SYT14

gene
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Also known as sytXIVFLJ34198

Summary

SYT14 (synaptotagmin 14, HGNC:23143) is a protein-coding gene on chromosome 1q32.2, encoding Synaptotagmin-14 (Q8NB59). May be involved in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues.

This gene is a member of the synaptotagmin gene family and encodes a protein similar to other family members that mediate membrane trafficking in synaptic transmission. The encoded protein is a calcium-independent synaptotagmin. Mutations in this gene are a cause of autosomal recessive spinocerebellar ataxia-11 (SCAR11), and a t(1;3) translocation of this gene has been associated with neurodevelopmental abnormalities. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 4.

Source: NCBI Gene 255928 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): autosomal recessive spinocerebellar ataxia 11 (Supportive, GenCC)
  • GWAS associations: 15
  • Clinical variants (ClinVar): 136 total — 1 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 18
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity unscored
  • MANE Select transcript: NM_001146262

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23143
Approved symbolSYT14
Namesynaptotagmin 14
Location1q32.2
Locus typegene with protein product
StatusApproved
AliasessytXIV, FLJ34198
Ensembl geneENSG00000143469
Ensembl biotypeprotein_coding
OMIM610949
Entrez255928

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000367015, ENST00000367019, ENST00000399639, ENST00000472886, ENST00000534859, ENST00000537238, ENST00000637265, ENST00000637945, ENST00000652023, ENST00000699295

RefSeq mRNA: 7 — MANE Select: NM_001146262 NM_001146261, NM_001146262, NM_001146264, NM_001256006, NM_001397544, NM_001397545, NM_153262

CCDS: CCDS31014, CCDS53470, CCDS58058, CCDS91157

Canonical transcript exons

ENST00000367019 — 9 exons

ExonStartEnd
ENSE00001443254209938217209938277
ENSE00001443255210160729210171315
ENSE00003523023209952709209952756
ENSE00003804324210013633210013797
ENSE00003805936210159421210159477
ENSE00003806100210100012210100461
ENSE00003807877210021039210021254
ENSE00003808025210155721210155910
ENSE00003809888210094322210094593

Expression profiles

Bgee: expression breadth broad, 89 present calls, max score 85.78.

FANTOM5 (CAGE): breadth broad, TPM avg 4.0062 / max 186.5970, expressed in 690 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
83762.4359562
83750.8954380
83730.2585141
83720.2375127
83740.107536
83710.071425

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.78gold quality
cortical plateUBERON:000534380.81gold quality
islet of LangerhansUBERON:000000680.21gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099179.73gold quality
ganglionic eminenceUBERON:000402375.88gold quality
cerebellar hemisphereUBERON:000224573.05gold quality
cerebellar cortexUBERON:000212972.99gold quality
stromal cell of endometriumCL:000225572.82gold quality
right hemisphere of cerebellumUBERON:001489072.58gold quality
cerebellumUBERON:000203771.25gold quality
ventricular zoneUBERON:000305371.00gold quality
adenohypophysisUBERON:000219669.02gold quality
prefrontal cortexUBERON:000045168.30gold quality
pituitary glandUBERON:000000768.14gold quality
corpus callosumUBERON:000233666.87gold quality
adrenal tissueUBERON:001830366.46gold quality
Brodmann (1909) area 9UBERON:001354065.72gold quality
anterior cingulate cortexUBERON:000983563.96gold quality
thyroid glandUBERON:000204663.21gold quality
hypothalamusUBERON:000189863.12gold quality
right frontal lobeUBERON:000281063.06gold quality
left lobe of thyroid glandUBERON:000112062.93gold quality
neocortexUBERON:000195062.87gold quality
frontal cortexUBERON:000187062.45gold quality
nucleus accumbensUBERON:000188262.17gold quality
dorsolateral prefrontal cortexUBERON:000983462.13gold quality
testisUBERON:000047361.49gold quality
right lobe of thyroid glandUBERON:000111961.35gold quality
brainUBERON:000095561.17gold quality
amygdalaUBERON:000187661.05gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-ENAD-27yes10.88
E-GEOD-83139yes8.67
E-ANND-3yes6.30
E-MTAB-5061yes5.85
E-MTAB-6379no4.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

