SNAP47

gene
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Also known as SVAP1SNAP-47

Summary

SNAP47 (synaptosome associated protein 47, HGNC:30669) is a protein-coding gene on chromosome 1q42.13, encoding Synaptosomal-associated protein 47 (Q5SQN1). Plays a role in intracellular membrane fusion.

Predicted to enable SNAP receptor activity and syntaxin binding activity. Predicted to be involved in synaptic vesicle fusion to presynaptic active zone membrane and synaptic vesicle priming. Predicted to act upstream of or within long-term synaptic potentiation. Located in BLOC-1 complex.

Source: NCBI Gene 116841 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 94 total
  • MANE Select transcript: NM_053052

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30669
Approved symbolSNAP47
Namesynaptosome associated protein 47
Location1q42.13
Locus typegene with protein product
StatusApproved
AliasesSVAP1, SNAP-47
Ensembl geneENSG00000143740
Ensembl biotypeprotein_coding
OMIM619659
Entrez116841

Gene structure

Transcript identifiers

Ensembl transcripts: 45 — 37 protein_coding, 7 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000315781, ENST00000366759, ENST00000366760, ENST00000418653, ENST00000426344, ENST00000470038, ENST00000475930, ENST00000478768, ENST00000480265, ENST00000480897, ENST00000491439, ENST00000606873, ENST00000617596, ENST00000679561, ENST00000679575, ENST00000680202, ENST00000680695, ENST00000680854, ENST00000680992, ENST00000681006, ENST00000681149, ENST00000681242, ENST00000681252, ENST00000681447, ENST00000681465, ENST00000681554, ENST00000681678, ENST00000681685, ENST00000681827, ENST00000681929, ENST00000857367, ENST00000857368, ENST00000857369, ENST00000857370, ENST00000857371, ENST00000857372, ENST00000857373, ENST00000857374, ENST00000928311, ENST00000928312, ENST00000972178, ENST00000972179, ENST00000972180, ENST00000972181, ENST00000972182

RefSeq mRNA: 7 — MANE Select: NM_053052 NM_001323930, NM_001323931, NM_001323932, NM_001323933, NM_001323934, NM_001323935, NM_053052

CCDS: CCDS81429

Canonical transcript exons

ENST00000617596 — 5 exons

ExonStartEnd
ENSE00001442552227780527227781226
ENSE00003664029227758995227759485
ENSE00003719098227766959227767083
ENSE00003731794227747692227748233
ENSE00003742491227735435227735499

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 96.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.0167 / max 86.1217, expressed in 1796 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
890312.72511786
89011.5774755
89020.3592196
89040.3550129

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207996.23gold quality
prefrontal cortexUBERON:000045194.10gold quality
left adrenal gland cortexUBERON:003582594.10gold quality
apex of heartUBERON:000209893.87gold quality
right frontal lobeUBERON:000281093.74gold quality
nucleus accumbensUBERON:000188293.68gold quality
left adrenal glandUBERON:000123493.57gold quality
middle temporal gyrusUBERON:000277193.50gold quality
left ovaryUBERON:000211993.48gold quality
adrenal cortexUBERON:000123593.26gold quality
anterior cingulate cortexUBERON:000983593.17gold quality
right ovaryUBERON:000211893.16gold quality
putamenUBERON:000187493.11gold quality
right adrenal gland cortexUBERON:003582793.11gold quality
Brodmann (1909) area 9UBERON:001354092.96gold quality
right adrenal glandUBERON:000123392.95gold quality
tibialis anteriorUBERON:000138592.88silver quality
caudate nucleusUBERON:000187392.78gold quality
cortical plateUBERON:000534392.74gold quality
neocortexUBERON:000195092.58gold quality
frontal cortexUBERON:000187092.54gold quality
dorsolateral prefrontal cortexUBERON:000983492.54gold quality
Brodmann (1909) area 23UBERON:001355492.41gold quality
primary visual cortexUBERON:000243692.14gold quality
left testisUBERON:000453392.08gold quality
adrenal glandUBERON:000236992.06gold quality
right testisUBERON:000453491.61gold quality
cerebral cortexUBERON:000095691.55gold quality
amygdalaUBERON:000187691.50gold quality
ovaryUBERON:000099291.39gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-CURD-112yes8.03
E-ANND-3yes4.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting SNAP47, 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-448799.9664.581252
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-60999.8264.26505
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-471999.7372.103329
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-5580-5P99.3866.961139
HSA-MIR-16-2-3P99.2970.601954
HSA-MIR-195-3P99.2970.611954
HSA-MIR-429098.5165.17907
HSA-MIR-548AT-3P98.3764.98580
HSA-MIR-548AY-3P98.3765.14562
HSA-MIR-477398.3567.301710
HSA-MIR-452385.6461.1664

