SYT6

gene
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Summary

SYT6 (synaptotagmin 6, HGNC:18638) is a protein-coding gene on chromosome 1p13.2, encoding Synaptotagmin-6 (Q5T7P8). 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.

The protein encoded by this gene belongs to the synaptotagmin family. Synaptotagmins share a common domain structure that includes a transmembrane domain and a cytoplasmic region composed of 2 C2 domains, and are involved in calcium-dependent exocytosis of synaptic vesicles. This protein has been shown to be a key component of the secretory machinery involved in acrosomal exocytosis. Alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 148281 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 66 total
  • MANE Select transcript: NM_001253772

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18638
Approved symbolSYT6
Namesynaptotagmin 6
Location1p13.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000134207
Ensembl biotypeprotein_coding
OMIM607718
Entrez148281

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 nonsense_mediated_decay

ENST00000369547, ENST00000607941, ENST00000608203, ENST00000608879, ENST00000609117, ENST00000609577, ENST00000610096, ENST00000610121, ENST00000610222, ENST00000641643

RefSeq mRNA: 7 — MANE Select: NM_001253772 NM_001253772, NM_001270805, NM_001366223, NM_001366224, NM_001366225, NM_001366226, NM_205848

CCDS: CCDS871, CCDS91026, CCDS91027

Canonical transcript exons

ENST00000610222 — 8 exons

ExonStartEnd
ENSE00000913486114103601114103721
ENSE00001150890114137495114138053
ENSE00001402005114093735114093803
ENSE00001450305114139615114139963
ENSE00001450309114089292114092082
ENSE00001669170114099094114099265
ENSE00003557305114153610114153869
ENSE00003565406114097727114097877

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 95.50.

FANTOM5 (CAGE): breadth broad, TPM avg 0.8629 / max 35.5128, expressed in 231 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
139360.6233200
139390.086544
139370.077443
139380.075846

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534395.50gold quality
pancreatic ductal cellCL:000207980.48silver quality
ganglionic eminenceUBERON:000402379.46gold quality
nucleus accumbensUBERON:000188274.15gold quality
hypothalamusUBERON:000189873.95gold quality
tibialis anteriorUBERON:000138572.41silver quality
caudate nucleusUBERON:000187372.04gold quality
primary visual cortexUBERON:000243670.68gold quality
putamenUBERON:000187470.57gold quality
ileal mucosaUBERON:000033170.02gold quality
kidney epitheliumUBERON:000481969.35gold quality
prefrontal cortexUBERON:000045168.22gold quality
body of pancreasUBERON:000115067.57gold quality
dorsal root ganglionUBERON:000004467.45gold quality
cerebellar vermisUBERON:000472066.75gold quality
C1 segment of cervical spinal cordUBERON:000646966.54gold quality
occipital lobeUBERON:000202166.32gold quality
anterior cingulate cortexUBERON:000983565.60gold quality
spinal cordUBERON:000224065.34gold quality
Brodmann (1909) area 23UBERON:001355464.67silver quality
ventricular zoneUBERON:000305364.45gold quality
neocortexUBERON:000195064.41gold quality
deltoidUBERON:000147664.29silver quality
cerebral cortexUBERON:000095663.44gold quality
forebrainUBERON:000189063.28gold quality
frontal cortexUBERON:000187063.01gold quality
amygdalaUBERON:000187662.94gold quality
Ammon’s hornUBERON:000195462.45gold quality
middle temporal gyrusUBERON:000277162.33gold quality
dorsolateral prefrontal cortexUBERON:000983461.69gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no4.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

94 targeting SYT6, 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-340-5P100.0072.504437
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-433-3P99.9869.371203
HSA-MIR-9-3P99.9670.882068
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-454-3P99.9174.011925
HSA-MIR-130599.9171.433443
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-1211999.8768.351653
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349

Literature-anchored findings (GeneRIF, showing 3)

