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SVBP small vasohibin binding protein [ Homo sapiens (human) ]

Gene ID: 374969, updated on 2-Nov-2024

Summary

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Official Symbol
SVBPprovided by HGNC
Official Full Name
small vasohibin binding proteinprovided by HGNC
Primary source
HGNC:HGNC:29204
See related
Ensembl:ENSG00000177868 MIM:617853; AllianceGenome:HGNC:29204
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CCDC23; NEDAHM
Summary
Enables microtubule binding activity and peptidase activator activity. Involved in axon development; proteolysis; and regulation of metallopeptidase activity. Acts upstream of or within negative regulation of endothelial cell migration; negative regulation of protein ubiquitination; and protein secretion. Located in apical part of cell. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 21.3), fat (RPKM 15.7) and 24 other tissues See more
Orthologs
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Genomic context

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See SVBP in Genome Data Viewer
Location:
1p34.2
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (42807052..42817397, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (42677541..42687878, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (43272723..43283068, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene chromosome 1 open reading frame 50 Neighboring gene TMEM269 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:43250662-43251403 Neighboring gene uncharacterized LOC107984946 Neighboring gene transmembrane protein 269 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 770 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 771 Neighboring gene erythroblast membrane associated protein (Scianna blood group) Neighboring gene uncharacterized LOC124904163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 897 Neighboring gene ZNF691 divergent transcript

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Loss of function of SVBP leads to autosomal recessive intellectual disability, microcephaly, ataxia, and hypotonia. Iqbal Z, et al. Genet Med, 2019 Aug. PMID 30607023
  2. Vasohibin 2 is transcriptionally activated and promotes angiogenesis in hepatocellular carcinoma. Xue X, et al. Oncogene, 2013 Mar 28. PMID 22614011
  3. Crystal structure of the tubulin tyrosine carboxypeptidase complex VASH1-SVBP. Adamopoulos A, et al. Nat Struct Mol Biol, 2019 Jul. PMID 31270470
  4. Structural basis of tubulin detyrosination by vasohibins. Li F, et al. Nat Struct Mol Biol, 2019 Jul. PMID 31235910, Free PMC Article
  5. Domain architecture of vasohibins required for their chaperone-dependent unconventional extracellular release. Kadonosono T, et al. Protein Sci, 2017 Mar. PMID 27879017, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The authors identified a core heterodimeric complex of human small vasohibin-binding protein (SVBP) and vasohibin 1 (VASH1) that catalyzes the detyrosination of a peptide derived from C-terminus of alpha-tubulin.
    Title: Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis.
  2. This study examined the crystal structures of human vasohibin 1 and 2 in complex with small vasohibin-binding protein (SVBP) in the absence and presence of different inhibitors and a C-terminal alpha-tubulin peptide.
    Title: Structural basis of tubulin detyrosination by the vasohibin-SVBP enzyme complex.
  3. This study describes the crystal and solution structure of the tubulin carboxypeptidase complex between vasohibin (VASH1) and small vasohibin-binding protein (SVBP), which folds in a long helix, which stabilizes the VASH1 catalytic domain.
    Title: Crystal structure of the tubulin tyrosine carboxypeptidase complex VASH1-SVBP.
  4. SVBP is not only involved in angiogenesis, but also has vital functions in the central nervous system. Biallelic loss-of-function variants in SVBP lead to intellectual disability.
    Title: Loss of function of SVBP leads to autosomal recessive intellectual disability, microcephaly, ataxia, and hypotonia.
  5. identified a novel UPS regulatory system in which essential domain architecture (VASH-PS) of VASHs, comprising regions VASH191-180 and VASH280-169 , regulate the cytosolic punctate structure formation in the absence of SVBP.
    Title: Domain architecture of vasohibins required for their chaperone-dependent unconventional extracellular release.
  6. VASH2 contributes to the angiogenesis in hepatocellular carcinoma via an SVBP-mediated paracrine mechanism.
    Title: Vasohibin 2 is transcriptionally activated and promotes angiogenesis in hepatocellular carcinoma.
  7. SVBP(CCDC23)acts as a secretory chaperone for VASH1.
    Title: Isolation of a small vasohibin-binding protein (SVBP) and its role in vasohibin secretion.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Neurodevelopmental disorder with ataxia, hypotonia, and microcephaly
MedGen: C5231413 OMIM: 618569 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables microtubule binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables peptidase activator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in axon development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within negative regulation of endothelial cell migration IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in negative regulation of protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within negative regulation of protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein secretion IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within protein secretion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proteolysis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of metallopeptidase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in apical part of cell IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in apical part of cell IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
small vasohibin-binding protein
Names
coiled-coil domain containing 23
coiled-coil domain-containing protein 23

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_199342.4 → NP_955374.1  small vasohibin-binding protein

    See identical proteins and their annotated locations for NP_955374.1

    Status: VALIDATED

    Source sequence(s)
    AL512353, BC029427, BM675639, BQ712089
    Consensus CDS
    CCDS474.1
    UniProtKB/Swiss-Prot
    A8K5P1, D3DPW7, Q8N300
    Related
    ENSP00000361599.4, ENST00000372521.9
    Conserved Domains (1) summary
    pfam15674
    Location:6 → 62
    CCDC23; Coiled-coil domain-containing protein 23

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    42807052..42817397 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017001226.2 → XP_016856715.1  small vasohibin-binding protein isoform X1

    UniProtKB/Swiss-Prot
    A8K5P1, D3DPW7, Q8N300
    Conserved Domains (1) summary
    pfam15674
    Location:6 → 62
    CCDC23; Coiled-coil domain-containing protein 23

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    42677541..42687878 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336446.1 → XP_054192421.1  small vasohibin-binding protein isoform X1

    UniProtKB/Swiss-Prot
    A8K5P1, D3DPW7, Q8N300
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N300.1 GenPept UniProtKB/Swiss-Prot:Q8N300

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