Literature-anchored findings (GeneRIF, showing 4)

  • Three proteins are identified: PAI-RBP1, C1orf142, and COTL1, which are differentially expressed in non-small cell lung cancer cell lines with different metastatic potential. (PMID:22373659)
  • SNAP47 Interacts with ATG14 to Promote VP1 Conjugation and CVB3 Propagation. (PMID:34440910)
  • A novel identified circular RNA, circSnap47, promotes heart failure progression via regulation of miR-223-3p/MAPK axis. (PMID:35900666)
  • The STX17-SNAP47-VAMP7/VAMP8 complex is the default SNARE complex mediating autophagosome-lysosome fusion. (PMID:38182888)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosnap47ENSDARG00000063445
mus_musculusSnap47ENSMUSG00000009894
rattus_norvegicusSnap47ENSRNOG00000022472

Paralogs (3): SNAP23 (ENSG00000092531), SNAP29 (ENSG00000099940), SNAP25 (ENSG00000132639)

Protein

Protein identifiers

Synaptosomal-associated protein 47Q5SQN1 (reviewed: Q5SQN1)

Alternative names: Epididymis luminal protein 170, Synaptosomal-associated 47 kDa protein

All UniProt accessions (11): Q5SQN1, A0A087X0B7, A0A087X2J6, A0A7P0T899, A0A7P0T8U4, A0A7P0T9T2, A0A7P0TBK4, A0A7P0Z4P6, H0Y627, H7C3C7, U3KPT7

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in intracellular membrane fusion.

Subunit / interactions. Forms a complex containing SNAP47, VAMP2 and STX1A. Associates with the BLOC-1 complex. Interacts with BLOC1S6.

Subcellular location. Endomembrane system. Cytoplasm. Perinuclear region.

Similarity. Belongs to the SVAP1 family.

Isoforms (4)

UniProt IDNamesCanonical?
Q5SQN1-11yes
Q5SQN1-22
Q5SQN1-33
Q5SQN1-44

RefSeq proteins (7): NP_001310859, NP_001310860, NP_001310861, NP_001310862, NP_001310863, NP_001310864, NP_444280* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000727T_SNARE_domDomain
IPR004182GRAMDomain
IPR011993PH-like_dom_sfHomologous_superfamily

Pfam: PF02893

UniProt features (11 total): sequence variant 4, domain 2, splice variant 2, chain 1, sequence conflict 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5SQN1-F170.800.17

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 183 (showing top): GOCC_VACUOLAR_MEMBRANE, GOBP_VESICLE_ORGANIZATION, GOBP_MEMBRANE_FUSION, GOBP_NEUROTRANSMITTER_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_MACROAUTOPHAGY, GOBP_CELL_CELL_SIGNALING, GOBP_EXOCYTOSIS, GOBP_VESICLE_FUSION_TO_PLASMA_MEMBRANE, GOBP_ORGANELLE_MEMBRANE_FUSION, MODULE_206, GOBP_SECRETION, GOBP_SIGNAL_RELEASE, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN

GO Biological Process (6): exocytosis (GO:0006887), synaptic vesicle priming (GO:0016082), synaptic vesicle fusion to presynaptic active zone membrane (GO:0031629), long-term synaptic potentiation (GO:0060291), exocytic insertion of neurotransmitter receptor to postsynaptic membrane (GO:0098967), vesicle-mediated transport in synapse (GO:0099003)

