SV2A

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

Basic information

Region (hg38): 1:149903318-149917844

Links

ENSG00000159164 ∙ ∙ OMIM:185860 ∙ HGNC:20566 ∙ Uniprot:Q7L0J3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• epilepsy (Limited), mode of inheritance: AD
• developmental and epileptic encephalopathy 113 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 113	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	Craniofacial; Musculoskeletal; Neurologic	26002053; 37985816

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SV2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SV2A 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	10	6	17
missense			45	1		46
nonsense		1				1
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	46	12	6

Variants in SV2A

This is a list of pathogenic ClinVar variants found in the SV2A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-149905064-T-C		not specified	Uncertain significance (Nov 12, 2021)
1-149905095-G-T			Likely benign (Apr 17, 2018)
1-149905121-C-T		not specified	Uncertain significance (Sep 23, 2023)
1-149905122-G-A			Benign (Jul 17, 2018)
1-149905134-G-A			Benign (Dec 31, 2019)
1-149905914-C-T		not specified	Uncertain significance (Oct 16, 2024)
1-149905947-C-T		not specified	Uncertain significance (Jun 03, 2024)
1-149905983-C-T		not specified	Uncertain significance (Jan 18, 2022)
1-149905984-A-G			Likely benign (Jan 30, 2018)
1-149906028-C-T		not specified	Uncertain significance (May 31, 2023)
1-149906762-G-A			Likely benign (Dec 31, 2019)
1-149906777-G-A			Benign (Dec 31, 2019)
1-149906784-G-A		not specified	Uncertain significance (Dec 21, 2022)
1-149906798-G-T		not specified	Uncertain significance (Jan 29, 2024)
1-149907704-G-A			Likely benign (Dec 14, 2018)
1-149907812-C-G		not specified	Uncertain significance (Feb 17, 2023)
1-149907819-C-T		not specified	Uncertain significance (Feb 08, 2025)
1-149907820-G-A		not specified	Uncertain significance (Mar 24, 2023)
1-149908066-C-T		not specified	Uncertain significance (May 26, 2023)
1-149908067-G-A		Developmental and epileptic encephalopathy 113	Pathogenic (Apr 04, 2024)
1-149908121-C-T		not specified	Uncertain significance (Sep 21, 2023)
1-149908128-C-T			Likely benign (Jan 01, 2023)
1-149908168-C-T		not specified	Uncertain significance (Jan 27, 2022)
1-149908190-C-T		not specified	Uncertain significance (Sep 13, 2023)
1-149909233-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SV2A	protein_coding	protein_coding	ENST00000369146	12	14565

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.228	0.772	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	328	455	0.721	0.0000285	4853
Missense in Polyphen		84	198.11	0.42401		2202
Synonymous	0.200	185	189	0.981	0.0000123	1501
Loss of Function	4.36	9	38.0	0.237	0.00000246	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000704	0.0000703
Middle Eastern	0.000109	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the control of regulated secretion in neural and endocrine cells, enhancing selectively low-frequency neurotransmission. Positively regulates vesicle fusion by maintaining the readily releasable pool of secretory vesicles (By similarity). {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: 0.345

Intolerance Scores

• loftool: 0.393
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.41

Haploinsufficiency Scores

• pHI: 0.903
• hipred: Y
• hipred_score: 0.639
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sv2a
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); 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); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: cellular calcium ion homeostasis;regulation of gamma-aminobutyric acid secretion;synaptic vesicle priming;transmembrane transport
• Cellular component: endoplasmic reticulum;plasma membrane;cell-cell junction;synaptic vesicle;integral component of membrane;integral component of synaptic vesicle membrane;dendrite;synaptic vesicle membrane;neuromuscular junction;neuron projection;neuronal cell body;presynaptic active zone;glutamatergic synapse;GABA-ergic synapse
• Molecular function: protein kinase binding;transmembrane transporter activity