SV2B

synaptic vesicle glycoprotein 2B, the group of Solute carrier family 22

Basic information

Region (hg38): 15:91099950-91302565

Links

ENSG00000185518 ∙ NCBI:9899 ∙ OMIM:185861 ∙ HGNC:16874 ∙ Uniprot:Q7L1I2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SV2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SV2B 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					1	1
missense			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	1

Variants in SV2B

This is a list of pathogenic ClinVar variants found in the SV2B region.

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

Position	Type	Phenotype	Significance	ClinVar
15-91226295-G-C		not specified	Uncertain significance (May 16, 2024)
15-91226303-G-A		not specified	Uncertain significance (Jun 23, 2021)
15-91226324-C-T		not specified	Uncertain significance (Feb 16, 2023)
15-91226325-G-A		not specified	Uncertain significance (Jan 02, 2024)
15-91226331-A-G		not specified	Uncertain significance (Feb 27, 2024)
15-91226348-G-C		not specified	Uncertain significance (Aug 13, 2021)
15-91226396-A-G		not specified	Uncertain significance (Apr 13, 2022)
15-91226418-G-A		not specified	Uncertain significance (Jun 04, 2024)
15-91226420-A-G		not specified	Uncertain significance (Nov 07, 2022)
15-91226500-C-A		not specified	Uncertain significance (Jul 19, 2023)
15-91226533-G-C		not specified	Uncertain significance (Oct 06, 2021)
15-91226579-C-T		not specified	Uncertain significance (Jun 18, 2021)
15-91226600-T-C		not specified	Uncertain significance (May 20, 2024)
15-91226603-G-A		not specified	Uncertain significance (Feb 15, 2023)
15-91226610-G-A		not specified	Uncertain significance (Apr 07, 2022)
15-91251905-A-T		not specified	Uncertain significance (May 26, 2022)
15-91251917-G-A		not specified	Likely benign (Mar 17, 2023)
15-91252371-T-C		not specified	Uncertain significance (Oct 18, 2021)
15-91252421-C-T		not specified	Uncertain significance (May 06, 2022)
15-91252491-C-T		not specified	Uncertain significance (Aug 02, 2021)
15-91252515-A-G		not specified	Uncertain significance (Mar 19, 2024)
15-91258450-C-T		not specified	Uncertain significance (Aug 02, 2023)
15-91258457-A-G		not specified	Uncertain significance (Feb 06, 2024)
15-91266640-C-T		not specified	Uncertain significance (Feb 27, 2024)
15-91266658-G-A		SV2B-related disorder	Likely benign (Jul 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SV2B	protein_coding	protein_coding	ENST00000394232	12	201360

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000570	1.00	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	327	392	0.835	0.0000209	4560
Missense in Polyphen		104	146.42	0.71028		1745
Synonymous	0.825	139	152	0.915	0.00000885	1269
Loss of Function	3.20	13	32.7	0.397	0.00000165	368

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.000399	0.000397
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000794	0.0000791
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000502	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably plays a role in the control of regulated secretion in neural and endocrine cells. {ECO:0000250}.
• Pathway: ECM-receptor interaction - Homo sapiens (human);Disease;Toxicity of botulinum toxin type A (BoNT/A);Toxicity of botulinum toxin type D (BoNT/D);Toxicity of botulinum toxin type F (BoNT/F);Uptake and actions of bacterial toxins;Neurotoxicity of clostridium toxins;Infectious disease;Toxicity of botulinum toxin type E (BoNT/E) (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• loftool: 0.468
• rvis_EVS: -1.17
• rvis_percentile_EVS: 5.99

Haploinsufficiency Scores

• pHI: 0.745
• hipred: Y
• hipred_score: 0.554
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.734

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sv2b
• Phenotype: normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: neurotransmitter transport;chemical synaptic transmission;transmembrane transport
• Cellular component: acrosomal vesicle;plasma membrane;synaptic vesicle;membrane;integral component of membrane;cell junction;synaptic vesicle membrane;neuron projection
• Molecular function: protein binding;transmembrane transporter activity