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VAMP5

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Summary

VAMP5 (vesicle associated membrane protein 5, HGNC:12646) is a protein-coding gene on chromosome 2p11.2, encoding Vesicle-associated membrane protein 5 (O95183). May participate in trafficking events that are associated with myogenesis, such as myoblast fusion and/or GLUT4 trafficking.

Synaptobrevins/VAMPs, syntaxins, and the 25-kD synaptosomal-associated protein are the main components of a protein complex involved in the docking and/or fusion of vesicles and cell membranes. The VAMP5 gene is a member of the vesicle-associated membrane protein (VAMP)/synaptobrevin family and the SNARE superfamily. This VAMP family member may participate in vesicle trafficking events that are associated with myogenesis.

Source: NCBI Gene 10791 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 31 total
  • MANE Select transcript: NM_006634

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:12646
Approved symbolVAMP5
Namevesicle associated membrane protein 5
Location2p11.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000168899
Ensembl biotypeprotein_coding
OMIM607029
Entrez10791

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000306384, ENST00000462451, ENST00000872734, ENST00000966848

RefSeq mRNA: 1 — MANE Select: NM_006634 NM_006634

CCDS: CCDS1980

Canonical transcript exons

ENST00000306384 — 3 exons

ExonStartEnd
ENSE000011354668558443185584493
ENSE000011549828559294885593406
ENSE000011549868559172585591862

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 98.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.3087 / max 219.7204, expressed in 1390 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
2122020.30871390

Top tissues by expression

280 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right lungUBERON:000216798.12gold quality
hindlimb stylopod muscleUBERON:000425297.82gold quality
upper lobe of left lungUBERON:000895297.81gold quality
left adrenal gland cortexUBERON:003582597.80gold quality
right adrenal glandUBERON:000123397.74gold quality
omental fat padUBERON:001041497.72gold quality
right adrenal gland cortexUBERON:003582797.69gold quality
peritoneumUBERON:000235897.68gold quality
left adrenal glandUBERON:000123497.59gold quality
monocyteCL:000057697.58gold quality
left uterine tubeUBERON:000130397.38gold quality
right atrium auricular regionUBERON:000663197.31gold quality
granulocyteCL:000009497.28gold quality
left coronary arteryUBERON:000162697.11gold quality
adipose tissue of abdominal regionUBERON:000780897.01gold quality
lower esophagus muscularis layerUBERON:003583396.98gold quality
mononuclear cellCL:000084296.97gold quality
lower esophagusUBERON:001347396.97gold quality
gastrocnemiusUBERON:000138896.92gold quality
leukocyteCL:000073896.87gold quality
apex of heartUBERON:000209896.87gold quality
esophagogastric junction muscularis propriaUBERON:003584196.85gold quality
descending thoracic aortaUBERON:000234596.81gold quality
adrenal cortexUBERON:000123596.72gold quality
mucosa of stomachUBERON:000119996.70gold quality
upper lobe of lungUBERON:000894896.65gold quality
right coronary arteryUBERON:000162596.63gold quality
coronary arteryUBERON:000162196.59gold quality
thoracic aortaUBERON:000151596.55gold quality
ascending aortaUBERON:000149696.51gold quality

Single-cell (SCXA)

Detected in 19 experiment(s), a significant marker in 17.

ExperimentMarker?Max mean expression
E-MTAB-9388yes1412.32
E-CURD-98yes1300.12
E-MTAB-8271yes1059.25
E-MTAB-10287yes80.26
E-MTAB-7008yes73.84
E-HCAD-1yes56.44
E-MTAB-10553yes50.42
E-HCAD-10yes47.13
E-GEOD-134144yes43.32
E-MTAB-8410yes33.08
E-MTAB-6701yes32.86
E-CURD-46yes27.59
E-MTAB-9467yes17.61
E-HCAD-9yes17.24
E-CURD-112yes12.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting VAMP5, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4283100.0066.422097
HSA-MIR-18A-3P99.5665.681092
HSA-MIR-5589-3P99.2968.301443
HSA-MIR-7156-3P98.2567.66859
HSA-MIR-4664-5P98.1765.071020
HSA-MIR-342-5P97.2564.10817

Literature-anchored findings (GeneRIF, showing 3)