227 targeting SYT14, 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-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-3646100.0073.565283
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5692A100.0074.406850
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-4776-3P100.0068.731340
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-126-5P100.0072.713180
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3163100.0077.238605
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3162-3P100.0065.37363
HSA-MIR-366299.9973.825684
HSA-MIR-428299.9975.366408
HSA-MIR-511-3P99.9968.851467
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-186-5P99.9970.833707
HSA-MIR-1213699.9872.815713
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-477599.9875.006394
HSA-MIR-569699.9872.364487
HSA-MIR-548P99.9872.253784
HSA-MIR-60799.9773.625593
HSA-MIR-50799.9770.111915
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-55799.9670.011640

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity Not yet evaluated (unscored). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 5)

  • Constitutional rearrangement of SYT14 may contribute to macrocephaly, cerebral atrophy, seizures and developmental delay. (PMID:17304550)
  • A homozygous missense mutation in SYT14, encoding synaptotagmin XIV was identified in a Japanese family in which two siblings have slow progression of a type of autosomal-recessive cerebellar ataxias. (PMID:21835308)
  • New DNA sequencing technologies are enabling us to investigate the whole or large targeted proportions of the genome in a rapid, affordable, and comprehensive way. Exome and targeted sequencing SYT14 genes causing ataxia. (PMID:22527681)
  • Whole-exome and targeted sequencing have defined the genetic basis of dizziness including new genes causing ataxia: GBA2, TGM6, ANO10 and SYT14 (PMID:24275721)
  • SYT14 mRNA expression was detected in the three glioma cell lines, and was highest in the U87MG cell line. The RNAi-mediated knockdown of SYT14 significantly decreased cell proliferation and colony formation in U87MG cells, and caused a moderate increase in apoptosis. Fewer S phase cells and more G2/M phase cells were observed. (PMID:29634997)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosyt14aENSDARG00000010934
mus_musculusSyt14ENSMUSG00000016200
rattus_norvegicusSyt14ENSRNOG00000046139

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), 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-14Q8NB59 (reviewed: Q8NB59)

Alternative names: Synaptotagmin XIV

All UniProt accessions (5): Q8NB59, A0A0A0MTK4, A0A1B0GTF1, A0A1B0GTZ1, A0A8V8TN09

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues. Is Ca(2+)-independent.

Subunit / interactions. Homodimer. Can also form heterodimers.

Subcellular location. Membrane.

Tissue specificity. Highly expressed in fetal and adult brain tissue.

Disease relevance. Spinocerebellar ataxia, autosomal recessive, 11 (SCAR11) [MIM:614229] A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCAR11 is associated with psychomotor retardation. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the synaptotagmin family.

Isoforms (7)

UniProt IDNamesCanonical?
Q8NB59-11yes
Q8NB59-22
Q8NB59-33
Q8NB59-44
Q8NB59-55
Q8NB59-66
Q8NB59-77

RefSeq proteins (7): NP_001139733, NP_001139734, NP_001139736, NP_001242935, NP_001384473, NP_001384474, NP_694994 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR035892C2_domain_sfHomologous_superfamily
IPR043541SYT14/14L/16Family

Pfam: PF00168

UniProt features (21 total): splice variant 8, sequence conflict 3, topological domain 2, sequence variant 2, domain 2, region of interest 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NB59-F165.500.29

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 111 (showing top): ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_DN, GOMF_LIPID_BINDING, GOMF_PHOSPHOLIPID_BINDING, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3, HOELZEL_NF1_TARGETS_UP, VDR_Q6, CHAMP1_TARGET_GENES, E2F5_TARGET_GENES, MIER1_TARGET_GENES, ZNF30_TARGET_GENES, ZNF618_TARGET_GENES, MIR3662, MIR607

GO Biological Process (0):

GO Molecular Function (2): phospholipid binding (GO:0005543), identical protein binding (GO:0042802)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
lipid binding1
protein binding1
cellular anatomical structure1

Protein interactions and networks

STRING

566 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SYT14FOSBP53539648
SYT14ANO10Q9NW15584
SYT14SERTAD4Q9NUC0519
SYT14GAL3ST4Q96RP7465
SYT14SYT2Q8N9I0462
SYT14AFG3L2Q9Y4W6455
SYT14LRRN1Q6UXK5424
SYT14CDADC1Q9BWV3417
SYT14COQ8AQ8NI60404
SYT14GCNT4Q9P109388
SYT14ATXN10Q9UBB4385
SYT14RIMS2Q9UQ26381
SYT14SYT12Q8IV01380
SYT14OR13F1Q8NGS4376
SYT14TAFA5Q7Z5A7375

IntAct

2 interactions, top by confidence:

ABTypeScore
USP7SYT14psi-mi:“MI:0407”(direct interaction)0.440

BioGRID (4): SYT14 (Affinity Capture-Western), SYT14 (Synthetic Lethality), SYT14 (Affinity Capture-RNA), SYT14 (Protein-peptide)

ESM2 similar proteins: A0FGR8, A4IJ05, A7MBL8, F1QGZ6, O08625, O08874, O54785, P15056, P24507, P28028, P34908, P53666, P53670, P53671, Q00944, Q04982, Q07139, Q16513, Q32L23, Q4VX76, Q5FWL4, Q5R8Q5, Q5RCK6, Q5SPC5, Q62136, Q62728, Q62807, Q6XYQ8, Q7TN84, Q80T23, Q812E4, Q86SS6, Q8BWW9, Q8N9U0, Q8NB59, Q8TDW5, Q8VHQ7, Q920M7, Q925C0, Q96C24

Diamond homologs: Q17RD7, Q58G82, Q5HZI2, Q7TN83, Q7TN84, Q8NB59, A4IJ05, O43581, P34693, P41823, P47708, P47709, P59926, P97610, Q06846, Q5R8Q5, Q62747, Q62807, Q8C6N3, Q8IV01, Q8NBV8, Q920M7, Q920N7, Q925B4, Q9BQS2, Q9BSW7, Q9H2B2, Q9R0N6, Q9R0N7, Q9Y2J0, X6R8R1, P24507, Q99N80

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic1
Uncertain significance85
Likely benign22
Benign20

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
30861NM_001146262.4(SYT14):c.1316G>A (p.Gly439Asp)Pathogenic
432092NM_001146262.4(SYT14):c.13+1G>ALikely pathogenic

SpliceAI

3158 predictions. Top by Δscore:

VariantEffectΔscore
1:209952705:ATAGG:Aacceptor_loss1.0000
1:209952706:TAGG:Tacceptor_loss1.0000
1:209952707:A:ATacceptor_loss1.0000
1:209952708:G:Tacceptor_loss1.0000
1:209952757:G:Cdonor_loss1.0000
1:209952758:T:Adonor_loss1.0000
1:210013631:A:AGacceptor_gain1.0000
1:210013632:G:GGacceptor_gain1.0000
1:210013632:GT:Gacceptor_gain1.0000
1:210013793:AATTT:Adonor_gain1.0000
1:210013794:ATTT:Adonor_gain1.0000
1:210013795:TTT:Tdonor_gain1.0000
1:210013796:TT:Tdonor_gain1.0000
1:210013796:TTG:Tdonor_loss1.0000
1:210013797:TGTA:Tdonor_loss1.0000
1:210013798:G:GGdonor_gain1.0000
1:210013798:GTA:Gdonor_loss1.0000
1:210013799:T:TCdonor_loss1.0000
1:210013800:AAGT:Adonor_loss1.0000
1:210013801:AG:Adonor_loss1.0000
1:210015162:A:AGacceptor_gain1.0000
1:210021033:A:AGacceptor_gain1.0000
1:210021034:A:Gacceptor_gain1.0000
1:210021036:TA:Tacceptor_loss1.0000
1:210021037:A:AGacceptor_gain1.0000
1:210021037:AGATA:Aacceptor_loss1.0000
1:210021038:G:GAacceptor_gain1.0000
1:210021038:GA:Gacceptor_gain1.0000
1:210021038:GAT:Gacceptor_gain1.0000
1:210021038:GATA:Gacceptor_gain1.0000

AlphaMissense

3770 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:210100127:T:CL277P1.000
1:210100202:T:CL302P1.000
1:210100268:T:CF324S1.000
1:210100325:T:AV343D1.000
1:210100331:T:CF345S1.000
1:210100337:T:CL347P1.000
1:210155824:T:CL423P1.000
1:210155829:T:GY425D1.000
1:210155845:G:AG430E1.000
1:210155851:T:CL432P1.000
1:210155871:G:CG439R1.000
1:210160738:T:AV455D1.000
1:210160750:T:CL459P1.000
1:210160849:C:AA492D1.000
1:210160854:T:CF494L1.000
1:210160856:T:AF494L1.000
1:210160856:T:GF494L1.000
1:210160861:T:CL496P1.000
1:210160876:T:CL501P1.000
1:210160888:T:AV505E1.000
1:210160926:G:CG518R1.000
1:210160927:G:AG518D1.000
1:210160941:G:CG523R1.000
1:210160942:G:AG523D1.000
1:210160942:G:TG523V1.000
1:210160977:T:AW535R1.000
1:210160977:T:CW535R1.000
1:210160978:G:CW535S1.000
1:210160979:G:CW535C1.000
1:210160979:G:TW535C1.000

