VAMP3

vesicle associated membrane protein 3, the group of Vesicle associated membrane proteins

Basic information

Region (hg38): 1:7771296-7781432

Links

ENSG00000049245

∙ NCBI:9341 ∙ OMIM:603657 ∙ HGNC:12644 ∙ Uniprot:Q15836 ∙ 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 VAMP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAMP3 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			7 clinvar			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in VAMP3

This is a list of pathogenic ClinVar variants found in the VAMP3 region.

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

Position	Phenotype	Significance	ClinVar
1-7773459-C-T	not specified	Uncertain significance (Dec 28, 2022)	2339974
1-7777226-G-A	not specified	Uncertain significance (May 01, 2024)	3331832
1-7777256-G-A	not specified	Uncertain significance (Oct 25, 2022)	2219922
1-7777272-C-T	not specified	Uncertain significance (Jan 25, 2023)	3188120
1-7777277-G-A	not specified	Uncertain significance (Jul 09, 2021)	2236144
1-7777289-A-G	not specified	Uncertain significance (Jan 18, 2023)	2476530
1-7778127-A-G	not specified	Uncertain significance (May 17, 2023)	2547082
1-7778136-A-G	not specified	Uncertain significance (Apr 05, 2023)	2527993

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VAMP3	protein_coding	protein_coding	ENST00000054666	5	10164

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00259	0.802	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.118	58	60.6	0.957	0.00000358	651
Missense in Polyphen		9	12.949	0.69502		177
Synonymous	-1.65	32	22.1	1.45	0.00000154	189
Loss of Function	1.05	5	8.26	0.605	5.01e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: SNARE involved in vesicular transport from the late endosomes to the trans-Golgi network. {ECO:0000269|PubMed:18195106}.;
Pathway: Phagosome - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;miR-targeted genes in lymphocytes - TarBase;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Arf6 trafficking events;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec: 0.169

Intolerance Scores

loftool: 0.526
rvis_EVS: -0.08
rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

pHI: 0.0882
hipred: Y
hipred_score: 0.628
ghis: 0.633

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.780

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Vamp3
Phenotype: immune system phenotype; homeostasis/metabolism phenotype; normal phenotype; hematopoietic system phenotype; 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);

Gene ontology

Biological process: positive regulation of receptor recycling;antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;exocytosis;vesicle docking involved in exocytosis;vesicle-mediated transport;calcium ion regulated exocytosis;substrate adhesion-dependent cell spreading;SNARE complex assembly;retrograde transport, endosome to Golgi;Golgi to plasma membrane protein transport;positive regulation of immunoglobulin secretion;membrane organization;membrane fusion;protein-containing complex assembly;mucus secretion;cellular response to interferon-gamma;negative regulation of secretion by cell;regulation of histamine secretion by mast cell
Cellular component: cytosol;plasma membrane;cell surface;integral component of membrane;apical plasma membrane;cell junction;transport vesicle;clathrin-coated vesicle;secretory granule;integral component of synaptic vesicle membrane;clathrin-coated vesicle membrane;phagocytic vesicle membrane;SNARE complex;trans-Golgi network membrane;neuron projection;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;recycling endosome;recycling endosome membrane
Molecular function: protein binding;syntaxin-1 binding