  • Our findings indicate that VAMP5 and VAMP8 are not involved in POAG in the Dutch population. (PMID:16110299)
  • VAMP5 polymorphisms were found to be associated with the total colonic aganglionosis of Hirschsprung disease. (PMID:26970437)
  • This study provided new evidence of epistatic association of VAMP5 and MCC with increased risk of Hirschsprung disease (PMID:29695640)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_reriovamp5ENSDARG00000068262
mus_musculusVamp5ENSMUSG00000073002
rattus_norvegicusVamp5ENSRNOG00000012659
drosophila_melanogasterSybFBGN0003660
caenorhabditis_elegansWBGENE00004898
caenorhabditis_elegansWBGENE00004899
caenorhabditis_elegansWBGENE00014084
caenorhabditis_elegansWBGENE00044062

Paralogs (10): VAMP3 (ENSG00000049245), SEC22C (ENSG00000093183), YKT6 (ENSG00000106636), VAMP4 (ENSG00000117533), VAMP8 (ENSG00000118640), SEC22A (ENSG00000121542), VAMP7 (ENSG00000124333), VAMP1 (ENSG00000139190), VAMP2 (ENSG00000220205), SEC22B (ENSG00000265808)

Protein

Protein identifiers

Vesicle-associated membrane protein 5 — O95183 (reviewed: O95183)

Alternative names: Myobrevin

All UniProt accessions (2): O95183, Q6FG93

UniProt curated annotations — full annotation on UniProt →

Function. May participate in trafficking events that are associated with myogenesis, such as myoblast fusion and/or GLUT4 trafficking.

Subcellular location. Cell membrane. Endomembrane system. Golgi apparatus. trans-Golgi network membrane.

Post-translational modifications. (Microbial infection) Targeted and hydrolyzed by C.botulinum neurotoxin type X (BoNT/X) which hydrolyzes the 40-Arg-|-Ser-41 bond and probably inhibits neurotransmitter release. It remains unknown whether BoNT/X is ever produced, or what organisms it targets.

Induction. During myogenesis.

Similarity. Belongs to the synaptobrevin family.

RefSeq proteins (1): NP_006625* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001388Synaptobrevin-likeFamily
IPR042166Vamp5Family
IPR042581VAMP5_R-SNARE_Domain
IPR042855V_SNARE_CCDomain

Pfam: PF00957

UniProt features (11 total): modified residue 3, topological domain 2, chain 1, sequence conflict 1, transmembrane region 1, domain 1, region of interest 1, site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95183-F180.600.27

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 40–41 ((microbial infection) cleavage; by c.botulinum neurotoxin type x (bont/x))

Post-translational modifications (3): 41, 48, 49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 271 (showing top): RNGTGGGC_UNKNOWN, GOBP_MUSCLE_TISSUE_DEVELOPMENT, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, KAAB_HEART_ATRIUM_VS_VENTRICLE_UP, GOCC_CELL_SURFACE, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_GOLGI_TO_PLASMA_MEMBRANE_TRANSPORT, GOCC_TRANS_GOLGI_NETWORK, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, GOBP_SKELETAL_MUSCLE_ORGAN_DEVELOPMENT, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, GOBP_GOLGI_TO_PLASMA_MEMBRANE_PROTEIN_TRANSPORT

GO Biological Process (5): muscle organ development (GO:0007517), skeletal muscle tissue development (GO:0007519), cell differentiation (GO:0030154), Golgi to plasma membrane protein transport (GO:0043001), vesicle-mediated transport (GO:0016192)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (12): late endosome (GO:0005770), trans-Golgi network (GO:0005802), plasma membrane (GO:0005886), cell surface (GO:0009986), intercalated disc (GO:0014704), cytoplasmic vesicle membrane (GO:0030659), organelle membrane (GO:0031090), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), Golgi apparatus (GO:0005794), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
membrane2
cytoplasm2
animal organ development1
muscle structure development1
striated muscle tissue development1
skeletal muscle organ development1
cellular developmental process1
Golgi to plasma membrane transport1
protein transport1
establishment of protein localization to plasma membrane1
protein localization to plasma membrane1
transport1
cellular process1
binding1
endosome1
Golgi apparatus subcompartment1
cell periphery1
cell-cell contact zone1
vesicle membrane1
cytoplasmic vesicle1
membrane-bounded organelle1
extracellular vesicle1
endomembrane system1
intracellular membrane-bounded organelle1
vacuole1
plasma membrane1

Protein interactions and networks

STRING

1106 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
VAMP5GOSR1O95249838
VAMP5YKT6O15498667
VAMP5VAMP8Q9BV40611
VAMP5VAMP7P51809596
VAMP5GGCXP38435586
VAMP5STX19Q8N4C7530
VAMP5PTPN13Q12923515
VAMP5CAV1Q03135490
VAMP5STX4Q12846482
VAMP5SNAP23O00161479
VAMP5STX11O75558472
VAMP5USP39Q53GS9469
VAMP5RNF181Q9P0P0461
VAMP5DENND11A4D1U4444
VAMP5STX3Q13277441

