SYT16

Summary

SYT16 (synaptotagmin 16, HGNC:23142) is a protein-coding gene on chromosome 14q23.2, encoding Synaptotagmin-16 (Q17RD7). May be involved in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues.

Predicted to enable phospholipid binding activity. Predicted to be located in membrane.

Source: NCBI Gene 83851 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 102 total
• MANE Select transcript: NM_001367656

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23142
Approved symbol	SYT16
Name	synaptotagmin 16
Location	14q23.2
Locus type	gene with protein product
Status	Approved
Aliases	yt14r, CHR14SYT, Strep14
Ensembl gene	ENSG00000139973
Ensembl biotype	protein_coding
OMIM	610950
Entrez	83851

Gene structure

Transcript identifiers

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

ENST00000554138, ENST00000554436, ENST00000555409, ENST00000568344, ENST00000636133, ENST00000683842, ENST00000883052, ENST00000939112, ENST00000965492, ENST00000965493

RefSeq mRNA: 10 — MANE Select: NM_001367656 NM_001367650, NM_001367652, NM_001367654, NM_001367656, NM_001367657, NM_001367659, NM_001367661, NM_001367663, NM_001387087, NM_001387088

CCDS: CCDS45121

Canonical transcript exons

ENST00000683842 — 8 exons

Exon	Start	End
ENSE00001336352	62069603	62069815
ENSE00001639571	62075135	62075391
ENSE00001680484	62080834	62081274
ENSE00002605273	62100394	62112550
ENSE00003469391	62084196	62084385
ENSE00003796241	61995876	61996542
ENSE00003797865	61970132	61970311
ENSE00003798407	61812703	61812810

Expression profiles

Bgee: expression breadth ubiquitous, 112 present calls, max score 99.28.

FANTOM5 (CAGE): breadth broad, TPM avg 1.5394 / max 98.0108, expressed in 224 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
140014	1.2060	125
140018	0.2417	80
140019	0.0415	12
140020	0.0215	4
140015	0.0107	3
140017	0.0074	2
140021	0.0063	3
140016	0.0042	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 23	UBERON:0013554	99.28	gold quality
endothelial cell	CL:0000115	98.67	gold quality
middle temporal gyrus	UBERON:0002771	98.16	gold quality
secondary oocyte	CL:0000655	97.49	gold quality
Brodmann (1909) area 46	UBERON:0006483	95.98	gold quality
oocyte	CL:0000023	95.46	gold quality
entorhinal cortex	UBERON:0002728	95.09	gold quality
postcentral gyrus	UBERON:0002581	94.44	gold quality
superior frontal gyrus	UBERON:0002661	94.29	gold quality
parietal lobe	UBERON:0001872	93.98	gold quality
primary visual cortex	UBERON:0002436	89.61	gold quality
occipital lobe	UBERON:0002021	89.26	gold quality
cortical plate	UBERON:0005343	87.84	gold quality
islet of Langerhans	UBERON:0000006	86.39	gold quality
lateral nuclear group of thalamus	UBERON:0002736	86.07	gold quality
lateral globus pallidus	UBERON:0002476	84.47	gold quality
prefrontal cortex	UBERON:0000451	82.99	gold quality
frontal cortex	UBERON:0001870	82.33	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.09	gold quality
temporal lobe	UBERON:0001871	82.06	gold quality
cerebral cortex	UBERON:0000956	81.96	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	81.73	gold quality
neocortex	UBERON:0001950	81.32	gold quality
Brodmann (1909) area 9	UBERON:0013540	79.68	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.54	gold quality
substantia nigra pars compacta	UBERON:0001965	79.52	gold quality
Ammon’s horn	UBERON:0001954	78.36	gold quality
forebrain	UBERON:0001890	77.38	gold quality
nucleus accumbens	UBERON:0001882	76.88	gold quality
left testis	UBERON:0004533	76.47	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-81547	yes	658.89
E-MTAB-5061	yes	13.26
E-ANND-3	yes	7.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

105 targeting SYT16, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-345-3P	99.89	70.23	1421
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769

Literature-anchored findings (GeneRIF, showing 3)

• Human synaptotagmin tandem C2 domains C2A-C2B have been expressed as a glutathione-S-transferase fusion protein in Escherichia coli, purified, and crystallized and the preliminary X-ray analysis reported. (PMID:16946482)
• SYT16 expression is significantly downregulated in human masticatory mucosa during wound healing (PMID:28005267)
• SYT16 is a prognostic biomarker and correlated with immune infiltrates in glioma: A study based on TCGA data. (PMID:32289666)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	syt16	ENSDARG00000030761
mus_musculus	Syt16	ENSMUSG00000044912
rattus_norvegicus	Syt16	ENSRNOG00000056012

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), 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-16 — Q17RD7 (reviewed: Q17RD7)

Alternative names: Chr14Syt, Synaptotagmin 14-like protein, Synaptotagmin XIV-related protein

All UniProt accessions (2): Q17RD7, A0A1B0GUW0

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.