GO Molecular Function (3): SNAP receptor activity (GO:0005484), syntaxin binding (GO:0019905), protein binding (GO:0005515)

GO Cellular Component (16): plasma membrane (GO:0005886), endomembrane system (GO:0012505), SNARE complex (GO:0031201), perinuclear region of cytoplasm (GO:0048471), presynapse (GO:0098793), cytoplasm (GO:0005737), postsynaptic density (GO:0014069), membrane (GO:0016020), dendrite (GO:0030425), BLOC-1 complex (GO:0031083), asymmetric synapse (GO:0032279), neuronal cell body (GO:0043025), synapse (GO:0045202), presynaptic active zone (GO:0048786), hippocampal mossy fiber to CA3 synapse (GO:0098686), glutamatergic synapse (GO:0098978)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure6
synapse3
vesicle-mediated transport2
vesicle fusion to plasma membrane2
synaptic vesicle exocytosis2
cytoplasm2
neuron to neuron synapse2
secretion by cell1
protein-containing complex assembly1
exocytic process1
synaptic vesicle membrane organization1
regulation of synaptic plasticity1
positive regulation of synaptic transmission1
exocytosis1
neurotransmitter receptor transport to postsynaptic membrane1
regulation of postsynaptic membrane neurotransmitter receptor levels1
protein-macromolecule adaptor activity1
membrane fusion1
fusogenic activity1
SNARE binding1
binding1
membrane1
cell periphery1
vacuole1
plasma membrane1
membrane protein complex1
intracellular anatomical structure1
asymmetric synapse1
postsynaptic specialization1
neuron projection1
dendritic tree1
BLOC complex1
postsynaptic density1
somatodendritic compartment1
cell body1
cell junction1
presynapse1
thorny excrescence1
hippocampal mossy fiber expansion1

Protein interactions and networks

STRING

1348 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SNAP47SNAP29O95721818
SNAP47VAMP2P19065812
SNAP47STX3Q13277797
SNAP47SNAP23O00161717
SNAP47STX1AQ16623713
SNAP47YKT6O15498676
SNAP47STX4Q12846661
SNAP47SYT2Q8N9I0617
SNAP47VAMP7P51809595
SNAP47AOC3Q16853591
SNAP47SNAP25P13795536
SNAP47TRIM67Q6ZTA4522
SNAP47VAMP4O75379518
SNAP47STX16O14662507
SNAP47JMJD4Q9H9V9501

IntAct

160 interactions, top by confidence:

ABTypeScore
Stx1aStxbp1psi-mi:“MI:0914”(association)0.920
STX18NBASpsi-mi:“MI:0914”(association)0.810
STX12SNAP47psi-mi:“MI:0915”(physical association)0.740
FAM9CSNAP29psi-mi:“MI:0914”(association)0.740
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
FAM9CNDC80psi-mi:“MI:0914”(association)0.670
USE1NBASpsi-mi:“MI:0914”(association)0.640
STX7SNAP23psi-mi:“MI:0914”(association)0.640
STX12SNAP23psi-mi:“MI:0914”(association)0.640
MAGEA6SNAP47psi-mi:“MI:0915”(physical association)0.560
GOLGA2SNAP47psi-mi:“MI:0915”(physical association)0.560
STX4SNAP47psi-mi:“MI:0915”(physical association)0.560
KLC3SNAP47psi-mi:“MI:0915”(physical association)0.560
CEP57L1SNAP47psi-mi:“MI:0915”(physical association)0.560
SNAP47FAM9Bpsi-mi:“MI:0915”(physical association)0.560
SNAP47FATE1psi-mi:“MI:0915”(physical association)0.560
SPAG5SNAP47psi-mi:“MI:0915”(physical association)0.560
SNAP47MID2psi-mi:“MI:0915”(physical association)0.560
SNAP47GOLGA2psi-mi:“MI:0915”(physical association)0.560
SNAP47CEP57L1psi-mi:“MI:0915”(physical association)0.560
FATE1SNAP47psi-mi:“MI:0915”(physical association)0.560

