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.

not_specified (81 variants)
Prostate_cancer (1 variants)
SV2B-related_disorder (1 variants)

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. These statistics are base on transcript: NM_001323032.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			81 clinvar	2 clinvar		83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	81	2	0

Loading clinvar variants...

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