to endosomal membranes with clathrin, transferrin and plasma membrane adapter AP1 and AP3 complexes.

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 SCYL2 gene
Compartment Confidence
golgi apparatus 5
endosome 5
cytosol 2
extracellular 1
mitochondrion 1
peroxisome 1
nucleus 1

Gene Ontology (GO) - Cellular Components for SCYL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005768 endosome IEA --
GO:0005794 Golgi apparatus IEA --
GO:0010008 endosome membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SCYL2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SCYL2 Gene

Pathways & Interactions for SCYL2 Gene

SuperPathways for SCYL2 Gene

PathCards logo More details on SuperPathways for SCYL2
No Data Available

Gene Ontology (GO) - Biological Process for SCYL2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002092 positive regulation of receptor internalization IDA 19643732
GO:0006468 protein phosphorylation IEA --
GO:0008333 endosome to lysosome transport IDA 19643732
GO:0090090 negative regulation of canonical Wnt signaling pathway IDA 19643732
GO:2000286 receptor internalization involved in canonical Wnt signaling pathway IDA 19643732
genes like me logo Genes that share ontologies with SCYL2: view

No data available for Pathways by source and SIGNOR curated interactions for SCYL2 Gene

Drugs & Compounds for SCYL2 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for SCYL2 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SCYL2 Gene

(8) REFSEQ mRNAs :
(12) Additional mRNA sequences :
(170) Selected AceView cDNA sequences:
(11) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SCYL2 Gene

SCY1-like 2 (S. cerevisiae):
Representative Sequences:

Clone Products

  • Addgene plasmids for SCYL2

Alternative Splicing Database (ASD) splice patterns (SP) for SCYL2 Gene

No ASD Table

Relevant External Links for SCYL2 Gene

GeneLoc Exon Structure for
SCYL2
ECgene alternative splicing isoforms for
SCYL2

Expression for SCYL2 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCYL2 Gene

mRNA expression in normal human tissues for SCYL2 Gene
mRNA expression by BioGPS for SCYL2 GenemRNA expression by GTEx for SCYL2 Gene

Protein differential expression in normal tissues from HIPED for SCYL2 Gene

This gene is overexpressed in Platelet (6.7) and Peripheral blood mononuclear cells (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SCYL2 Gene



Protein tissue co-expression partners for SCYL2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SCYL2 Gene:

SCYL2

SOURCE GeneReport for Unigene cluster for SCYL2 Gene:

Hs.506481

Evidence on tissue expression from TISSUES for SCYL2 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with SCYL2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCYL2 Gene

Orthologs for SCYL2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SCYL2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia SCYL2 34
  • 100 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia SCYL2 33 34
  • 94.44 (n)
dog
(Canis familiaris)
 Mammalia SCYL2 33 34
  • 93.9 (n)
oppossum
(Monodelphis domestica)
 Mammalia SCYL2 34
  • 90 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia SCYL2 34
  • 90 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Scyl2 33
  • 89.34 (n)
mouse
(Mus musculus)
 Mammalia Scyl2 33 16 34
  • 88.81 (n)
chicken
(Gallus gallus)
 Aves SCYL2 33 34
  • 79.84 (n)
lizard
(Anolis carolinensis)
 Reptilia SCYL2 34
  • 83 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia scyl2 33
  • 74.21 (n)
zebrafish
(Danio rerio)
 Actinopterygii SCYL2 34
  • 71 (a)
 OneToOne
si:ch211-244b2.1 33
  • 66.74 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG1951 33 34
  • 54.57 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP002142 33
  • 49.49 (n)
worm
(Caenorhabditis elegans)
 Secernentea ZC581.9 34
  • 21 (a)
 OneToOne
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes SCY1 34 36
  • 23 (a)
 OneToOne
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 57 (a)
 OneToOne
Species where no ortholog for SCYL2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)

Evolution for SCYL2 Gene

ENSEMBL:
Gene Tree for SCYL2 (if available)
TreeFam:
Gene Tree for SCYL2 (if available)

Paralogs for SCYL2 Gene

Pseudogenes.org Pseudogenes for SCYL2 Gene

genes like me logo Genes that share paralogs with SCYL2: view

No data available for Paralogs for SCYL2 Gene

Variants for SCYL2 Gene

Sequence variations from dbSNP and Humsavar for SCYL2 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
VAR_041370 A lung adenocarcinoma sample p.Gln863His
rs1000002371 -- 100,332,102(+) A/G intron_variant
rs1000015151 -- 100,297,739(+) C/A intron_variant
rs1000070133 -- 100,266,201(+) C/T upstream_transcript_variant
rs1000137175 -- 100,304,068(+) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SCYL2 Gene

Variant ID Type Subtype PubMed ID
esv2364259 CNV deletion 18987734
esv2518688 CNV deletion 19546169
esv2672785 CNV deletion 23128226
esv2746277 CNV deletion 23290073
esv3549674 CNV deletion 23714750
esv3580426 CNV loss 25503493
nsv1070124 CNV deletion 25765185
nsv559964 CNV gain 21841781
nsv958649 CNV deletion 24416366
nsv977143 CNV duplication 23825009

Variation tolerance for SCYL2 Gene

Residual Variation Intolerance Score: 7.58% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.91; 67.72% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCYL2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCYL2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCYL2 Gene

Disorders for SCYL2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SCYL2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
cataract 8, multiple types
  • ctrct8
- elite association - COSMIC cancer census association via MalaCards
Search SCYL2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SCYL2

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SCYL2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCYL2 Gene

Publications for SCYL2 Gene

  1. Clathrin-dependent association of CVAK104 with endosomes and the trans-Golgi network. (PMID: 16914521) Düwel M … Ungewickell EJ (Molecular biology of the cell 2006) 3 4 22 58
  2. CVAK104 is a novel poly-L-lysine-stimulated kinase that targets the beta2-subunit of AP2. (PMID: 15809293) Conner SD … Schmid SL (The Journal of biological chemistry 2005) 2 3 4 58
  3. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 58
  4. CVAK104 is a novel regulator of clathrin-mediated SNARE sorting. (PMID: 17587408) Borner GH … Robinson MS (Traffic (Copenhagen, Denmark) 2007) 2 3 58
  5. Role of the AP2 beta-appendage hub in recruiting partners for clathrin-coated vesicle assembly. (PMID: 16903783) Schmid EM … McMahon HT (PLoS biology 2006) 3 4 58

Products for SCYL2 Gene

  • Addgene plasmids for SCYL2

Sources for SCYL2 Gene

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