  • Acrosomal exocytosis is regulated through the PKC-mediated phosphorylation of conserved threonines in the polybasic regions of synaptotagmin VI. (PMID:16111671)
  • SYT6 is hypermethylated in renal cell carcinoma. (PMID:18639284)
  • synaptotagmin must be dephosphorylated at a specific window of time and phosphorylated synaptotagmin has an active role at early stages of the acrosomal exocytosis. (PMID:20551332)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosyt6bENSDARG00000031463
danio_reriosyt6aENSDARG00000076730
mus_musculusSyt6ENSMUSG00000027849
rattus_norvegicusSyt6ENSRNOG00000019163

Paralogs (31): SYT7 (ENSG00000011347), SYT13 (ENSG00000019505), SYT1 (ENSG00000067715), RPH3A (ENSG00000089169), SYTL4 (ENSG00000102362), SYT17 (ENSG00000103528), SYT10 (ENSG00000110975), SYT5 (ENSG00000129990), SYT11 (ENSG00000132718), SYT4 (ENSG00000132872), 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-6Q5T7P8 (reviewed: Q5T7P8)

Alternative names: Synaptotagmin VI

All UniProt accessions (8): A0A286YEX2, A0A7I2PMW4, Q5T7P8, I6L9C3, V9GY33, V9GYB1, V9GYC4, V9GYY7

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. May mediate Ca(2+)-regulation of exocytosis in acrosomal reaction in sperm.

Subunit / interactions. Isoform 1: Homodimer; disulfide-linked via the cysteine motif. Isoform 1: Can also form heterodimers with SYT3, SYT7, SYT9 and SYT10. Isoform 1: Interacts with STX1A, STX1B and STX2; the interaction is Ca(2+)-dependent. Isoform 2: Is not able to form homodimer and heterodimers.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Synaptic vesicle membrane Membrane Cytoplasm. Cytosol. Cell 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.

Isoforms (2)

UniProt IDNamesCanonical?
Q5T7P8-11yes
Q5T7P8-22

RefSeq proteins (7): NP_001240701, NP_001257734, NP_001353152, NP_001353153, NP_001353154, NP_001353155, NP_995320 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR001565SynaptotagminDomain
IPR035892C2_domain_sfHomologous_superfamily

Pfam: PF00168

UniProt features (28 total): binding site 16, region of interest 3, topological domain 2, domain 2, chain 1, transmembrane region 1, modified residue 1, splice variant 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5T7P8-F173.960.45

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): 260; 260; 266; 318; 318; 319; 320; 320; 320; 323; 326; 326

Post-translational modifications (1): 216

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 168 (showing top): GOBP_SINGLE_FERTILIZATION, FREAC2_01, BENPORATH_ES_WITH_H3K27ME3, MYOGENIN_Q6, GCANCTGNY_MYOD_Q6, GOBP_REGULATION_OF_EXOCYTOSIS, GOBP_VESICLE_MEDIATED_TRANSPORT, FOXO1_01, GGGTGGRR_PAX4_03, USF_C, CAGCTG_AP4_Q5, EFC_Q6, FOXD3_01, GOBP_CELL_CELL_SIGNALING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT

GO Biological Process (4): chemical synaptic transmission (GO:0007268), vesicle-mediated transport (GO:0016192), regulation of calcium ion-dependent exocytosis (GO:0017158), acrosomal vesicle exocytosis (GO:0060478)

GO Molecular Function (7): SNARE binding (GO:0000149), syntaxin binding (GO:0019905), clathrin binding (GO:0030276), protein homodimerization activity (GO:0042803), metal ion binding (GO:0046872), calcium ion sensor activity (GO:0061891), protein binding (GO:0005515)

GO Cellular Component (11): cytosol (GO:0005829), plasma membrane (GO:0005886), cytoplasmic side of plasma membrane (GO:0009898), membrane (GO:0016020), synaptic vesicle membrane (GO:0030672), exocytic vesicle (GO:0070382), perinuclear endoplasmic reticulum (GO:0097038), cytoplasm (GO:0005737), transport vesicle membrane (GO:0030658), cytoplasmic vesicle (GO:0031410), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
calcium-ion regulated exocytosis2
protein binding2
cytoplasm2
transport vesicle2
anterograde trans-synaptic signaling1
transport1
cellular process1
regulation of regulated secretory pathway1
acrosome reaction1
SNARE binding1
identical protein binding1
protein dimerization activity1
cation binding1
calcium ion binding1
metal ion sensor activity1
binding1
membrane1
cell periphery1
plasma membrane1
cytoplasmic side of membrane1
synaptic vesicle1
exocytic vesicle membrane1
secretory vesicle1
endoplasmic reticulum1
perinuclear region of cytoplasm1
intracellular anatomical structure1
cytoplasmic vesicle membrane1
bounding membrane of organelle1
intracellular vesicle1
cell junction1

