VAMP8

vesicle associated membrane protein 8, the group of Vesicle associated membrane proteins

Basic information

Region (hg38): 2:85561561-85582031

Links

ENSG00000118640 ∙ NCBI:8673 ∙ OMIM:603177 ∙ HGNC:12647 ∙ Uniprot:Q9BV40 ∙ 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 VAMP8 gene.

• Inborn genetic diseases (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAMP8 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			4			4
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	4	0	1

Variants in VAMP8

This is a list of pathogenic ClinVar variants found in the VAMP8 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-85561615-C-A			Benign (Jul 09, 2018)
2-85579034-A-G		not specified	Uncertain significance (Dec 14, 2021)
2-85579040-G-C		not specified	Uncertain significance (Dec 09, 2023)
2-85579121-A-G		not specified	Uncertain significance (Nov 15, 2023)
2-85579124-A-T		not specified	Uncertain significance (Jul 31, 2023)
2-85579138-C-T		not specified	Uncertain significance (Nov 10, 2022)
2-85581684-A-G		not specified	Uncertain significance (Apr 25, 2022)
2-85581859-T-C			Benign (Nov 02, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VAMP8	protein_coding	protein_coding	ENST00000263864	3	20470

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.107	0.786	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.849	39	57.1	0.684	0.00000335	647
Missense in Polyphen		12	17.874	0.67136		230
Synonymous	-0.535	24	20.9	1.15	0.00000123	189
Loss of Function	1.26	2	5.05	0.396	2.80e-7	54

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000577	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000278	0.0000264
Middle Eastern	0.0000577	0.0000544
South Asian	0.0000669	0.0000653
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: SNAREs, soluble N-ethylmaleimide-sensitive factor- attachment protein receptors, are essential proteins for fusion of cellular membranes. SNAREs localized on opposing membranes assemble to form a trans-SNARE complex, an extended, parallel four alpha-helical bundle that drives membrane fusion. VAMP8 is a SNARE involved in autophagy through the direct control of autophagosome membrane fusion with the lysososome membrane via its interaction with the STX17-SNAP29 binary t-SNARE complex (PubMed:23217709, PubMed:25686604). Also required for dense-granule secretion in platelets (PubMed:12130530). Plays also a role in regulated enzyme secretion in pancreatic acinar cells (By similarity). Involved in the abscission of the midbody during cell division, which leads to completely separate daughter cells (By similarity). Involved in the homotypic fusion of early and late endosomes (By similarity). {ECO:0000250|UniProtKB:Q9WUF4, ECO:0000269|PubMed:12130530, ECO:0000269|PubMed:23217709, ECO:0000269|PubMed:25686604}.
• Pathway: Platelet activation - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Neutrophil degranulation;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Innate Immune System;Immune System;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.240

Intolerance Scores

• loftool: 0.656
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.285
• hipred: Y
• hipred_score: 0.621
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vamp8
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system 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); digestive/alimentary phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;protein transport;autophagosome membrane docking;eosinophil degranulation;neutrophil degranulation;viral entry into host cell;membrane organization;mucus secretion;autophagosome maturation;regulation of protein localization to plasma membrane;negative regulation of secretion by cell;positive regulation of histamine secretion by mast cell
• Cellular component: cytoplasm;lysosomal membrane;early endosome;cytosol;plasma membrane;membrane;integral component of membrane;clathrin-coated vesicle membrane;secretory granule membrane;phagocytic vesicle membrane;SNARE complex;early endosome membrane;late endosome membrane;vesicle;azurophil granule membrane;specific granule membrane;perinuclear region of cytoplasm;recycling endosome;recycling endosome membrane;extracellular exosome;tertiary granule membrane;mucin granule
• Molecular function: protein binding;chloride channel inhibitor activity