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

Summary

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. 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, Apr 2022]
Expression: Ubiquitous expression in testis (RPKM 21.3), fat (RPKM 15.7) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p34.2

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (42807052..42817397, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (42677541..42687878, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (43272723..43283068, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH98844 (e-PCR)
- UniSTS:91164

G32266 (e-PCR)
- UniSTS:116865

SHGC-74676 (e-PCR)
- UniSTS:63897

A005Q11 (e-PCR)
- UniSTS:62910

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)

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

42807052..42817397 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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