SYT9

gene
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Summary

SYT9 (synaptotagmin 9, HGNC:19265) is a protein-coding gene on chromosome 11p15.4, encoding Synaptotagmin-9 (Q86SS6). 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.

Predicted to enable SNARE binding activity; calcium ion sensor activity; and calcium-dependent phospholipid binding activity. Predicted to be involved in chemical synaptic transmission; regulation of vesicle-mediated transport; and vesicle-mediated transport. Predicted to be located in clathrin-coated endocytic vesicle membrane. Predicted to be active in hippocampal mossy fiber to CA3 synapse; plasma membrane; and secretory vesicle.

Source: NCBI Gene 143425 — RefSeq curated summary.

At a glance

  • GWAS associations: 12
  • Clinical variants (ClinVar): 58 total
  • MANE Select transcript: NM_175733

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19265
Approved symbolSYT9
Namesynaptotagmin 9
Location11p15.4
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000170743
Ensembl biotypeprotein_coding
OMIM613528
Entrez143425

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 nonsense_mediated_decay, 1 protein_coding

ENST00000318881, ENST00000524820, ENST00000532592

RefSeq mRNA: 1 — MANE Select: NM_175733 NM_175733

CCDS: CCDS7778

Canonical transcript exons

ENST00000318881 — 7 exons

ExonStartEnd
ENSE0000112668973133957313941
ENSE0000129137672519047252331
ENSE0000216610874667927469043
ENSE0000348640773030397303390
ENSE0000353872274160427416162
ENSE0000355408574205067420635
ENSE0000362680774179577418128

Expression profiles

Bgee: expression breadth ubiquitous, 153 present calls, max score 91.15.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2631 / max 92.0230, expressed in 262 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1128880.6337205
1128870.4017158
1128900.117659
1128890.110167

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
medial globus pallidusUBERON:000247791.15gold quality
globus pallidusUBERON:000187589.10gold quality
cerebellar vermisUBERON:000472083.25silver quality
corpus callosumUBERON:000233682.93gold quality
lateral nuclear group of thalamusUBERON:000273682.92silver quality
subthalamic nucleusUBERON:000190681.58silver quality
vena cavaUBERON:000408781.34gold quality
cerebellumUBERON:000203781.26gold quality
dorsal plus ventral thalamusUBERON:000189781.25gold quality
cerebellar cortexUBERON:000212981.04gold quality
cerebellar hemisphereUBERON:000224580.85gold quality
inferior vagus X ganglionUBERON:000536380.48silver quality
lateral globus pallidusUBERON:000247680.45silver quality
cardia of stomachUBERON:000116280.43gold quality
pylorusUBERON:000116680.43silver quality
ventral tegmental areaUBERON:000269179.98silver quality
body of tongueUBERON:001187679.96gold quality
substantia nigra pars reticulataUBERON:000196679.70silver quality
substantia nigra pars compactaUBERON:000196579.55silver quality
superior surface of tongueUBERON:000737179.51gold quality
tongueUBERON:000172379.47gold quality
right hemisphere of cerebellumUBERON:001489079.44gold quality
medulla oblongataUBERON:000189679.40silver quality
pericardiumUBERON:000240779.34gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.13gold quality
ponsUBERON:000098879.11silver quality
spinal cordUBERON:000224078.83gold quality
pharyngeal mucosaUBERON:000035578.82gold quality
C1 segment of cervical spinal cordUBERON:000646978.82gold quality
midbrainUBERON:000189178.81gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no3.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

146 targeting SYT9, 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-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-60799.9773.625593
HSA-MIR-314899.9775.066478
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-146A-5P99.9668.93988
HSA-MIR-146B-5P99.9669.13977
HSA-MIR-7153-5P99.9468.891006
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-449399.9066.48977
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-568299.8972.561005
HSA-MIR-449699.8868.892236
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-605-3P99.8869.221833
HSA-MIR-806799.8669.592260
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-659-3P99.8570.691620
HSA-MIR-607999.8468.541170
HSA-MIR-544A99.8468.661965
HSA-MIR-3180-5P99.8269.122422

Literature-anchored findings (GeneRIF, showing 3)

  • SYT9 expression is significantly downregulated in human masticatory mucosa during wound healing (PMID:28005267)
  • The intronic SYT9 variant rs11041321, which exhibits a significant genome-wide association with circulating homocysteine, was associated with the occurrence of congenital cardiac septal defects (CCSDs). This finding helps to characterize the unexpected role of SYT9 in homocysteine metabolism and the development of CCSDs, which further highlighted the interplay of diet, genetics, and human birth defects (PMID:28834160)
  • The Zika virus infection remodels the expression of the synaptotagmin-9 secretory protein. (PMID:37677740)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosyt9aENSDARG00000003994
danio_reriosyt9bENSDARG00000029239
mus_musculusSyt9ENSMUSG00000062542
rattus_norvegicusSyt9ENSRNOG00000019613

