SYT5

gene
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Summary

SYT5 (synaptotagmin 5, HGNC:11513) is a protein-coding gene on chromosome 19q13.42, encoding Synaptotagmin-5 (O00445). May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis.

Synaptotagmins, such as SYT5, are a family of type III membrane proteins characterized by cytoplasmic repeats related to protein kinase C (see MIM 176960) regulatory (C2) domains, which are thought to bind calcium. Synaptotagmins may act both as negative regulators of vesicle fusion, allowing fusion in the presence of calcium, and as calcium receptors or sensor molecules (summary by Hudson and Birnbaum, 1995 [PubMed 7597049]).

Source: NCBI Gene 6861 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 63 total
  • MANE Select transcript: NM_003180

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11513
Approved symbolSYT5
Namesynaptotagmin 5
Location19q13.42
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000129990
Ensembl biotypeprotein_coding
OMIM600782
Entrez6861

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 14 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000354308, ENST00000537500, ENST00000585461, ENST00000587067, ENST00000588305, ENST00000589172, ENST00000590851, ENST00000590859, ENST00000592470, ENST00000592935, ENST00000592956, ENST00000868679, ENST00000868681, ENST00000868684, ENST00000868686, ENST00000868688, ENST00000868689, ENST00000948087

RefSeq mRNA: 2 — MANE Select: NM_003180 NM_001297774, NM_003180

CCDS: CCDS12919, CCDS74455

Canonical transcript exons

ENST00000354308 — 9 exons

ExonStartEnd
ENSE000013998345517896355179086
ENSE000014202935518011755180289
ENSE000027640715517119655173684
ENSE000032186185517819655178368
ENSE000035320465517570955175876
ENSE000036264705517517255175339
ENSE000036599815517600555176124
ENSE000036612405517488255174999
ENSE000036726215517451755174650

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 97.61.

FANTOM5 (CAGE): breadth broad, TPM avg 5.7764 / max 231.4682, expressed in 433 samples.

FANTOM5 promoters (15 alternative TSS)

Promoter IDTPM avgSamples expressed
1827361.8463268
1827451.6576162
1827431.3456180
1827390.144554
1827350.105459
1827440.102549
1827370.097160
1827420.086048
1827410.082151
1827380.079539

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534397.61gold quality
prefrontal cortexUBERON:000045196.86gold quality
right frontal lobeUBERON:000281096.52gold quality
cingulate cortexUBERON:000302795.54gold quality
anterior cingulate cortexUBERON:000983595.52gold quality
nucleus accumbensUBERON:000188295.23gold quality
caudate nucleusUBERON:000187395.17gold quality
dorsolateral prefrontal cortexUBERON:000983494.67gold quality
Brodmann (1909) area 9UBERON:001354094.12gold quality
frontal cortexUBERON:000187093.69gold quality
putamenUBERON:000187493.59gold quality
Brodmann (1909) area 10UBERON:001354193.51gold quality
amygdalaUBERON:000187693.30gold quality
neocortexUBERON:000195093.30gold quality
pituitary glandUBERON:000000792.38gold quality
telencephalonUBERON:000189391.53gold quality
cerebral cortexUBERON:000095691.48gold quality
adenohypophysisUBERON:000219691.35gold quality
forebrainUBERON:000189091.24gold quality
islet of LangerhansUBERON:000000690.31gold quality
hypothalamusUBERON:000189890.18gold quality
Ammon’s hornUBERON:000195488.75gold quality
brainUBERON:000095587.97gold quality
frontal poleUBERON:000279587.57gold quality
central nervous systemUBERON:000101787.45gold quality
temporal lobeUBERON:000187187.40gold quality
superior frontal gyrusUBERON:000266185.63gold quality
Brodmann (1909) area 46UBERON:000648383.90gold quality
postcentral gyrusUBERON:000258183.72gold quality
middle frontal gyrusUBERON:000270283.71silver quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-5yes14.61
E-ANND-3yes4.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting SYT5, 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-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-607799.9968.042299
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-219A-5P99.9173.36735
HSA-MIR-4782-3P99.8873.31735
HSA-MIR-6766-3P99.8873.38732
HSA-MIR-449299.8768.253611
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-6752-5P99.5967.321243
HSA-MIR-6751-5P99.5664.991145
HSA-MIR-486-3P99.5166.821901
HSA-MIR-608199.4866.071446
HSA-MIR-330-3P99.4169.952521
HSA-MIR-889-5P99.4168.751025
HSA-MIR-7109-5P99.1866.131057
HSA-MIR-125399.1267.081688
HSA-MIR-465199.0667.572002
HSA-MIR-60898.9367.832013
HSA-MIR-508-3P98.6669.62887
HSA-MIR-7155-5P98.6566.141290
HSA-MIR-3135B98.6165.331470
HSA-MIR-92A-1-5P98.2864.51631
HSA-MIR-93-3P98.1566.651309
HSA-MIR-6819-5P97.9666.591071
HSA-MIR-6847-5P97.9366.741808
HSA-MIR-6737-5P97.7566.541044
HSA-MIR-467597.6964.82774
HSA-MIR-474197.6964.14883

