Aliases for SVBP Gene

Aliases for SVBP Gene

  • Small Vasohibin Binding Protein 2 3 5
  • Coiled-Coil Domain Containing 23 2 3
  • Small Vasohibin-Binding Protein 3 4
  • CCDC23 3 4
  • Coiled-Coil Domain-Containing Protein 23 3
  • Coiled Coil Domain-Containing Protein 23 4
  • MGC45441 2
  • NEDAHM 3
  • SVBP 5

External Ids for SVBP Gene

Previous HGNC Symbols for SVBP Gene

  • CCDC23

Summaries for SVBP Gene

GeneCards Summary for SVBP Gene

SVBP (Small Vasohibin Binding Protein) is a Protein Coding gene. Diseases associated with SVBP include Neurodevelopmental Disorder With Ataxia, Hypotonia, And Microcephaly and Microcephaly.

UniProtKB/Swiss-Prot Summary for SVBP Gene

  • Enhances the tyrosine carboxypeptidase activity of VASH1 and VASH2, thereby promoting the removal of the C-terminal tyrosine residue of alpha-tubulin (PubMed:29146869, PubMed:31270470, PubMed:31235911, PubMed:31324789, PubMed:31171830, PubMed:31235910). This activity is critical for spindle function and accurate chromosome segregation during mitosis since microtuble detyronisation regulates mitotic spindle length and postioning (PubMed:31171830). Also required to enhance the solubility and secretion of VASH1 and VASH2 (PubMed:20736312, PubMed:27879017, PubMed:30607023). Plays a role in axon and excitatory synapse formation (PubMed:31235911).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SVBP Gene

Genomics for SVBP Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SVBP 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 SVBP on the GeneHancer Hub at the UCSC Golden Path

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

Genomic Locations for SVBP Gene

Genomic Locations for SVBP Gene
chr1:42,807,052-42,817,397
(GRCh38/hg38)
Size:
10,346 bases
Orientation:
Minus strand
chr1:43,272,723-43,283,059
(GRCh37/hg19)
Size:
10,337 bases
Orientation:
Minus strand

Genomic View for SVBP Gene

Genes around SVBP on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SVBP Gene

Proteins for SVBP Gene

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

    Protein Symbol:
    Q8N300-SVBP_HUMAN
    Recommended name:
    Small vasohibin-binding protein
    Protein Accession:
    Q8N300
    Secondary Accessions:
    • A8K5P1
    • D3DPW7

    Protein attributes for SVBP Gene

    Size:
    66 amino acids
    Molecular mass:
    7808 Da
    Quaternary structure:
    • Interacts with VASH1 and VASH2.

    Three dimensional structures from OCA and Proteopedia for SVBP Gene

neXtProt entry for SVBP Gene

Post-translational modifications for SVBP Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SVBP Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SVBP Gene

Domains & Families for SVBP Gene

Gene Families for SVBP Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for SVBP Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SVBP Gene

GenScript: Design optimal peptide antigens:
  • Coiled-coil domain-containing protein 23 (CCD23_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N300

UniProtKB/Swiss-Prot:

SVBP_HUMAN :
  • Belongs to the SVBP family.
Family:
  • Belongs to the SVBP family.
genes like me logo Genes that share domains with SVBP: view

Function for SVBP Gene

Molecular function for SVBP Gene

UniProtKB/Swiss-Prot Function:
Enhances the tyrosine carboxypeptidase activity of VASH1 and VASH2, thereby promoting the removal of the C-terminal tyrosine residue of alpha-tubulin (PubMed:29146869, PubMed:31270470, PubMed:31235911, PubMed:31324789, PubMed:31171830, PubMed:31235910). This activity is critical for spindle function and accurate chromosome segregation during mitosis since microtuble detyronisation regulates mitotic spindle length and postioning (PubMed:31171830). Also required to enhance the solubility and secretion of VASH1 and VASH2 (PubMed:20736312, PubMed:27879017, PubMed:30607023). Plays a role in axon and excitatory synapse formation (PubMed:31235911).

Phenotypes From GWAS Catalog for SVBP Gene

Gene Ontology (GO) - Molecular Function for SVBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 29146869
GO:0008017 microtubule binding IDA 31324789
genes like me logo Genes that share ontologies with SVBP: view
genes like me logo Genes that share phenotypes with SVBP: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SVBP Gene

Localization for SVBP Gene

Subcellular locations from UniProtKB/Swiss-Prot for SVBP Gene

Cytoplasm. Secreted. Cytoplasm, cytoskeleton. Note=Detected both intracellularly and extracellularly (By similarity). Within cells, localizes mainly to the apical part of the cell (By similarity). {ECO:0000250 UniProtKB:Q99LQ4}.