Paralogs (31): SYT7 (ENSG00000011347), SYT13 (ENSG00000019505), SYT1 (ENSG00000067715), RPH3A (ENSG00000089169), SYTL4 (ENSG00000102362), SYT17 (ENSG00000103528), SYT10 (ENSG00000110975), SYT5 (ENSG00000129990), 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), SYT12 (ENSG00000173227), RPH3AL (ENSG00000181031), C2CD4C (ENSG00000183186), C2CD4A (ENSG00000198535), SYT15 (ENSG00000204176), C2CD4B (ENSG00000205502), SYT3 (ENSG00000213023), C2CD4D (ENSG00000225556), DOC2B (ENSG00000272636), SYT15B (ENSG00000277758)

Protein

Protein identifiers

Synaptotagmin-9Q86SS6 (reviewed: Q86SS6)

Alternative names: Synaptotagmin IX

All UniProt accessions (3): Q86SS6, B3KNT7, E9PDN4

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.

Subunit / interactions. Homodimer; disulfide-linked via the cysteine motif. Can also form heterodimers with SYT3, SYT6, SYT7 and SYT10.

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

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

Domain organisation. The cysteine motif mediates homo- or heterodimer formation via formation of disulfide bonds.

Similarity. Belongs to the synaptotagmin family.

RefSeq proteins (1): NP_783860* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR001565SynaptotagminDomain
IPR035892C2_domain_sfHomologous_superfamily

Pfam: PF00168

UniProt features (28 total): binding site 16, sequence variant 4, topological domain 2, domain 2, chain 1, transmembrane region 1, modified residue 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86SS6-F175.270.48

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 (16): 309; 309; 310; 311; 311; 311; 314; 317; 317; 383; 389; 443

Post-translational modifications (1): 177

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-6794361Neurexins and neuroligins
R-HSA-8856825Cargo recognition for clathrin-mediated endocytosis
R-HSA-8856828Clathrin-mediated endocytosis
R-HSA-112316Neuronal System
R-HSA-199991Membrane Trafficking
R-HSA-5653656Vesicle-mediated transport
R-HSA-6794362Protein-protein interactions at synapses

MSigDB gene sets: 165 (showing top): GOBP_REGULATION_OF_VESICLE_FUSION, ACTACCT_MIR196A_MIR196B, NKX25_02, GOCC_SECRETORY_GRANULE, GOBP_VESICLE_ORGANIZATION, GOBP_MEMBRANE_FUSION, GOBP_REGULATION_OF_EXOCYTOSIS, GOBP_NEUROTRANSMITTER_TRANSPORT, RACCACAR_AML_Q6, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, SP1_Q2_01, GOBP_CELL_CELL_SIGNALING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT

GO Biological Process (5): chemical synaptic transmission (GO:0007268), vesicle-mediated transport (GO:0016192), regulation of calcium ion-dependent exocytosis (GO:0017158), positive regulation of vesicle fusion (GO:0031340), calcium-dependent activation of synaptic vesicle fusion (GO:0099502)

GO Molecular Function (8): SNARE binding (GO:0000149), phosphatidylserine binding (GO:0001786), calcium-dependent phospholipid binding (GO:0005544), phosphatidylinositol-4,5-bisphosphate binding (GO:0005546), identical protein binding (GO:0042802), metal ion binding (GO:0046872), calcium ion sensor activity (GO:0061891), protein binding (GO:0005515)