Literature-anchored findings (GeneRIF, showing 4)

  • results suggest a novel putative functional role for the GST-synaptotagmin V complex in human breast cancers. As this association of GST M1-synaptotagmin was not seen in adjacent non-cancerous tissues, this can be used as a marker for breast cancers. (PMID:15820774)
  • This protein has been found differentially expressed in thalami from patients with schizophrenia. (PMID:20471030)
  • crystals of synaptotagmin 5 belonged to the hexagonal space group P6(5), with unit-cell parameters a = b = 93.97, c = 28.05 A. (PMID:22102235)
  • Ca(2+)-binding pocket of synaptotagmin 5 C2A domain (PMID:27793683)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusSyt5ENSMUSG00000004961
rattus_norvegicusSyt5ENSRNOG00000018217

Paralogs (31): SYT7 (ENSG00000011347), SYT13 (ENSG00000019505), SYT1 (ENSG00000067715), RPH3A (ENSG00000089169), SYTL4 (ENSG00000102362), SYT17 (ENSG00000103528), SYT10 (ENSG00000110975), SYT11 (ENSG00000132718), SYT4 (ENSG00000132872), SYT6 (ENSG00000134207), SYTL2 (ENSG00000137501), SYT16 (ENSG00000139973), SYTL1 (ENSG00000142765), SYT14 (ENSG00000143469), SYT2 (ENSG00000143858), SYTL5 (ENSG00000147041), SYT8 (ENSG00000149043), DOC2A (ENSG00000149927), SYTL3 (ENSG00000164674), TC2N (ENSG00000165929), SYT9 (ENSG00000170743), SYT12 (ENSG00000173227), RPH3AL (ENSG00000181031), C2CD4C (ENSG00000183186), C2CD4A (ENSG00000198535), SYT15 (ENSG00000204176), C2CD4B (ENSG00000205502), SYT3 (ENSG00000213023), C2CD4D (ENSG00000225556), DOC2B (ENSG00000272636), SYT15B (ENSG00000277758)

Protein

Protein identifiers

Synaptotagmin-5O00445 (reviewed: O00445)

Alternative names: Synaptotagmin V

All UniProt accessions (7): O00445, K7EJ95, K7EJC4, K7EJS7, K7EQ59, M0QYJ7, Q4FD32

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in Ca(2+)-dependent exocytosis of secretory vesicles through Ca(2+) and phospholipid binding to the C2 domain or may serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis. Regulates the Ca(2+)-dependent secretion of norepinephrine in PC12 cells. Required for export from the endocytic recycling compartment to the cell surface.

Subunit / interactions. Homodimer. Interacts with both alpha- and beta-tubulin.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Synaptic vesicle membrane. Recycling endosome membrane.

Cofactor. Binds 3 Ca(2+) ions per subunit. The ions are bound to the C2 domains.

Similarity. Belongs to the synaptotagmin family.