BioGRID (213): SNAP47 (Two-hybrid), SNAP47 (Two-hybrid), SNAP47 (Two-hybrid), SNAP47 (Two-hybrid), SNAP47 (Two-hybrid), SNAP47 (Two-hybrid), KLC3 (Two-hybrid), FAM9B (Two-hybrid), CEP57L1 (Two-hybrid), SNAP47 (Affinity Capture-MS), SNAP47 (Affinity Capture-MS), SNAP47 (Affinity Capture-MS), SNAP47 (Affinity Capture-MS), SNAP47 (Affinity Capture-MS), SNAP47 (Affinity Capture-MS)

ESM2 similar proteins: A2BID5, A4D1P6, A5WW21, A6QP11, B2RYI0, E9PUQ8, E9PXF8, O14976, O15068, P0CI65, P32019, P57075, P70600, P97874, Q008S8, Q0P4A7, Q0V9N0, Q14289, Q16760, Q2HJE1, Q2I6J0, Q3U213, Q5FVC7, Q5R6T6, Q5SQN1, Q5SVR0, Q5ZK62, Q5ZLL7, Q5ZLR6, Q63406, Q64096, Q66K14, Q6IVG4, Q6NTN5, Q6P6S0, Q6TEN6, Q6ZQK5, Q7TMQ7, Q7TT49, Q7TT50

Diamond homologs: A6QP11, Q0P4A7, Q5SQN1, Q6P6S0, Q8R570

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 115 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.

Reactome pathways:

PathwayPartnersFoldFDR
Intra-Golgi traffic519.4×2e-04
trans-Golgi Network Vesicle Budding518.9×2e-04
Intra-Golgi and retrograde Golgi-to-ER traffic914.1×4e-06
COPII-mediated vesicle transport512.2×6e-04
Golgi-to-ER retrograde transport611.9×2e-04
COPI-dependent Golgi-to-ER retrograde traffic711.6×8e-05
ER-Phagosome pathway59.7×1e-03
Cargo recognition for clathrin-mediated endocytosis57.8×2e-03

GO biological processes:

GO termPartnersFoldFDR
vesicle fusion1062.0×2e-13
obsolete vesicle docking755.3×9e-09
membrane fusion532.2×5e-05
Golgi to plasma membrane protein transport527.1×9e-05
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum517.4×6e-04
exocytosis812.5×3e-05
cellular response to type II interferon510.7×4e-03
intracellular protein transport138.7×7e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance70
Likely benign7
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2354 predictions. Top by Δscore:

VariantEffectΔscore
1:227732675:ACC:Aacceptor_loss1.0000
1:227732677:C:CCacceptor_gain1.0000
1:227733023:TCATC:Tacceptor_gain1.0000
1:227733024:CATC:Cacceptor_gain1.0000
1:227733024:CATCC:Cacceptor_gain1.0000
1:227733025:ATCCT:Aacceptor_loss1.0000
1:227733026:TC:Tacceptor_gain1.0000
1:227733026:TCCTG:Tacceptor_loss1.0000
1:227733027:CC:Cacceptor_gain1.0000
1:227733028:C:Aacceptor_loss1.0000
1:227733028:C:CCacceptor_gain1.0000
1:227733029:T:Aacceptor_loss1.0000
1:227733408:CATTA:Cdonor_loss1.0000
1:227733409:ATTAC:Adonor_loss1.0000
1:227733410:TTAC:Tdonor_loss1.0000
1:227733411:TACCA:Tdonor_loss1.0000
1:227733412:A:Cdonor_loss1.0000
1:227733469:T:TAdonor_gain1.0000
1:227733642:CCAG:Cacceptor_gain1.0000
1:227733643:CAGC:Cacceptor_gain1.0000
1:227733901:CCTCA:Cdonor_loss1.0000
1:227733902:CTCA:Cdonor_loss1.0000
1:227733905:A:ACdonor_gain1.0000
1:227733905:ACCAG:Adonor_loss1.0000
1:227733906:C:CCdonor_gain1.0000
1:227733906:CCAG:Cdonor_gain1.0000
1:227734721:T:Adonor_gain1.0000
1:227734977:T:Adonor_gain1.0000
1:227735015:AGGT:Adonor_gain1.0000
1:227735024:G:Cdonor_gain1.0000

