SYT10

gene
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Summary

SYT10 (synaptotagmin 10, HGNC:19266) is a protein-coding gene on chromosome 12p11.1, encoding Synaptotagmin-10 (Q6XYQ8). Ca(2+) sensor specifically required for the Ca(2+)-dependent exocytosis of secretory vesicles containing IGF1 in neurons of the olfactory bulb.

Predicted to enable several functions, including calcium ion binding activity; calcium ion sensor activity; and calcium-dependent phospholipid binding activity. Predicted to be involved in positive regulation of calcium ion-dependent exocytosis; presynaptic dense core vesicle exocytosis; and sensory perception of smell. Predicted to be located in transport vesicle membrane. Predicted to be active in several cellular components, including exocytic vesicle; glutamatergic synapse; and presynapse.

Source: NCBI Gene 341359 — RefSeq curated summary.

At a glance

  • GWAS associations: 45
  • Clinical variants (ClinVar): 86 total
  • MANE Select transcript: NM_198992

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19266
Approved symbolSYT10
Namesynaptotagmin 10
Location12p11.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000110975
Ensembl biotypeprotein_coding
Entrez341359

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 1 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000228567, ENST00000539102, ENST00000567656

RefSeq mRNA: 1 — MANE Select: NM_198992 NM_198992

CCDS: CCDS8732

Canonical transcript exons

ENST00000228567 — 7 exons

ExonStartEnd
ENSE000011334343337423833376901
ENSE000011334413343937233439819
ENSE000035015523338234933382520
ENSE000036036643340678933407356
ENSE000036283753338517133385291
ENSE000036400243342613833426495
ENSE000036812523337983233379961

Expression profiles

Bgee: expression breadth broad, 93 present calls, max score 80.66.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1824 / max 23.8052, expressed in 291 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
1304180.9649248
2066660.1550107
1304190.043517
1304170.01906

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.66gold quality
sural nerveUBERON:001548873.85gold quality
right uterine tubeUBERON:000130268.97gold quality
tibial nerveUBERON:000132365.65gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099161.23gold quality
superior frontal gyrusUBERON:000266160.82gold quality
muscle layer of sigmoid colonUBERON:003580560.57gold quality
fallopian tubeUBERON:000388958.82gold quality
prefrontal cortexUBERON:000045158.47gold quality
rectumUBERON:000105257.74gold quality
pituitary glandUBERON:000000757.04gold quality
colonic epitheliumUBERON:000039754.71gold quality
nucleus accumbensUBERON:000188254.59gold quality
colonUBERON:000115553.46gold quality
adult mammalian kidneyUBERON:000008252.89gold quality
frontal cortexUBERON:000187052.69gold quality
embryoUBERON:000092252.16silver quality
ganglionic eminenceUBERON:000402352.16silver quality
duodenumUBERON:000211452.03gold quality
adenohypophysisUBERON:000219652.03gold quality
ventricular zoneUBERON:000305351.78silver quality
kidneyUBERON:000211351.53gold quality
intestineUBERON:000016051.37gold quality
metanephros cortexUBERON:001053349.95gold quality
caudate nucleusUBERON:000187349.16gold quality
hypothalamusUBERON:000189849.13gold quality
stomachUBERON:000094548.91gold quality
fundus of stomachUBERON:000116048.50gold quality
smooth muscle tissueUBERON:000113548.45gold quality
corpus callosumUBERON:000233648.42silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no4.55
E-GEOD-124858no1.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

95 targeting SYT10, 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-126-5P100.0072.713180
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-9-5P100.0072.282361
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-477599.9875.006394
HSA-MIR-548N99.9871.944170
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-60799.9773.625593
HSA-MIR-590-3P99.9674.346478
HSA-MIR-365899.9673.874379
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-129799.9173.413162
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-806399.9169.763146
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607

Literature-anchored findings (GeneRIF, showing 1)

  • This cDNA clone is 3287 bp and contains an open reading frame from 299 to 1870 encoding a putative protein of 523 amino acids. It shares 94.6 and 94.8% homology to rat Syt 10 and mouse Syt 10 at protein level, respectively. (PMID:14756426)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosyt10ENSDARG00000045750
mus_musculusSyt10ENSMUSG00000063260
rattus_norvegicusSyt10ENSRNOG00000014296

