SVBP

protein-coding

small vasohibin binding protein

Gene 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, Jul 2025]

Previous symbols:

CCDC23

MANE transcript

NM_199342.4

Inheritance

AD, AR

ClinVar variants

P:6U:11

Top phenotype

Neurodevelopmental disorder with ataxia, hypotonia, and microcephaly

gnomAD constraint

pLI —, LoF o/e 1.15

Max pathogenic AF

—

Genomic locus

chr1:42,807,052-42,817,397

External References & Databases

Ensembl (ENSG00000177868)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

syndromic intellectual disabilitySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0000508

Submitter: Orphanet

neurodevelopmental disorder with ataxia, hypotonia, and microcephalySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032816

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Neurodevelopmental disorder with ataxia, hypotonia, and microcephalyAR

Manifestation: Musculoskeletal; Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 30607023

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SVBP variants in ClinVar

8 Conditions Cataloged

Inborn genetic diseasesTotal: 9

not providedTotal: 4

Neurodevelopmental disorder with ataxia, hypotonia, and microcephalyTotal: 4

Lower limb spasticityTotal: 2

Intellectual disabilityTotal: 2

MicrocephalyTotal: 2

SVBP-related disorderTotal: 1

Neurodevelopmental disorder with ataxiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_199342.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense		1 clinvar	9 clinvar			10
nonsense		2 clinvar				2
start loss						0
frameshift	1 clinvar	2 clinvar	1 clinvar			4
splice donor/acceptor (+/-2bp)						0
Total	1	5	11	0	0	17

Highest pathogenic variant AF is 0.0000047888725

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_199342.4	RefSeq	NP_955374.1	2	MANE Select
ENST00000372521.9	Ensembl	ENSP00000361599.4	2	MANE Select
ENST00000372522.5	Ensembl	ENSP00000361600.1	2	Standard
ENST00000881555.1	Ensembl	ENSP00000551614.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteolysis
protein secretion
negative regulation of endothelial cell migration
negative regulation of protein ubiquitination

Molecular Function

protein binding

Cellular Component

extracellular region
cytoplasm
apical part of cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372521
Coding exons: 2
Length: 10232
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125747
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.374	26	32.0	0.814	0.00000136	432
Missense (PolyPhen)		4	5.9659	0.67048		92
Synonymous	0.674	8	10.8	0.740	4.65e-7	111
Loss of Function	-0.258	4	3.48	1.15	1.47e-7	43

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: 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). Also required to enhance the solubility and secretion of VASH1 and VASH2 (PubMed:20736312, PubMed:27879017). {ECO:0000269|PubMed:20736312, ECO:0000269|PubMed:27879017, ECO:0000269|PubMed:29146869}.;

Intolerance Scores

RVIS EVS: 0.15
RVIS percentile EVS: 63.81

Essentials

Essential (gene trap): N