AlphaMissense

2744 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:227747975:T:CF125S0.992
1:227747800:T:AW67R0.985
1:227747800:T:CW67R0.985
1:227759213:T:AI284K0.984
1:227759300:T:AI313N0.984
1:227747842:T:CF81L0.983
1:227747844:C:AF81L0.983
1:227747844:C:GF81L0.983
1:227747764:T:AW55R0.981
1:227747764:T:CW55R0.981
1:227747802:G:CW67C0.980
1:227747802:G:TW67C0.980
1:227747843:T:CF81S0.980
1:227759357:T:GM332R0.980
1:227747776:T:GY59D0.977
1:227759213:T:GI284R0.975
1:227759357:T:AM332K0.974
1:227748025:T:CF142L0.973
1:227748027:C:AF142L0.973
1:227748027:C:GF142L0.973
1:227759186:T:CL275P0.972
1:227759270:T:AI303N0.970
1:227747929:T:CF110L0.969
1:227747931:C:AF110L0.969
1:227747931:C:GF110L0.969
1:227747977:A:CS126R0.969
1:227747979:C:AS126R0.969
1:227747979:C:GS126R0.969
1:227759192:T:AV277D0.969
1:227747816:T:CL72P0.968

dbSNP variants (sampled 300 via entrez): RS1000063862 (1:227779384 G>A), RS1000114768 (1:227765252 A>G), RS1000119087 (1:227765460 A>G), RS1000195863 (1:227765942 T>G), RS1000199559 (1:227767934 C>T), RS1000252452 (1:227765000 G>A), RS1000272274 (1:227736405 C>A), RS1000462676 (1:227763943 G>C), RS1000483316 (1:227768210 A>C,T), RS1000489218 (1:227749149 C>T), RS1000541743 (1:227758119 C>T), RS1000598162 (1:227763728 T>C), RS1000628627 (1:227746578 G>C), RS1000713555 (1:227752477 G>A), RS1000727486 (1:227773437 A>T)

Disease associations

OMIM: gene MIM:619659 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

StudyTraitp-value
GCST003542_210Night sleep phenotypes7.000000e-06
GCST008163_362Height2.000000e-09
GCST012227_1221Hip circumference adjusted for BMI2.000000e-09
GCST90020025_1288Waist-to-hip ratio adjusted for BMI5.000000e-08
GCST90020027_1588Waist-hip index4.000000e-09
GCST90020028_419Hip circumference adjusted for BMI4.000000e-08
GCST90020029_635Waist circumference adjusted for body mass index3.000000e-09
GCST90020029_636Waist circumference adjusted for body mass index8.000000e-13
GCST90020029_637Waist circumference adjusted for body mass index3.000000e-13
GCST90020029_638Waist circumference adjusted for body mass index8.000000e-10

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0008039BMI-adjusted hip circumference
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases methylation2
Cisplatinaffects cotreatment, increases expression, decreases expression, decreases response to substance2
alpha-pineneaffects cotreatment, affects expression, increases abundance1
pirinixic acidincreases activity, affects binding, decreases expression1
aflatoxin B2increases methylation1
methacrylaldehydeincreases abundance, affects cotreatment, affects expression1
jinfukangaffects cotreatment, increases expression1
Arsenic Trioxidedecreases expression1
Leflunomidedecreases expression1
Acroleinaffects cotreatment, affects expression, increases abundance1
Air Pollutantsaffects cotreatment, affects expression, increases abundance1
Ozoneaffects cotreatment, affects expression, increases abundance1
Smokedecreases expression1
Aflatoxin B1increases methylation1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1
Volatile Organic Compoundsaffects cotreatment, affects expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.