Paralogs (31): SYT7 (ENSG00000011347), SYT13 (ENSG00000019505), SYT1 (ENSG00000067715), RPH3A (ENSG00000089169), SYTL4 (ENSG00000102362), SYT17 (ENSG00000103528), 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), 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-10Q6XYQ8 (reviewed: Q6XYQ8)

Alternative names: Synaptotagmin X

All UniProt accessions (2): Q6XYQ8, F5GZB8

UniProt curated annotations — full annotation on UniProt →

Function. Ca(2+) sensor specifically required for the Ca(2+)-dependent exocytosis of secretory vesicles containing IGF1 in neurons of the olfactory bulb. Exocytosis of IGF1 is required for sensory perception of smell. Not involved in Ca(2+)-dependent synaptic vesicle exocytosis. Acts through Ca(2+) and phospholipid binding to the C2 domain: Ca(2+) induces binding of the C2-domains to phospholipid membranes and to assembled SNARE-complexes; both actions contribute to triggering exocytosis.

Subunit / interactions. Homodimer; disulfide-linked via the cysteine motif. Can also form heterodimers with SYT3, SYT6, SYT7 and SYT9.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle membrane.

Tissue specificity. Expressed only in pancreas, lung and kidney.

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. The first C2 domain mediates Ca(2+)-dependent phospholipid binding.

Similarity. Belongs to the synaptotagmin family.

RefSeq proteins (1): NP_945343* (*=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-Q6XYQ8-F173.680.42

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): 320; 320; 321; 322; 322; 322; 325; 328; 328; 394; 400; 454

Post-translational modifications (1): 136

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-6794361Neurexins and neuroligins
R-HSA-9768919NPAS4 regulates expression of target genes
R-HSA-112316Neuronal System
R-HSA-212436Generic Transcription Pathway
R-HSA-6794362Protein-protein interactions at synapses
R-HSA-73857RNA Polymerase II Transcription
R-HSA-74160Gene expression (Transcription)
R-HSA-9634815Transcriptional Regulation by NPAS4

MSigDB gene sets: 121 (showing top): GOBP_POSITIVE_REGULATION_OF_CALCIUM_ION_DEPENDENT_EXOCYTOSIS, GOBP_REGULATION_OF_EXOCYTOSIS, GOBP_SENSORY_PERCEPTION_OF_CHEMICAL_STIMULUS, GOBP_NEUROTRANSMITTER_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_CELL_CELL_SIGNALING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, chr12p11, GOBP_EXOCYTOSIS, GOBP_POSITIVE_REGULATION_OF_REGULATED_SECRETORY_PATHWAY, GOBP_POSITIVE_REGULATION_OF_EXOCYTOSIS, GOBP_SECRETION, GOBP_REGULATION_OF_REGULATED_SECRETORY_PATHWAY, GOBP_REGULATION_OF_CALCIUM_ION_DEPENDENT_EXOCYTOSIS, TGANTCA_AP1_C

GO Biological Process (6): exocytosis (GO:0006887), chemical synaptic transmission (GO:0007268), sensory perception of smell (GO:0007608), vesicle-mediated transport (GO:0016192), regulation of calcium ion-dependent exocytosis (GO:0017158), positive regulation of calcium ion-dependent exocytosis (GO:0045956)

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), protein homodimerization activity (GO:0042803), protein heterodimerization activity (GO:0046982), calcium ion sensor activity (GO:0061891), identical protein binding (GO:0042802), metal ion binding (GO:0046872)