Protein interactions and networks

STRING

936 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYT6EFR3AQ14156478
SYT6RORBQ92753471
SYT6SYNDIG1LA6NDD5470
SYT6CPLX3Q8WVH0452
SYT6PGLYRP4Q96LB8432
SYT6GNG7O60262418
SYT6FARP2O94887416
SYT6CEP41Q9BYV8413
SYT6OR52N1Q8NH53411
SYT6DLGAP3O95886409
SYT6SYNPRQ8TBG9406
SYT6CUX2O14529405
SYT6OR52N5Q8NH56405
SYT6ERC2O15083403
SYT6PRDM8Q9NQV8402
SYT6DRD1P21728402

IntAct

10 interactions, top by confidence:

ABTypeScore
SYT6psi-mi:“MI:0915”(physical association)0.400
YES1HSPB1psi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350
TMPRSS11ERAB4Apsi-mi:“MI:0914”(association)0.350
SYT6SYT10psi-mi:“MI:0914”(association)0.350
SYT6SUPT5Hpsi-mi:“MI:0914”(association)0.350

BioGRID (132): SYT6 (Two-hybrid), SYT6 (Two-hybrid), SYT6 (Two-hybrid), SYT6 (Two-hybrid), SYT6 (Two-hybrid), SYT6 (Two-hybrid), SYT6 (Two-hybrid), SYT6 (Two-hybrid), SYT6 (Two-hybrid), SYT6 (Two-hybrid), ZBTB8A (Two-hybrid), BRCA1 (Two-hybrid), SYT10 (Affinity Capture-MS), SYT3 (Affinity Capture-MS), CETN3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0B4J1F4, A0A0G2JXN2, A2AWP8, A2RRH5, C9J798, O43374, O70277, O95294, P04629, P59926, Q0GA42, Q13368, Q14318, Q16512, Q29RM4, Q2HY40, Q2T9P3, Q2TBA3, Q5BIM1, Q5M7W1, Q5R5M3, Q5R811, Q5T7P8, Q5XIS9, Q62746, Q6PFQ7, Q6PFY8, Q7TNM2, Q7TP90, Q7Z4K8, Q8BG60, Q8BHT7, Q8BQC3, Q8C6N3, Q8CIW5, Q8IZ69, Q8NCT1, Q920N2, Q92546, Q925B4

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

3 interactions.

AEffectBMechanism
PRKCB“up-regulates activity”phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance56
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1450 predictions. Top by Δscore:

VariantEffectΔscore
1:114099089:CCTA:Cdonor_gain1.0000
1:114099090:CTACC:Cdonor_loss1.0000
1:114099092:A:ACdonor_gain1.0000
1:114099093:C:CCdonor_gain1.0000
1:114099093:CCGAT:Cdonor_gain1.0000
1:114099261:GGGAT:Gacceptor_gain1.0000
1:114099263:GATC:Gacceptor_loss1.0000
1:114099264:ATCTG:Aacceptor_loss1.0000
1:114099266:C:CCacceptor_gain1.0000
1:114099266:C:Tacceptor_loss1.0000
1:114099268:G:Cacceptor_gain1.0000
1:114099271:CCAA:Cacceptor_gain1.0000
1:114099272:C:Tacceptor_gain1.0000
1:114099272:CAA:Cacceptor_gain1.0000
1:114099273:A:Tacceptor_gain1.0000
1:114099274:A:ACacceptor_gain1.0000
1:114099274:A:Cacceptor_gain1.0000
1:114099281:C:CTacceptor_gain1.0000
1:114099282:A:Tacceptor_gain1.0000
1:114137493:A:ACdonor_gain1.0000
1:114137494:C:CCdonor_gain1.0000
1:114137494:CA:Cdonor_gain1.0000
1:114137494:CACT:Cdonor_gain1.0000
1:114137494:CACTT:Cdonor_gain1.0000
1:114139611:TCACC:Tdonor_loss1.0000
1:114139612:CACC:Cdonor_loss1.0000
1:114139613:ACCTG:Adonor_loss1.0000
1:114099263:GAT:Gacceptor_gain0.9900
1:114099272:C:CTacceptor_loss0.9900
1:114103596:GGTAC:Gdonor_loss0.9900