Isoforms (2)

UniProt IDNamesCanonical?
O00445-11yes
O00445-22

RefSeq proteins (2): NP_001284703, NP_003171* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR001565SynaptotagminDomain
IPR035892C2_domain_sfHomologous_superfamily

Pfam: PF00168

UniProt features (43 total): binding site 17, strand 9, topological domain 2, splice variant 2, sequence variant 2, helix 2, domain 2, chain 1, transmembrane region 1, mutagenesis site 1, sequence conflict 1, turn 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
5H4YX-RAY DIFFRACTION1.9
5H4ZX-RAY DIFFRACTION3.01

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O00445-F184.160.59

Functional residue map

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

Ligand- & substrate-binding residues (17): 139; 145; 197; 197; 198; 199; 199; 199; 202; 205; 205; 270

Mutagenesis-validated functional residues (1):

PositionPhenotype
202does not affect ca(2+) affinity as measured by isothermal titration calorimetry of the mutant protein.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-422356Regulation of insulin secretion
R-HSA-1430728Metabolism
R-HSA-163685Integration of energy metabolism

MSigDB gene sets: 210 (showing top): GOBP_REGULATION_OF_VESICLE_FUSION, MORF_FLT1, MODULE_274, MORF_MSH3, GOCC_SECRETORY_GRANULE, GOBP_VESICLE_ORGANIZATION, MORF_BRCA1, GOBP_MEMBRANE_FUSION, GOBP_REGULATION_OF_EXOCYTOSIS, GOBP_NEUROTRANSMITTER_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, MORF_ESR1, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, MORF_RAD51L3, GOBP_CELL_CELL_SIGNALING

GO Biological Process (5): chemical synaptic transmission (GO:0007268), vesicle-mediated transport (GO:0016192), regulation of calcium ion-dependent exocytosis (GO:0017158), calcium-dependent activation of synaptic vesicle fusion (GO:0099502), regulation of synaptic vesicle exocytosis (GO:2000300)

GO Molecular Function (10): SNARE binding (GO:0000149), phosphatidylserine binding (GO:0001786), calcium ion binding (GO:0005509), calcium-dependent phospholipid binding (GO:0005544), phosphatidylinositol-4,5-bisphosphate binding (GO:0005546), syntaxin binding (GO:0019905), clathrin binding (GO:0030276), protein heterodimerization activity (GO:0046982), calcium ion sensor activity (GO:0061891), metal ion binding (GO:0046872)

GO Cellular Component (15): plasma membrane (GO:0005886), axon (GO:0030424), synaptic vesicle membrane (GO:0030672), dense core granule (GO:0031045), neuronal cell body (GO:0043025), perinuclear region of cytoplasm (GO:0048471), recycling endosome membrane (GO:0055038), exocytic vesicle (GO:0070382), neuronal dense core vesicle membrane (GO:0099012), proximal neuron projection (GO:1990769), endosome (GO:0005768), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410), neuron projection (GO:0043005), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Integration of energy metabolism1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of regulated secretory pathway2
synaptic vesicle exocytosis2
protein binding2
phospholipid binding2
neuron projection2
cytoplasm2
cellular anatomical structure2
anterograde trans-synaptic signaling1
transport1
cellular process1
calcium-ion regulated exocytosis1
positive regulation of synaptic vesicle fusion to presynaptic active zone membrane1
regulation of neurotransmitter secretion1
anion binding1
modified amino acid binding1
metal ion binding1
phosphatidylinositol phosphate binding1
phosphatidylinositol bisphosphate binding1
SNARE binding1
protein dimerization activity1
calcium ion binding1
metal ion sensor activity1
cation binding1
membrane1
cell periphery1
synaptic vesicle1
exocytic vesicle membrane1
secretory granule1
somatodendritic compartment1
cell body1
endosome membrane1
recycling endosome1
transport vesicle1
secretory vesicle1
dense core granule membrane1
neuronal dense core vesicle1
endomembrane system1
cytoplasmic vesicle1
intracellular vesicle1
plasma membrane bounded cell projection1