GO Cellular Component (7): plasma membrane (GO:0005886), transport vesicle membrane (GO:0030658), exocytic vesicle (GO:0070382), presynapse (GO:0098793), glutamatergic synapse (GO:0098978), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
Protein-protein interactions at synapses1
Transcriptional Regulation by NPAS41
RNA Polymerase II Transcription1
Neuronal System1
Gene expression (Transcription)1
Generic Transcription Pathway1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
calcium-ion regulated exocytosis2
protein binding2
phospholipid binding2
protein dimerization activity2
transport vesicle2
synapse2
cellular anatomical structure2
vesicle-mediated transport1
secretion by cell1
vesicle fusion to plasma membrane1
anterograde trans-synaptic signaling1
sensory perception of chemical stimulus1
transport1
cellular process1
regulation of regulated secretory pathway1
regulation of calcium ion-dependent exocytosis1
positive regulation of regulated secretory pathway1
anion binding1
modified amino acid binding1
metal ion binding1
phosphatidylinositol phosphate binding1
phosphatidylinositol bisphosphate binding1
identical protein binding1
calcium ion binding1
metal ion sensor activity1
cation binding1
membrane1
cell periphery1
cytoplasmic vesicle membrane1
bounding membrane of organelle1
secretory vesicle1
cytoplasm1
intracellular vesicle1

Protein interactions and networks

STRING

894 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYT10KIAA1755Q5JYT7542
SYT10SNAP25P13795531
SYT10UNC13AQ9UPW8500
SYT10SYT13Q7L8C5472
SYT10AFAP1L1Q8TED9471
SYT10RPH3ALQ9UNE2460
SYT10CCDC141Q6ZP82458
SYT10CPPED1Q9BRF8447
SYT10VAMP1P23763433
SYT10SYT1P21579429
SYT10KLHL2O95198420
SYT10TDRD5Q8NAT2420
SYT10MED13LQ71F56418
SYT10CPNE8Q86YQ8418
SYT10RNPEPQ9H4A4416

IntAct

7 interactions, top by confidence:

ABTypeScore
SYT3PGK2psi-mi:“MI:0914”(association)0.530
SYT6SYT10psi-mi:“MI:0914”(association)0.350
SYT3YES1psi-mi:“MI:0914”(association)0.350

BioGRID (8): SYT10 (Affinity Capture-MS), SYT10 (Affinity Capture-MS), SYT10 (Affinity Capture-MS), SYT10 (Affinity Capture-MS), SYT10 (Affinity Capture-MS), SYT10 (Affinity Capture-Western), SYT10 (Affinity Capture-MS), SYT10 (Affinity Capture-MS)

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

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance74
Likely benign2
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1484 predictions. Top by Δscore:

VariantEffectΔscore
12:33382345:ATAC:Adonor_loss1.0000
12:33382346:TA:Tdonor_loss1.0000
12:33382347:A:Cdonor_loss1.0000
12:33382352:T:Cdonor_gain1.0000
12:33382516:AGGAT:Aacceptor_gain1.0000
12:33382517:GGAT:Gacceptor_gain1.0000
12:33382518:GAT:Gacceptor_gain1.0000
12:33382518:GATC:Gacceptor_loss1.0000
12:33382521:C:CCacceptor_gain1.0000
12:33382521:C:Tacceptor_loss1.0000
12:33382522:T:Cacceptor_loss1.0000
12:33385287:CTTTC:Cacceptor_gain1.0000
12:33376902:C:CCacceptor_gain0.9900
12:33382342:CACAT:Cdonor_loss0.9900
12:33382343:ACATA:Adonor_loss0.9900
12:33382347:A:ACdonor_gain0.9900
12:33382348:C:CCdonor_gain0.9900
12:33382348:CCTAT:Cdonor_gain0.9900
12:33382518:GATCT:Gacceptor_gain0.9900
12:33382519:AT:Aacceptor_gain0.9900
12:33382519:ATCT:Aacceptor_gain0.9900
12:33407371:A:Cacceptor_gain0.9900
12:33426131:T:Adonor_gain0.9900
12:33426132:CCTTA:Cdonor_loss0.9900
12:33426133:CTTAC:Cdonor_loss0.9900
12:33426134:TTA:Tdonor_loss0.9900
12:33426135:T:TGdonor_loss0.9900
12:33426136:A:ACdonor_gain0.9900
12:33426136:ACCGG:Adonor_loss0.9900
12:33426137:C:Adonor_loss0.9900