AlphaMissense

3358 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:114097765:A:GW493R1.000
1:114097765:A:TW493R1.000
1:114097807:A:GW479R1.000
1:114097807:A:TW479R1.000
1:114097854:C:TG463E1.000
1:114097855:C:GG463R1.000
1:114097855:C:TG463R1.000
1:114099097:T:AD454V1.000
1:114099097:T:GD454A1.000
1:114099102:G:CD452E1.000
1:114099102:G:TD452E1.000
1:114099103:T:AD452V1.000
1:114099103:T:CD452G1.000
1:114099103:T:GD452A1.000
1:114099104:C:GD452H1.000
1:114099109:A:TV450D1.000
1:114099121:A:GL446P1.000
1:114099156:A:CF434L1.000
1:114099156:A:TF434L1.000
1:114099158:A:GF434L1.000
1:114099181:G:TP426H1.000
1:114099208:G:AT417I1.000
1:114099208:G:CT417R1.000
1:114099208:G:TT417K1.000
1:114099252:T:AK402N1.000
1:114099252:T:GK402N1.000
1:114099260:A:CY400D1.000
1:114099262:G:CP399R1.000
1:114099262:G:TP399H1.000
1:114103617:G:CD392E1.000

dbSNP variants (sampled 300 via entrez): RS1000003805 (1:114121160 T>C), RS1000038834 (1:114102641 T>C), RS1000044549 (1:114107137 G>C), RS1000077167 (1:114144034 A>T), RS1000180327 (1:114106983 ACT>A), RS1000206540 (1:114149826 C>T), RS1000248024 (1:114112345 T>C), RS1000274742 (1:114115713 C>A,G), RS1000329555 (1:114110646 G>C), RS1000368965 (1:114155825 T>C), RS1000398474 (1:114147136 G>A), RS1000415971 (1:114117482 G>T), RS1000448750 (1:114110455 G>T), RS1000526780 (1:114148808 A>T), RS1000531659 (1:114125512 A>G)

Disease associations

OMIM: gene MIM:607718 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST001762_512Obesity-related traits2.000000e-06
GCST001762_676Obesity-related traits2.000000e-06
GCST001816_1Breast cancer (prognosis)8.000000e-06
GCST010002_392Refractive error8.000000e-20

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004578homocysteine measurement
EFO:0005134amino acid measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D018270Carcinoma, Ductal, BreastC04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

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
Valproic Acidaffects cotreatment, increases expression, affects expression, decreases methylation3
Benzo(a)pyreneaffects methylation2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
arseniteincreases methylation1
sodium arseniteincreases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Acetaminophendecreases expression1
Hydralazineaffects cotreatment, increases expression1
Methapyrileneincreases methylation1
Rotenonedecreases expression1
Thimerosaldecreases expression1
1-Methyl-4-phenylpyridiniumdecreases expression1
Cadmium Chlorideincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03414970PHASE3ACTIVE_NOT_RECRUITINGHypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344PHASE2TERMINATEDDocetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999PHASE2NOT_YET_RECRUITINGRandomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364PHASE1/PHASE2SUSPENDEDHigh Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855PHASE1/PHASE2COMPLETEDTalimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908EARLY_PHASE1COMPLETEDBroccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041EARLY_PHASE1COMPLETEDIntraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974Not specifiedACTIVE_NOT_RECRUITINGNipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198Not specifiedTERMINATEDOncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397Not specifiedUNKNOWNMRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532Not specifiedCOMPLETEDLiving Well After Breast Surgery
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): breast ductal adenocarcinoma