Tissue specificity. Expressed in brain.

Similarity. Belongs to the synaptotagmin family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q17RD7-1	1	yes
Q17RD7-2	2
Q17RD7-3	3
Q17RD7-4	4

RefSeq proteins (10): NP_001354579, NP_001354581, NP_001354583, NP_001354585, NP_001354586, NP_001354588, NP_001354590, NP_001354592, NP_001374016, NP_001374017 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000008	C2_dom	Domain
IPR035892	C2_domain_sf	Homologous_superfamily
IPR043541	SYT14/14L/16	Family

Pfam: PF00168

UniProt features (20 total): compositionally biased region 4, splice variant 4, region of interest 4, sequence conflict 3, domain 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q17RD7-F1	60.82	0.24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 69 (showing top): FOXO1_01, CAGCTG_AP4_Q5, CEBP_Q2, YAMASHITA_METHYLATED_IN_PROSTATE_CANCER, chr14q23, HAND1E47_01, RFX1_01, YKACATTT_UNKNOWN, GOMF_LIPID_BINDING, GOMF_PHOSPHOLIPID_BINDING, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, ER_Q6_01, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, MEF2_01, GATA1_05

GO Biological Process (0):

GO Molecular Function (3): phospholipid binding (GO:0005543), identical protein binding (GO:0042802), protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
lipid binding	1
protein binding	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

760 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SYT16	FOSB	P53539	638
SYT16	CFAP20DC	Q6ZVT6	469
SYT16	IQUB	Q8NA54	447
SYT16	GSTM3	P21266	418
SYT16	EXOC5	O00471	418
SYT16	LINC02914	Q52M58	417
SYT16	EXOC8	Q8IYI6	406
SYT16	TMEM222	Q9H0R3	391
SYT16	SYT13	Q7L8C5	384
SYT16	ELOF1	P60002	383
SYT16	UNC13A	Q9UPW8	382
SYT16	RAB3C	Q96E17	379
SYT16	RIMS1	Q86UR5	372
SYT16	DZANK1	Q9NVP4	367
SYT16	ZCCHC18	P0CG32	365

IntAct

107 interactions, top by confidence:

A	B	Type	Score
RABAC1	SYT16	psi-mi:“MI:0915”(physical association)	0.830
SYT16	RABAC1	psi-mi:“MI:0915”(physical association)	0.830
SYT16	AGTRAP	psi-mi:“MI:0915”(physical association)	0.740
RTN4	SYT16	psi-mi:“MI:0915”(physical association)	0.740
SYT16	RTN4	psi-mi:“MI:0915”(physical association)	0.740
AGTRAP	SYT16	psi-mi:“MI:0915”(physical association)	0.740
ZBTB14	SYT16	psi-mi:“MI:0915”(physical association)	0.560
PHC2	SYT16	psi-mi:“MI:0915”(physical association)	0.560
	SYT16	psi-mi:“MI:0915”(physical association)	0.560
SYT16	ZBTB14	psi-mi:“MI:0915”(physical association)	0.560
SYT16	PHC2	psi-mi:“MI:0915”(physical association)	0.560
SYT16		psi-mi:“MI:0915”(physical association)	0.560
SYT16	APOC4	psi-mi:“MI:0915”(physical association)	0.560
SYT16	CMTM5	psi-mi:“MI:0915”(physical association)	0.560
SYT16	AGTRAP	psi-mi:“MI:0915”(physical association)	0.560
SYT16	TMEM239	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (53): SYT16 (Two-hybrid), SYT16 (Two-hybrid), SYT16 (Two-hybrid), SYT16 (Two-hybrid), SYT16 (Two-hybrid), SYT16 (Two-hybrid), SEMG2 (Affinity Capture-MS), SEMG1 (Affinity Capture-MS), DUSP14 (Affinity Capture-MS), DSG4 (Affinity Capture-MS), PKP3 (Affinity Capture-MS), HIST1H1B (Affinity Capture-MS), SERPINB5 (Affinity Capture-MS), LRRC15 (Affinity Capture-MS), SELENBP1 (Affinity Capture-MS)