AlphaMissense

3456 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:33379849:A:GW495R1.000
12:33379849:A:TW495R1.000
12:33379891:A:GW481R1.000
12:33379891:A:TW481R1.000
12:33379938:C:TG465E1.000
12:33382364:A:TV452D1.000
12:33382412:A:GF436S1.000
12:33382436:G:TP428H1.000
12:33382499:A:GL407P1.000
12:33382511:A:TV403D1.000
12:33385200:A:GL390P1.000
12:33385208:G:CC387W1.000
12:33385210:A:GC387R1.000
12:33385218:A:TV384D1.000
12:33385233:C:GR379P1.000
12:33406874:C:TG331E1.000
12:33406875:C:AG331W1.000
12:33379839:A:CL498W0.999
12:33379847:C:AW495C0.999
12:33379847:C:GW495C0.999
12:33379889:C:AW481C0.999
12:33379889:C:GW481C0.999
12:33379890:C:GW481S0.999
12:33379938:C:AG465V0.999
12:33379939:C:GG465R0.999
12:33379939:C:TG465R0.999
12:33382352:T:GD456A0.999
12:33382358:T:GD454A0.999
12:33382376:A:GL448P0.999
12:33382411:A:CF436L0.999

dbSNP variants (sampled 300 via entrez): RS1000045311 (12:33434856 C>A,T), RS1000103954 (12:33392605 T>C), RS1000177843 (12:33380339 T>C), RS1000194539 (12:33377553 A>G), RS1000227721 (12:33387018 A>G), RS1000282256 (12:33428618 G>A), RS1000337785 (12:33416610 A>C,G), RS1000358293 (12:33422995 C>A), RS1000389072 (12:33406228 A>T), RS1000389364 (12:33422852 A>G), RS1000530421 (12:33410750 A>G), RS1000556059 (12:33441184 A>G), RS1000611723 (12:33428950 G>T), RS1000791899 (12:33411085 T>G), RS1000982772 (12:33404596 C>G,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

45 associations (top):

StudyTraitp-value
GCST001969_4Heart rate6.000000e-24
GCST003818_39Resting heart rate7.000000e-34
GCST003984_3Parkinson’s disease4.000000e-21
GCST004732_4Heart rate variability traits (pvRSA/HF)2.000000e-14
GCST004732_6Heart rate variability traits (pvRSA/HF)6.000000e-15
GCST004733_11Heart rate variability traits (RMSSD)2.000000e-22
GCST004733_20Heart rate variability traits (RMSSD)3.000000e-20
GCST004734_4Heart rate variability traits (SDNN)7.000000e-13
GCST004734_5Heart rate variability traits (SDNN)3.000000e-15
GCST005787_10Heart rate response to exercise2.000000e-11
GCST005787_7Heart rate response to exercise3.000000e-10
GCST005788_19Heart rate response to recovery post exercise1.000000e-26
GCST005789_2Resting heart rate4.000000e-12
GCST005789_21Resting heart rate5.000000e-11
GCST005845_8Heart rate increase in response to exercise3.000000e-30
GCST005846_13Heart rate response to recovery post exercise (10 sec)5.000000e-66
GCST005847_14Heart rate response to recovery post exercise (20 sec)3.000000e-58
GCST005848_2Heart rate response to recovery post exercise (50 sec)8.000000e-54
GCST005849_5Heart rate response to recovery post exercise (40 sec)2.000000e-57
GCST005850_11Heart rate response to recovery post exercise (30 sec)4.000000e-56
GCST007217_7RR interval (heart rate)6.000000e-09
GCST007565_131Morning person1.000000e-27
GCST007565_200Morning person7.000000e-31
GCST007565_204Morning person3.000000e-35
GCST007565_212Morning person3.000000e-40
GCST007565_31Morning person2.000000e-14
GCST007565_71Morning person4.000000e-22
GCST007576_332Chronotype3.000000e-40
GCST009391_1141Metabolite levels8.000000e-06
GCST010242_238HDL cholesterol levels1.000000e-08

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0008003heart rate variability measurement
EFO:0009184heart rate response to exercise
EFO:0009185heart rate response to recovery post exercise
EFO:0004831RR interval
EFO:0008328chronotype measurement
EFO:0010458alpha-hydroxybutyric acid measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004327electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases expression, increases methylation2
CGP 52608affects binding, increases reaction1
Resveratrolaffects cotreatment, decreases expression1
Ethanolincreases expression1
Caffeinedecreases expression1
Copperaffects cotreatment, decreases expression1
Tobacco Smoke Pollutiondecreases 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.