GO Cellular Component (9): plasma membrane (GO:0005886), clathrin-coated endocytic vesicle membrane (GO:0030669), synaptic vesicle membrane (GO:0030672), dense core granule (GO:0031045), exocytic vesicle (GO:0070382), hippocampal mossy fiber to CA3 synapse (GO:0098686), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Protein-protein interactions at synapses1
Clathrin-mediated endocytosis1
Membrane Trafficking1
Vesicle-mediated transport1
Neuronal System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein binding2
phospholipid binding2
anterograde trans-synaptic signaling1
transport1
cellular process1
calcium-ion regulated exocytosis1
regulation of regulated secretory pathway1
vesicle fusion1
positive regulation of organelle organization1
regulation of vesicle fusion1
positive regulation of transport1
synaptic vesicle exocytosis1
positive regulation of synaptic vesicle fusion to presynaptic active zone membrane1
anion binding1
modified amino acid binding1
phosphatidylinositol phosphate binding1
phosphatidylinositol bisphosphate binding1
cation binding1
calcium ion binding1
metal ion sensor activity1
binding1
membrane1
cell periphery1
clathrin-coated vesicle membrane1
endocytic vesicle membrane1
clathrin-coated endocytic vesicle1
synaptic vesicle1
exocytic vesicle membrane1
secretory granule1
transport vesicle1
secretory vesicle1
thorny excrescence1
neuron to neuron synapse1
hippocampal mossy fiber expansion1
cellular anatomical structure1
cytoplasm1
intracellular vesicle1
cell junction1

Protein interactions and networks

STRING

762 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYT9TUBB2AQ13885711
SYT9TRPV1Q8NER1690
SYT9TUBBP05218670
SYT9ZNF614Q8N883540
SYT9VAMP8Q9BV40509
SYT9STON2Q8WXE9462
SYT9VAMP3Q15836450
SYT9STX1AQ16623427
SYT9SNAPINO95295425
SYT9SLC18A2Q05940421
SYT9DLGAP3O95886412
SYT9VAMP2P19065412
SYT9NLGN4XQ8N0W4385
SYT9SLC18A3Q16572384
SYT9ZNF793Q6ZN11375

IntAct

12 interactions, top by confidence:

ABTypeScore
SLC39A5FAM171A2psi-mi:“MI:0914”(association)0.640
TMBIM6SYT9psi-mi:“MI:0915”(physical association)0.560
TMEM50ASYT9psi-mi:“MI:0915”(physical association)0.560
UPK1BSYT9psi-mi:“MI:0915”(physical association)0.560
SYT9LRP6psi-mi:“MI:0914”(association)0.350
UPK1BSYT9psi-mi:“MI:0915”(physical association)0.000

BioGRID (26): SYT9 (Two-hybrid), SYT9 (Affinity Capture-MS), SYT9 (Reconstituted Complex), SYT9 (Affinity Capture-Western), TUBB (Reconstituted Complex), TUBB (Affinity Capture-Western), DNAJC5 (FRET), SYT9 (Two-hybrid), SYT9 (Two-hybrid), TMEM50A (Two-hybrid), SYT9 (Co-purification), SYT9 (Proximity Label-MS), SYT9 (Proximity Label-MS), SYT9 (Proximity Label-MS), SYNCRIP (Reconstituted Complex)

ESM2 similar proteins: A0A8I3NFE2, A0FGR8, A0FGR9, A2AP18, A4IJ05, O08625, O08874, O15357, O75038, P51432, P70218, P70268, Q01970, Q12851, Q3TZZ7, Q3U7R1, Q4VX76, Q5DTI8, Q5FWL4, Q5M7N9, Q5R8Q5, Q5RAG2, Q5RCK6, Q5RJH2, Q61161, Q62807, Q63433, Q6DN12, Q6XYQ8, Q7ZWU7, Q812E4, Q86SS6, Q8K394, Q8TDW5, Q920M7, Q925C0, Q92918, Q99JE6, Q99N48, Q9BSJ8

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

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance49
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2134 predictions. Top by Δscore:

VariantEffectΔscore
11:7252332:G:GAdonor_loss1.0000
11:7252332:G:GGdonor_gain1.0000
11:7252333:T:Adonor_loss1.0000
11:7303035:GCA:Gacceptor_loss1.0000
11:7303036:CAGAT:Cacceptor_loss1.0000
11:7303037:A:AGacceptor_gain1.0000
11:7303037:A:Cacceptor_loss1.0000
11:7303038:G:GAacceptor_loss1.0000
11:7303038:G:GGacceptor_gain1.0000
11:7313942:G:GGdonor_gain1.0000
11:7417945:T:TAacceptor_gain1.0000
11:7252330:AG:Adonor_gain0.9900
11:7252331:GG:Gdonor_gain0.9900
11:7303038:GA:Gacceptor_gain0.9900
11:7303038:GAT:Gacceptor_gain0.9900
11:7303038:GATA:Gacceptor_gain0.9900
11:7303038:GATAT:Gacceptor_gain0.9900
11:7303228:G:GGdonor_gain0.9900
11:7303395:G:GGdonor_gain0.9900
11:7313392:AAG:Aacceptor_gain0.9900
11:7313393:A:Gacceptor_gain0.9900
11:7313902:G:GTdonor_gain0.9900
11:7313937:CCAAT:Cdonor_gain0.9900
11:7313940:AT:Adonor_gain0.9900
11:7313941:TGT:Tdonor_loss0.9900
11:7313943:TG:Tdonor_loss0.9900
11:7313944:G:GCdonor_loss0.9900
11:7313945:A:ACdonor_loss0.9900
11:7313946:G:Tdonor_loss0.9900
11:7321395:G:Tdonor_gain0.9900