dbSNP variants (sampled 300 via entrez): RS1000003766 (1:210042913 G>T), RS1000009397 (1:210027513 G>A), RS1000034855 (1:210000884 A>G), RS1000037799 (1:209999587 C>T), RS1000047591 (1:210128993 A>G,T), RS1000048582 (1:209957080 T>A,G), RS1000052459 (1:210086272 A>C,G), RS1000090300 (1:209993205 C>T), RS1000096424 (1:209999165 C>T), RS1000109524 (1:210120340 G>A), RS1000118230 (1:210036776 A>G), RS1000126188 (1:209945127 C>A), RS1000170439 (1:209942866 T>A), RS1000196581 (1:210079520 C>T), RS1000202184 (1:209936845 A>G,T)

Disease associations

OMIM: gene MIM:610949 | disease phenotypes: MIM:614229

GenCC curated gene-disease

DiseaseClassificationInheritance
autosomal recessive spinocerebellar ataxia 11SupportiveAutosomal recessive

Mondo (1): autosomal recessive spinocerebellar ataxia 11 (MONDO:0013645)

Orphanet (1): Autosomal recessive cerebellar ataxia-psychomotor delay syndrome (Orphanet:284271)

HPO phenotypes

18 total (18 of 18 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000617Abnormality of ocular smooth pursuit
HP:0000639Nystagmus
HP:0001249Intellectual disability
HP:0001251Ataxia
HP:0001260Dysarthria
HP:0001263Global developmental delay
HP:0001272Cerebellar atrophy
HP:0001288Gait disturbance
HP:0002015Dysphagia
HP:0002070Limb ataxia
HP:0002078Truncal ataxia
HP:0002317Unsteady gait
HP:0003677Slowly progressive
HP:0006855Cerebellar vermis atrophy
HP:0007772Impaired smooth pursuit
HP:0007979Gaze-evoked horizontal nystagmus
HP:0011463Childhood onset

GWAS associations

15 associations (top):

StudyTraitp-value
GCST003089_3Manic episodes in bipolar disorder7.000000e-06
GCST003996_12Monobrow2.000000e-11
GCST004866_6Alopecia areata2.000000e-06
GCST006270_1Drug-induced liver injury in interferon-beta-treated multiple sclerosis2.000000e-08
GCST006946_19Worry too long after an embarrassing experience4.000000e-08
GCST008295_36Number of decayed, missing and filled tooth surfaces or use of dentures2.000000e-08
GCST008306_24Dentures7.000000e-08
GCST008522_13Bitter alcoholic beverage consumption1.000000e-07
GCST008757_8Alcohol consumption1.000000e-10
GCST008810_49Smoking initiation (ever regular vs never regular)3.000000e-08
GCST009665_11Breast cancer8.000000e-07
GCST010002_351Refractive error1.000000e-13
GCST010988_269Adult body size2.000000e-10
GCST90000050_8Age at first birth3.000000e-10
GCST90020053_1Frailty index1.000000e-09

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0007706manic or hypomanic episode
EFO:0007906synophrys measurement
EFO:0009589worry measurement
EFO:0010078dentures
EFO:0010092bitter alcoholic beverage consumption measurement
EFO:0005670smoking initiation
EFO:0009101age at first birth measurement
EFO:0009885frailty measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2205986SYT1433.501interferon beta-1a;interferon beta-1b

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, decreases methylation7
bisphenol Aincreases expression, decreases methylation2
sodium arseniteaffects cotreatment, increases abundance, increases expression2
potassium chromate(VI)affects cotreatment, decreases expression2
Aflatoxin B1decreases methylation, increases methylation2
perfluorotetradecanoic acidincreases expression1
titanium dioxideincreases expression1
trichostatin Aincreases expression1
mono-(2-ethylhexyl)phthalatedecreases expression1
perfluorooctanoic acidaffects expression1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
epigallocatechin gallateaffects cotreatment, decreases expression1
chromium hexavalent iondecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, increases expression1
incobotulinumtoxinAincreases expression1
MT19c compoundincreases expression1
Decitabinedecreases expression, decreases reaction1
Vorinostatincreases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneincreases methylation1
Estradiolaffects cotreatment, increases expression1
Manganeseincreases abundance, increases expression, affects cotreatment1
Silicon Dioxideincreases expression1
Smokedecreases expression, decreases reaction1
Gold Compoundsincreases expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

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