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 SVBP gene
Compartment Confidence
cytoskeleton 4
extracellular 3
nucleus 3
cytosol 2

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 SVBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA --
GO:0045177 apical part of cell IDA 20736312
genes like me logo Genes that share ontologies with SVBP: view

Pathways & Interactions for SVBP Gene

PathCards logo

SuperPathways for SVBP Gene

No Data Available

Interacting Proteins for SVBP Gene

STRING Interaction Network Preview (showing top 1 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000361599 Q8N300-SVBP_HUMAN for SVBP Gene via STRING IID

Gene Ontology (GO) - Biological Process for SVBP Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IDA 29146869
GO:0009306 protein secretion IDA 20736312
GO:0010596 negative regulation of endothelial cell migration IGI 20736312
GO:0031397 negative regulation of protein ubiquitination IDA 20736312
GO:0061564 axon development IMP 31324789
genes like me logo Genes that share ontologies with SVBP: view

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

Drugs & Compounds for SVBP Gene

No Compound Related Data Available

Transcripts for SVBP Gene

mRNA/cDNA for SVBP Gene

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

CRISPR Products

Inhibitory RNA Products

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

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

No ASD Table

Relevant External Links for SVBP Gene

GeneLoc Exon Structure for
SVBP

Expression for SVBP Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)
  • Heart (Cardiovascular System)

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SVBP

Evidence on tissue expression from TISSUES for SVBP Gene

  • Nervous system(4.5)
  • Lung(4.3)
  • Heart(2.4)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with SVBP: view

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SVBP Gene

Orthologs for SVBP Gene

This gene was present in the common ancestor of chordates.

Orthologs for SVBP Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CCDC23 30 31
  • 100 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CCDC23 30 31
  • 94.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CCDC23 30 31
  • 94.44 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ccdc23 30
  • 90.4 (n)
Mouse
(Mus musculus)
Mammalia Ccdc23 30 31
  • 89.39 (n)
OneToOne
Svbp 17
Oppossum
(Monodelphis domestica)
Mammalia CCDC23 31
  • 61 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CCDC23 31
  • 70 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii CCDC23 31
  • 68 (a)
OneToOne
Species where no ortholog for SVBP 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)
  • Chicken (Gallus gallus)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Platypus (Ornithorhynchus anatinus)
  • 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 Squirt (Ciona savignyi)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SVBP Gene

ENSEMBL:
Gene Tree for SVBP (if available)
TreeFam:
Gene Tree for SVBP (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SVBP: view image

Paralogs for SVBP Gene

No data available for Paralogs for SVBP Gene

Variants for SVBP Gene

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

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
635968 Pathogenic: Microcephaly; Intellectual disability; Lower limb spasticity; NEURODEVELOPMENTAL DISORDER WITH ATAXIA, HYPOTONIA, AND MICROCEPHALY 42,816,463(-) G/A NONSENSE
635969 Pathogenic: Microcephaly; Intellectual disability; Lower limb spasticity; NEURODEVELOPMENTAL DISORDER WITH ATAXIA, HYPOTONIA, AND MICROCEPHALY 42,816,502(-) ATTCT/A FRAMESHIFT_VARIANT
806113 Uncertain Significance: not provided 42,816,516(-) G/GT FRAMESHIFT_VARIANT

Additional dbSNP identifiers (rs#s) for SVBP Gene

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

Variant ID Type Subtype PubMed ID
esv2668067 CNV deletion 23128226
esv3577249 CNV gain 25503493
esv3585854 CNV loss 21293372

Variation tolerance for SVBP Gene

Residual Variation Intolerance Score: 54.2% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SVBP Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for SVBP Gene

MalaCards: The human disease database

(4) MalaCards diseases for SVBP Gene - From: OMIM, ClinVar, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SVBP in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SVBP_HUMAN
  • Neurodevelopmental disorder with ataxia, hypotonia, and microcephaly (NEDAHM) [MIM:618569]: An autosomal recessive neurodevelopmental disorder characterized by intellectual disability, microcephaly, ataxia, and muscular hypotonia. {ECO:0000269 PubMed:30607023}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with SVBP: view

No data available for Genatlas for SVBP Gene

Publications for SVBP Gene

  1. Isolation of a small vasohibin-binding protein (SVBP) and its role in vasohibin secretion. (PMID: 20736312) Suzuki Y … Sato Y (Journal of cell science 2010) 2 3 4
  2. Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis. (PMID: 31171830) Liao S … Xu C (Cell research 2019) 3 4
  3. Structural basis of tubulin detyrosination by the vasohibin-SVBP enzyme complex. (PMID: 31235911) Wang N … Huang H (Nature structural & molecular biology 2019) 3 4
  4. Structural basis of tubulin detyrosination by VASH2/SVBP heterodimer. (PMID: 31324789) Zhou C … Liu Z (Nature communications 2019) 3 4
  5. Structural basis of tubulin detyrosination by vasohibins. (PMID: 31235910) Li F … Yu H (Nature structural & molecular biology 2019) 3 4

Products for SVBP Gene

Sources for SVBP Gene