SV2C

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

Basic information

Region (hg38): 5:76083382-76353939

Links

ENSG00000122012 ∙ NCBI:22987 ∙ OMIM:610291 ∙ HGNC:30670 ∙ Uniprot:Q496J9 ∙ 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 SV2C gene.

• Inborn genetic diseases (33 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SV2C 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	2	3
missense			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	33	2	3

Variants in SV2C

This is a list of pathogenic ClinVar variants found in the SV2C region.

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

Position	Type	Phenotype	Significance	ClinVar
5-76131781-C-T		SV2C-related disorder	Likely benign (Nov 06, 2019)
5-76131838-G-A		not specified	Uncertain significance (Dec 06, 2021)
5-76131867-T-A		not specified	Uncertain significance (Mar 01, 2024)
5-76131895-T-C		not specified	Uncertain significance (Nov 07, 2022)
5-76131952-G-A		not specified	Uncertain significance (Dec 07, 2021)
5-76132034-G-A		not specified	Uncertain significance (Dec 21, 2023)
5-76132055-C-G		not specified	Likely benign (Dec 14, 2023)
5-76132055-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-76132110-G-A		SV2C-related disorder	Benign (Oct 16, 2019)
5-76132111-C-T		SV2C-related disorder	Likely benign (Feb 07, 2022)
5-76132219-G-A		not specified	Uncertain significance (Jun 13, 2023)
5-76132245-C-T			Benign (Apr 24, 2018)
5-76132249-G-A		SV2C-related disorder	Likely benign (Jan 06, 2020)
5-76132264-G-A		not specified	Uncertain significance (Jan 27, 2022)
5-76132299-C-T		SV2C-related disorder	Likely benign (Feb 20, 2019)
5-76132322-G-C		not specified	Uncertain significance (Nov 15, 2021)
5-76132339-G-A			Benign (May 18, 2018)
5-76194934-T-A		not specified	Uncertain significance (May 05, 2023)
5-76194967-G-A		not specified	Uncertain significance (Nov 01, 2022)
5-76195051-T-C		not specified	Uncertain significance (Aug 02, 2021)
5-76209738-T-C		not specified	Uncertain significance (Sep 17, 2021)
5-76209789-G-A		not specified	Uncertain significance (Jul 26, 2023)
5-76209850-C-T		SV2C-related disorder	Likely benign (Apr 08, 2019)
5-76209852-C-T		not specified	Uncertain significance (Jan 29, 2024)
5-76209872-A-G		not specified	Uncertain significance (Sep 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SV2C	protein_coding	protein_coding	ENST00000502798	12	270768

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000244	1.00	125274	1	77	125352	0.000311

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.868	369	419	0.881	0.0000232	4794
Missense in Polyphen		143	174.38	0.82007		1952
Synonymous	-1.40	184	161	1.14	0.00000969	1363
Loss of Function	3.28	14	34.9	0.401	0.00000166	415

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00125
Ashkenazi Jewish	0.00	0.00
East Asian	0.000283	0.000274
Finnish	0.00	0.00
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000283	0.000274
South Asian	0.000393	0.000392
Other	0.000165	0.000164

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. {ECO:0000250|UniProtKB:Q9Z2I6}.; FUNCTION: (Microbial infection) Possible receptor for C.botulinum neurotoxin type D (BoNT/D, botD); note that type D does not usually infect humans. {ECO:0000269|PubMed:21483489}.
• 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 (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.28

Haploinsufficiency Scores

• pHI: 0.172
• hipred: Y
• hipred_score: 0.554
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.685

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sv2c
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

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