ESM2 similar proteins: A0FIN4, A6NI15, B1WBU4, D2HNW6, D4A7U2, O35906, O43734, P10914, P14316, P15314, P17433, P17947, P23570, P23906, P97303, P97432, Q01892, Q17RD7, Q1LY51, Q1RML4, Q3SZP0, Q4V7B1, Q501R9, Q505G8, Q5EBA3, Q5SUE8, Q66HA2, Q6AI12, Q6BDS1, Q6P3D7, Q6PKU1, Q6ZNC4, Q7TN83, Q8BSV3, Q8HWS3, Q8N5J4, Q8N7W2, Q8R4E0, Q8VHI4, Q90876

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, A6NLJ0, B7Z1M9, P0CG09, Q2KJ18, Q8NCU7, Q8TF44, P24507, Q99N80

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	96
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1631 predictions. Top by Δscore:

Variant	Effect	Δscore
14:62069797:G:GT	donor_gain	1.0000
14:62075127:A:AG	acceptor_gain	1.0000
14:62075128:A:G	acceptor_gain	1.0000
14:62075133:A:AG	acceptor_gain	1.0000
14:62075134:G:GG	acceptor_gain	1.0000
14:61996538:GCAAG:G	donor_gain	0.9900
14:61996543:GTAA:G	donor_loss	0.9900
14:61996544:T:A	donor_loss	0.9900
14:62069601:A:AG	acceptor_gain	0.9900
14:62069602:G:GG	acceptor_gain	0.9900
14:62075130:TTTAG:T	acceptor_loss	0.9900
14:62075131:TTA:T	acceptor_loss	0.9900
14:62075132:TAGAT:T	acceptor_loss	0.9900
14:62075133:A:G	acceptor_loss	0.9900
14:62075134:G:GA	acceptor_loss	0.9900
14:62075134:GA:G	acceptor_gain	0.9900
14:62075134:GAT:G	acceptor_gain	0.9900
14:62075134:GATT:G	acceptor_gain	0.9900
14:62075134:GATTT:G	acceptor_gain	0.9900
14:62075397:T:G	donor_gain	0.9900
14:62081273:GC:G	donor_gain	0.9900
14:62084194:AGAGT:A	acceptor_gain	0.9900
14:62084195:GA:G	acceptor_gain	0.9900
14:62084195:GAGTG:G	acceptor_gain	0.9900
14:62084390:GT:G	donor_gain	0.9900
14:62004810:T:G	donor_gain	0.9800
14:62075124:T:TA	acceptor_gain	0.9800
14:62075387:CAGAG:C	donor_loss	0.9800
14:62075388:AGAG:A	donor_loss	0.9800
14:62075390:AG:A	donor_loss	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000026211 (14:62071841 C>T), RS1000028973 (14:62069055 C>A), RS1000036723 (14:62055916 C>T), RS1000039064 (14:61907347 A>G), RS1000041764 (14:61986339 T>A), RS1000052773 (14:62020655 C>A), RS1000062912 (14:61858184 C>T), RS1000070837 (14:61858426 A>G), RS1000077137 (14:61898111 G>A), RS1000103139 (14:62020333 A>G), RS1000117287 (14:61859565 C>G), RS1000122936 (14:61999312 G>A), RS1000127853 (14:62043745 T>C), RS1000133750 (14:61919552 T>A), RS1000138335 (14:61817483 C>G,T)

Disease associations

OMIM: gene MIM:610950 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST000747_3	Self-rated health	3.000000e-06
GCST002336_6	Telomere length	4.000000e-06
GCST002337_154	Amyotrophic lateral sclerosis (sporadic)	6.000000e-07
GCST002404_3	Longevity (90 years and older)	9.000000e-06
GCST002730_5	Hepatitis	3.000000e-09
GCST007576_180	Chronotype	7.000000e-09
GCST007645_3	Estimated glomerular filtration rate after 1 year in renal transplantation (recipient effect)	3.000000e-06
GCST009514_4	Recurrence of mild malaria attacks	6.000000e-06
GCST010988_538	Adult body size	2.000000e-14

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004778	self rated health
EFO:0008328	chronotype measurement
EFO:0005199	renal transplant outcome measurement
EFO:0004952	disease recurrence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression, increases methylation	2
Progesterone	decreases expression	2
ferrous chloride	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects cotreatment, affects response to substance	1
diallyl trisulfide	increases expression	1
CGP 52608	affects binding, increases reaction	1
Diethylhexyl Phthalate	increases expression	1
Lipopolysaccharides	affects cotreatment, increases expression, affects response to substance	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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