SVBP

small vasohibin binding protein

Basic information

Region (hg38): 1:42807052-42817397

Previous symbols: [ "CCDC23" ]

Links

ENSG00000177868 ∙ NCBI:374969 ∙ OMIM:617853 ∙ HGNC:29204 ∙ Uniprot:Q8N300 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• syndromic intellectual disability (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with ataxia, hypotonia, and microcephaly	AR	General	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	Musculoskeletal; Neurologic	30607023

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SVBP gene.

• Neurodevelopmental disorder with ataxia, hypotonia, and microcephaly (1 variants)
• Microcephaly;Intellectual disability;Lower limb spasticity (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SVBP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense		1	5			6
nonsense		1				1
start loss						0
frameshift	1	1	1			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	3	6	0	0

Variants in SVBP

This is a list of pathogenic ClinVar variants found in the SVBP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-42807419-C-T		Inborn genetic diseases	Uncertain significance (Aug 05, 2024)
1-42807456-C-G		Inborn genetic diseases	Uncertain significance (May 11, 2022)
1-42807460-T-C		Inborn genetic diseases	Uncertain significance (Aug 08, 2023)
1-42807469-A-G		SVBP-related disorder	Likely pathogenic (Apr 27, 2023)
1-42816438-CTT-C			Likely pathogenic (Dec 01, 2021)
1-42816441-T-C		Inborn genetic diseases	Uncertain significance (May 28, 2024)
1-42816450-T-C		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
1-42816454-G-C		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
1-42816463-G-A		Lower limb spasticity;Microcephaly;Intellectual disability • Neurodevelopmental disorder with ataxia, hypotonia, and microcephaly • Neurodevelopmental disorder with ataxia	Pathogenic/Likely pathogenic (Oct 04, 2024)
1-42816502-ATTCT-A		Microcephaly;Intellectual disability;Lower limb spasticity • Neurodevelopmental disorder with ataxia, hypotonia, and microcephaly	Pathogenic (Apr 04, 2019)
1-42816516-G-GT			Uncertain significance (Dec 01, 2017)
1-42816517-T-C		Inborn genetic diseases	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SVBP	protein_coding	protein_coding	ENST00000372521	2	10232

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00113	0.404	125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.374	26	32.0	0.814	0.00000136	432
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.325
• ghis: 0.543

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Svbp

Gene ontology

• Biological process: proteolysis;protein secretion;negative regulation of endothelial cell migration;negative regulation of protein ubiquitination
• Cellular component: extracellular region;cytoplasm;apical part of cell
• Molecular function: protein binding