IntAct

227 interactions, top by confidence:

ABTypeScore
SNAP29VAMP5psi-mi:“MI:0915”(physical association)0.830
VAMP5STX4psi-mi:“MI:0915”(physical association)0.830
VAMP5SNAP29psi-mi:“MI:0915”(physical association)0.830
STX16VAMP5psi-mi:“MI:0915”(physical association)0.740
VAMP5STX16psi-mi:“MI:0915”(physical association)0.740
VAMP5STX5psi-mi:“MI:0915”(physical association)0.740
VAMP5ERGIC3psi-mi:“MI:0915”(physical association)0.670
VAMP5SNAP23psi-mi:“MI:0915”(physical association)0.560
SNAP23VAMP5psi-mi:“MI:0915”(physical association)0.560
VAMP5SDC3psi-mi:“MI:0915”(physical association)0.560
VAMP5ERVFRD-1psi-mi:“MI:0915”(physical association)0.560
VAMP5IL7Rpsi-mi:“MI:0915”(physical association)0.560
VAMP5REEP4psi-mi:“MI:0915”(physical association)0.560
VAMP5SORT1psi-mi:“MI:0915”(physical association)0.560
VAMP5SEC11Cpsi-mi:“MI:0915”(physical association)0.560
VAMP5ZDHHC15psi-mi:“MI:0915”(physical association)0.560
VAMP5SLC39A2psi-mi:“MI:0915”(physical association)0.560
VAMP5IL10RApsi-mi:“MI:0915”(physical association)0.560

BioGRID (209): VAMP5 (Two-hybrid), VAMP5 (Two-hybrid), VAMP5 (Two-hybrid), VAMP5 (Two-hybrid), VAMP5 (Two-hybrid), VAMP5 (Two-hybrid), VAMP5 (Affinity Capture-MS), ACTL6A (Affinity Capture-MS), BET1L (Affinity Capture-MS), BTF3 (Affinity Capture-MS), CEP44 (Affinity Capture-MS), COPA (Affinity Capture-MS), CSE1L (Affinity Capture-MS), DENND1A (Affinity Capture-MS), DHX29 (Affinity Capture-MS)

ESM2 similar proteins: O02495, O15155, O23429, O35623, O94651, O95183, P13701, P18489, P23763, P32867, P34351, P35589, P47192, P47193, P47194, P63024, P63025, P63026, P63027, P63044, P63045, P78768, P93654, Q04338, Q09730, Q0V7N0, Q15836, Q20574, Q27236, Q2KJD2, Q4R8T0, Q54GB3, Q5RBX2, Q60WU2, Q62442, Q62896, Q63666, Q6TMJ9, Q7XIE2, Q8VXX9

Diamond homologs: O02495, O48850, O49377, O70404, O70480, O75379, O95183, P13701, P18489, P23763, P31109, P33328, P34351, P35589, P47192, P47193, P47194, P63024, P63025, P63026, P63027, P63044, P63045, Q0V7N0, Q12255, Q15836, Q27236, Q2KHY2, Q2KJD2, Q32L97, Q3T0Y8, Q4R8T0, Q5REQ5, Q60WU2, Q62442, Q63666, Q6TMJ9, Q92356, Q9BV40, Q9FMR5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 69 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
obsolete vesicle docking787.9×3e-10
vesicle fusion549.3×6e-06
exocytosis717.4×1e-05
intracellular protein transport88.5×3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

31 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance25
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

564 predictions. Top by Δscore:

VariantEffectΔscore
2:85591721:CCA:Cacceptor_loss1.0000
2:85591723:A:AGacceptor_gain1.0000
2:85591724:G:GAacceptor_loss1.0000
2:85591724:G:GGacceptor_gain1.0000
2:85591724:GGCA:Gacceptor_gain1.0000
2:85591857:GA:Gdonor_gain1.0000
2:85591858:A:Gdonor_gain1.0000
2:85591863:GT:Gdonor_gain1.0000
2:85592933:T:TAacceptor_gain1.0000
2:85592934:G:Aacceptor_gain1.0000
2:85592947:GA:Gacceptor_gain1.0000
2:85591858:ATATG:Adonor_loss0.9900
2:85591859:TATGG:Tdonor_loss0.9900
2:85591860:ATG:Adonor_loss0.9900
2:85591860:ATGGT:Adonor_gain0.9900
2:85591861:TGGT:Tdonor_gain0.9900
2:85591862:GG:Gdonor_loss0.9900
2:85591862:GGTG:Gdonor_gain0.9900
2:85591863:G:GGdonor_loss0.9900
2:85591865:G:GGdonor_gain0.9900
2:85591877:G:Tdonor_gain0.9900
2:85592936:G:Aacceptor_gain0.9900
2:85592940:A:AGacceptor_gain0.9900
2:85592943:CGCA:Cacceptor_loss0.9900
2:85592945:CAG:Cacceptor_gain0.9900
2:85592946:A:AGacceptor_gain0.9900
2:85592946:A:Tacceptor_loss0.9900
2:85592946:AGA:Aacceptor_gain0.9900
2:85592947:G:GAacceptor_gain0.9900
2:85592947:GAG:Gacceptor_gain0.9900