AlphaMissense

3241 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:7313562:G:AG222E1.000
11:7313568:T:CL224P1.000
11:7313607:T:CL237P1.000
11:7313627:G:CA244P1.000
11:7313637:T:CL247S1.000
11:7313637:T:GL247W1.000
11:7313648:G:CD251H1.000
11:7313649:A:CD251A1.000
11:7313667:A:GD257G1.000
11:7313670:C:AP258H1.000
11:7313670:C:GP258R1.000
11:7313672:T:GY259D1.000
11:7313676:T:AV260D1.000
11:7313718:C:TT274I1.000
11:7313724:T:AV276D1.000
11:7313731:A:CR278S1.000
11:7313731:A:TR278S1.000
11:7313745:C:AP283H1.000
11:7313750:T:CF285L1.000
11:7313752:T:AF285L1.000
11:7313752:T:GF285L1.000
11:7313805:T:AL303H1.000
11:7313805:T:CL303P1.000
11:7313823:A:CD309A1.000
11:7313823:A:TD309V1.000
11:7313825:T:CF310L1.000
11:7313827:T:AF310L1.000
11:7313827:T:GF310L1.000
11:7313829:A:CD311A1.000
11:7313829:A:TD311V1.000

dbSNP variants (sampled 300 via entrez): RS1000001245 (11:7270100 T>A,C), RS1000051028 (11:7262916 G>A,C), RS1000053869 (11:7401668 T>A), RS1000063979 (11:7237845 A>T), RS1000071053 (11:7328460 G>A), RS1000091370 (11:7445957 C>A), RS1000126131 (11:7378426 G>T), RS1000136516 (11:7269327 C>T), RS1000139862 (11:7394458 A>G), RS1000140365 (11:7415239 G>C), RS1000146497 (11:7368941 A>G), RS1000159323 (11:7247285 T>C), RS1000162638 (11:7430735 C>G,T), RS1000163569 (11:7349641 C>G), RS1000179528 (11:7263980 G>A,T)

Disease associations

OMIM: gene MIM:613528 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

StudyTraitp-value
GCST001414_22Phospholipid levels (plasma)3.000000e-08
GCST002284_9QRS duration in Tripanosoma cruzi seropositivity2.000000e-07
GCST002285_14Chagas cardiomyopathy in Tripanosoma cruzi seropositivity6.000000e-06
GCST002935_9Lead levels1.000000e-06
GCST006035_10Breast cancer and/or colorectal cancer2.000000e-06
GCST006086_19Familial lung cancer8.000000e-06
GCST006998_6Cerebrospinal fluid p-tau levels in mild cognitive impairment4.000000e-07
GCST007676_63-month functional outcome in ischaemic stroke (modified Rankin score)4.000000e-06
GCST010600_4Dietary fat liking1.000000e-06
GCST010725_20Malaria4.000000e-69
GCST010725_33Malaria2.000000e-67
GCST010725_51Malaria1.000000e-55

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0006953family history of lung cancer
EFO:0004760t-tau measurement
EFO:0009603stroke outcome severity measurement
EFO:0010816dietary fat liking measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Aflatoxin B1affects expression, decreases methylation3
mercuric bromidedecreases expression, affects cotreatment2
Benzo(a)pyrenedecreases expression, increases methylation2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Valproic Acidincreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, decreases expression2
methylmercuric chloridedecreases expression1
methyleugenoldecreases expression1
propionaldehydeincreases expression1
bisphenol Aaffects cotreatment, increases methylation, decreases methylation1
ethyl-p-hydroxybenzoatedecreases expression1
trichostatin Adecreases expression, increases expression1
butyraldehydeincreases expression1
pentanalincreases expression1
CGP 52608affects binding, increases reaction1
entinostatincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Sunitinibdecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Aldehydesincreases expression1
Doxorubicindecreases expression1
Niclosamidedecreases expression1
Tretinoinincreases expression1
Triclosandecreases expression1
8-Bromo Cyclic Adenosine Monophosphateincreases expression1
Cyclosporinedecreases expression1
Okadaic Acidincreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Chagas cardiomyopathy