Protein interactions and networks

STRING

616 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYT5UBXN2BQ14CS0462
SYT5NCKIPSDQ9NZQ3418
SYT5RDH13Q8NBN7417
SYT5ARFRP1Q13795414
SYT5STXBP1P61764410
SYT5VAMP2P19065382
SYT5MPZL1O95297372
SYT5NCKAP5LQ9HCH0370
SYT5TMEM94Q12767369
SYT5TFPTP0C1Z6367
SYT5SNAP25P13795364
SYT5SYN2Q92777350
SYT5VAMP3Q15836343
SYT5STX1AQ16623343
SYT5VAMP8Q9BV40336

IntAct

19 interactions, top by confidence:

ABTypeScore
SYT5SYT1psi-mi:“MI:0914”(association)0.530
SYT1SYT5psi-mi:“MI:0914”(association)0.530
SYT2SYT5psi-mi:“MI:0915”(physical association)0.400
SYT5HTR6psi-mi:“MI:0915”(physical association)0.370
SYT5SHANK3psi-mi:“MI:0915”(physical association)0.370
POLR2ESYT5psi-mi:“MI:0915”(physical association)0.370
MAPTSHTN1psi-mi:“MI:0914”(association)0.350
CACNA1CSYT5psi-mi:“MI:0914”(association)0.350
CACNA1CIGLL5psi-mi:“MI:0914”(association)0.350
CACNA1CCACNB4psi-mi:“MI:0914”(association)0.350
CACNA1CDISP2psi-mi:“MI:0914”(association)0.350
HCN1POTEFpsi-mi:“MI:0914”(association)0.350
DNAJC5SYT5psi-mi:“MI:2364”(proximity)0.270
RAB1ASYT5psi-mi:“MI:0915”(physical association)0.000

BioGRID (17): ATP6V1C2 (Affinity Capture-MS), PALM2 (Affinity Capture-MS), SYT1 (Affinity Capture-MS), SYT1 (Affinity Capture-MS), ATP6V1C2 (Affinity Capture-MS), PALM2 (Affinity Capture-MS), DNAJC5 (FRET), SYT5 (Two-hybrid), SYT5 (Negative Genetic), SYT5 (Affinity Capture-Western), SYT5 (Two-hybrid), PALM2 (Affinity Capture-MS), ATP6V1C2 (Affinity Capture-MS), NEU2 (Affinity Capture-MS), SYT1 (Affinity Capture-MS)

ESM2 similar proteins: A0FGR8, A0FGR9, O00445, O08835, O35681, O75038, P05129, P10688, P10829, P10895, P21579, P21707, P21709, P24505, P24506, P29101, P40748, P41823, P46096, P46097, P47861, P48018, P51178, P54760, P63318, P63319, P70611, Q06418, Q14183, Q3TZZ7, Q3U7R1, Q4R4U2, Q5DTI8, Q5FWL4, Q5M7N9, Q5R4J5, Q5RAG2, Q60HC0, Q7TNF0, Q8K2J0

Diamond homologs: A0A075F932, A0FGR8, A4IJ05, K8FE10, O00445, O00750, O08625, O08835, O35681, O43581, P04409, P05128, P05129, P05130, P05696, P10102, P10829, P13677, P17252, P20444, P21521, P21579, P21707, P24505, P24506, P24507, P29101, P34693, P40748, P40749, P41823, P41885, P46096, P46097, P47191, P47708, P47709, P47861, P48018, P50232

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance58
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1471 predictions. Top by Δscore:

VariantEffectΔscore
19:55173695:C:CTacceptor_gain1.0000
19:55173697:C:CTacceptor_gain1.0000
19:55173698:G:Tacceptor_gain1.0000
19:55174511:GCTCA:Gdonor_loss1.0000
19:55174512:CTCAC:Cdonor_loss1.0000
19:55174513:TCACC:Tdonor_loss1.0000
19:55174514:CACCT:Cdonor_loss1.0000
19:55174515:ACCTG:Adonor_loss1.0000
19:55174516:C:CAdonor_loss1.0000
19:55174646:TGGAT:Tacceptor_gain1.0000
19:55174647:GGAT:Gacceptor_gain1.0000
19:55174648:GAT:Gacceptor_gain1.0000
19:55174649:AT:Aacceptor_gain1.0000
19:55174651:C:CCacceptor_gain1.0000
19:55174651:CTGGG:Cacceptor_loss1.0000
19:55174879:CACCT:Cdonor_loss1.0000
19:55174880:ACCTG:Adonor_loss1.0000
19:55174881:C:Gdonor_loss1.0000
19:55174899:T:TAdonor_gain1.0000
19:55174995:TCCTG:Tacceptor_gain1.0000
19:55174996:CCTGC:Cacceptor_gain1.0000
19:55174997:CTG:Cacceptor_gain1.0000
19:55174998:TG:Tacceptor_gain1.0000
19:55174999:GCTGA:Gacceptor_loss1.0000
19:55175000:C:CCacceptor_gain1.0000
19:55175000:C:Gacceptor_loss1.0000
19:55175001:T:Gacceptor_loss1.0000
19:55175167:CTCA:Cdonor_loss1.0000
19:55175168:TCA:Tdonor_loss1.0000
19:55175169:CA:Cdonor_loss1.0000

AlphaMissense

2471 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:55173532:C:AW371C1.000
19:55173532:C:GW371C1.000
19:55173623:C:TG341E1.000
19:55174566:G:TP304H1.000
19:55174641:A:TV279D1.000
19:55174921:C:GA263P1.000
19:55174929:A:TV260D1.000
19:55173534:A:GW371R0.999
19:55173534:A:TW371R0.999
19:55173623:C:AG341V0.999
19:55173624:C:AG341W0.999
19:55174583:C:AK298N0.999
19:55174583:C:GK298N0.999
19:55174593:G:AT295I0.999
19:55174645:A:CY278D0.999
19:55174647:G:TP277Q0.999
19:55174911:A:GL266P0.999
19:55174911:A:TL266Q0.999
19:55174935:A:TV258D0.999
19:55174941:A:GL256P0.999
19:55174941:A:TL256H0.999
19:55174968:A:GL247P0.999
19:55174968:A:TL247H0.999
19:55174986:C:AG241V0.999
19:55174986:C:TG241E0.999
19:55174987:C:AG241W0.999
19:55174987:C:GG241R0.999
19:55174987:C:TG241R0.999
19:55175257:C:TG208E0.999
19:55175764:G:AT162I0.999

dbSNP variants (sampled 300 via entrez): RS1000398942 (19:55181322 C>T), RS1000832513 (19:55178806 AC>A), RS1000859461 (19:55176642 G>A), RS1000953753 (19:55176902 G>A), RS1001604146 (19:55175436 G>A,T), RS1001947434 (19:55180923 C>T), RS1002301356 (19:55171988 A>G), RS1002755077 (19:55172324 G>A), RS1002870750 (19:55174204 G>A,C), RS1003191616 (19:55173039 G>T), RS1003215614 (19:55181937 C>G,T), RS1003307740 (19:55173369 G>A,C), RS1003681498 (19:55178006 G>A), RS1003954823 (19:55179282 C>G,T), RS1004430210 (19:55173443 G>A)

Disease associations

OMIM: gene MIM:600782 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST90002400_98Plateletcrit4.000000e-09
GCST90002401_300Platelet distribution width6.000000e-10

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007985platelet crit
EFO:0007984platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects acetylation, affects methylation, increases expression3
Air Pollutantsincreases abundance, increases expression2
Smokedecreases expression, increases abundance, increases expression2
aristolochic acid Iincreases expression1
sotorasibaffects cotreatment, decreases expression1
ethyl-p-hydroxybenzoatedecreases expression1
CGP 52608affects binding, increases reaction1
monomethylarsonous acidaffects acetylation, affects methylation1
abrineincreases expression1
trametinibaffects cotreatment, decreases expression1
NVP-BKM120affects cotreatment, decreases expression1
Resveratrolaffects cotreatment, decreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation, decreases methylation1
Methotrexatedecreases expression1
Niclosamideincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Tobacco Smoke Pollutiondecreases expression1
Tretinoinincreases expression1
Valproic Acidincreases methylation1
Particulate Matterincreases abundance, increases 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.