AlphaMissense

750 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:85592957:T:CF51L0.970
2:85592959:C:AF51L0.970
2:85592959:C:GF51L0.970
2:85591783:G:CR21P0.946
2:85591842:T:CS41P0.942
2:85591852:T:CL44P0.929
2:85591790:C:AN23K0.928
2:85591790:C:GN23K0.928
2:85591831:T:CL37P0.928
2:85591840:G:CR40P0.927
2:85591781:G:AM20I0.900
2:85591781:G:CM20I0.900
2:85591781:G:TM20I0.900
2:85591758:G:CA13P0.895
2:85592948:A:CS48R0.892
2:85592950:C:AS48R0.892
2:85592950:C:GS48R0.892
2:85591810:G:CR30P0.891
2:85591789:A:TN23I0.890
2:85593041:G:CG79R0.865
2:85591855:T:CL45P0.857
2:85591791:T:CF24L0.836
2:85591793:C:AF24L0.836
2:85591793:C:GF24L0.836
2:85591849:A:CQ43P0.832
2:85592951:T:CS49P0.824
2:85592958:T:CF51S0.823
2:85591788:A:TN23Y0.822
2:85592958:T:GF51C0.814
2:85591750:A:CQ10P0.808

dbSNP variants (sampled 300 via entrez): RS1000071228 (2:85587633 C>T), RS1000186252 (2:85585309 C>CT), RS1000494913 (2:85592527 G>A), RS1000601908 (2:85587278 G>A), RS1000640763 (2:85593553 T>C), RS1000798170 (2:85586844 G>A), RS1001074631 (2:85586089 G>A), RS1001117277 (2:85586485 A>G), RS1001168263 (2:85586534 C>T), RS1001188473 (2:85587212 T>C), RS1001470386 (2:85593881 G>A), RS1001771698 (2:85588021 C>T), RS1002654297 (2:85585502 G>T), RS1003214624 (2:85584579 GCTGGGGCCTCCC>G), RS1003248215 (2:85583894 T>C)

Disease associations

OMIM: gene MIM:607029 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

9 associations (top):

StudyTraitp-value
GCST001148_4Prostate cancer3.000000e-15
GCST003116_32Coronary artery disease4.000000e-10
GCST003117_3Myocardial infarction3.000000e-10
GCST004787_22Coronary artery disease (myocardial infarction, percutaneous transluminal coronary angioplasty, coronary artery bypass grafting, angina or chromic ischemic heart disease)2.000000e-13
GCST005196_204Coronary artery disease2.000000e-23
GCST90000025_757Appendicular lean mass1.000000e-12
GCST90002401_379Platelet distribution width1.000000e-17
GCST90002405_129Reticulocyte count1.000000e-10
GCST90002406_22Reticulocyte fraction of red cells2.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004980appendicular lean mass
EFO:0007984platelet component distribution width
EFO:0007986reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, decreases expression6
Benzo(a)pyreneaffects methylation, increases expression3
Acetaminophendecreases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tobacco Smoke Pollutionincreases expression, affects expression2
aristolochic acid Iincreases expression1
bisphenol Faffects cotreatment, increases methylation1
trichostatin Aincreases expression1
tris(2-butoxyethyl) phosphateaffects expression1
sodium arseniteincreases expression1
nickel sulfateincreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
ICG 001increases expression1
dorsomorphinaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Temozolomidedecreases expression1
Sunitinibdecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Arsenicaffects expression1
Cadmiumincreases abundance, increases expression1
Calcitriolaffects cotreatment, increases expression1
Cisplatinincreases expression1
Doxorubicindecreases expression1
Estradioldecreases expression1
Silicon Dioxideincreases expression1
Smokeincreases expression1
Testosteroneaffects cotreatment, increases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot