SYT17

Summary

SYT17 (synaptotagmin 17, HGNC:24119) is a protein-coding gene on chromosome 16p12.3, encoding Synaptotagmin-17 (Q9BSW7). Plays a role in dendrite formation by melanocytes.

Predicted to enable SNARE binding activity; calcium ion sensor activity; and calcium-dependent phospholipid binding activity. Involved in positive regulation of dendrite extension and regulation of postsynaptic neurotransmitter receptor internalization. Is active in glutamatergic synapse and postsynapse.

Source: NCBI Gene 51760 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 83 total
• MANE Select transcript: NM_016524

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24119
Approved symbol	SYT17
Name	synaptotagmin 17
Location	16p12.3
Locus type	gene with protein product
Status	Approved
Aliases	Syt-17
Ensembl gene	ENSG00000103528
Ensembl biotype	protein_coding
Entrez	51760

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000355377, ENST00000562034, ENST00000562274, ENST00000562711, ENST00000565183, ENST00000566261, ENST00000568115, ENST00000568433, ENST00000570264, ENST00000971661

RefSeq mRNA: 4 — MANE Select: NM_016524 NM_001308157, NM_001330509, NM_001410903, NM_016524

CCDS: CCDS10575, CCDS76835, CCDS81952, CCDS92119

Canonical transcript exons

ENST00000355377 — 8 exons

Exon	Start	End
ENSE00000675952	19183528	19184147
ENSE00000675953	19223045	19223165
ENSE00000675954	19224683	19224838
ENSE00001412244	19168240	19168661
ENSE00001920768	19266880	19268332
ENSE00003480253	19173430	19173578
ENSE00003547891	19180391	19180539
ENSE00003684450	19172760	19172777

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 95.74.

FANTOM5 (CAGE): breadth broad, TPM avg 2.4449 / max 47.3402, expressed in 694 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152990	1.7229	631
152991	0.3990	189
152993	0.0964	31
152994	0.0851	29
152992	0.0516	27
152997	0.0515	24
152996	0.0284	7
152995	0.0101	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
middle temporal gyrus	UBERON:0002771	95.74	gold quality
endothelial cell	CL:0000115	93.80	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.32	gold quality
oocyte	CL:0000023	92.52	gold quality
substantia nigra pars reticulata	UBERON:0001966	92.37	gold quality
CA1 field of hippocampus	UBERON:0003881	91.68	gold quality
entorhinal cortex	UBERON:0002728	91.24	gold quality
secondary oocyte	CL:0000655	90.24	gold quality
substantia nigra pars compacta	UBERON:0001965	89.89	gold quality
cingulate cortex	UBERON:0003027	89.41	gold quality
anterior cingulate cortex	UBERON:0009835	89.37	gold quality
temporal lobe	UBERON:0001871	89.35	gold quality
orbitofrontal cortex	UBERON:0004167	89.27	gold quality
superior frontal gyrus	UBERON:0002661	89.16	gold quality
Ammon’s horn	UBERON:0001954	88.46	gold quality
palpebral conjunctiva	UBERON:0001812	88.23	gold quality
amygdala	UBERON:0001876	88.07	gold quality
Brodmann (1909) area 46	UBERON:0006483	87.57	gold quality
substantia nigra	UBERON:0002038	87.02	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	86.46	gold quality
cerebral cortex	UBERON:0000956	86.34	gold quality
midbrain	UBERON:0001891	86.25	gold quality
adenohypophysis	UBERON:0002196	86.14	gold quality
pituitary gland	UBERON:0000007	86.06	gold quality
hypothalamus	UBERON:0001898	85.98	gold quality
pigmented layer of retina	UBERON:0001782	85.61	gold quality
neocortex	UBERON:0001950	85.60	gold quality
parietal lobe	UBERON:0001872	85.57	gold quality
prefrontal cortex	UBERON:0000451	85.54	gold quality
postcentral gyrus	UBERON:0002581	85.44	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.76
E-CURD-10	no	21.88

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting SYT17, 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-8485	100.00	77.57	4731
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-3660	99.68	67.33	1149
HSA-MIR-4526	99.68	67.07	1136
HSA-MIR-26A-1-3P	99.64	66.81	788
HSA-MIR-26A-2-3P	99.64	66.82	786
HSA-MIR-6757-3P	99.63	66.88	1089
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-519D-5P	99.41	69.30	2057
HSA-MIR-297	99.40	69.58	1418
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-542-3P	99.34	67.58	1270
HSA-MIR-593-5P	99.34	69.50	965
HSA-MIR-5582-5P	99.27	71.42	1879
HSA-MIR-3922-3P	99.25	64.96	1136
HSA-MIR-3176	99.25	64.35	954

Literature-anchored findings (GeneRIF, showing 1)

• The results suggest that B/K proteins play a role as potential substrates for PKA in the area where they are expressed. (PMID:16672768)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	syt17	ENSDARG00000060741
mus_musculus	Syt17	ENSMUSG00000058420
rattus_norvegicus	Syt17	ENSRNOG00000017136

Paralogs (31): SYT7 (ENSG00000011347), SYT13 (ENSG00000019505), SYT1 (ENSG00000067715), RPH3A (ENSG00000089169), SYTL4 (ENSG00000102362), 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), 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-17 — Q9BSW7 (reviewed: Q9BSW7)

Alternative names: Protein B/K, Synaptotagmin XVII

All UniProt accessions (8): Q9BSW7, H3BMD4, H3BN78, H3BQZ6, H3BRH9, H3BSP0, H3BSU5, H3BSX1

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in dendrite formation by melanocytes.

Subcellular location. Membrane.

Tissue specificity. Expressed abundantly in brain (frontal and temporal lobes, hippocampus, hypothalamus, amygdala, substantia nigra, and pituitary), kidney, and prostate. Expressed in fetal brain, kidney and lung. Expressed in melanocytes.

Similarity. Belongs to the synaptotagmin family.

RefSeq proteins (4): NP_001295086, NP_001317438, NP_001397832, NP_057608* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000008	C2_dom	Domain
IPR001565	Synaptotagmin	Domain
IPR014705	Syt17_C2B	Domain
IPR035892	C2_domain_sf	Homologous_superfamily
IPR047897	Synaptotagmin-15/17_C2A	Domain

Pfam: PF00168

UniProt features (18 total): strand 6, turn 3, domain 2, modified residue 2, chain 1, helix 1, region of interest 1, compositionally biased region 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2ENP	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BSW7-F1	71.22	0.41

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 118, 119

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 214 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, MYOGENIN_Q6, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, GOBP_NEURON_PROJECTION_EXTENSION, GOBP_REGULATION_OF_DEVELOPMENTAL_GROWTH, GCANCTGNY_MYOD_Q6, GOBP_GROWTH, GOBP_REGULATION_OF_EXOCYTOSIS, SABATES_COLORECTAL_ADENOMA_SIZE_DN, GOBP_NEUROGENESIS, TGACCTY_ERR1_Q2, GOBP_VESICLE_MEDIATED_TRANSPORT, CAGCTG_AP4_Q5, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5

GO Biological Process (5): vesicle-mediated transport (GO:0016192), regulation of calcium ion-dependent exocytosis (GO:0017158), cell differentiation (GO:0030154), regulation of postsynaptic neurotransmitter receptor internalization (GO:0099149), positive regulation of dendrite extension (GO:1903861)

GO Molecular Function (4): SNARE binding (GO:0000149), calcium-dependent phospholipid binding (GO:0005544), calcium ion sensor activity (GO:0061891), protein binding (GO:0005515)

GO Cellular Component (6): trans-Golgi network (GO:0005802), plasma membrane (GO:0005886), exocytic vesicle (GO:0070382), postsynapse (GO:0098794), glutamatergic synapse (GO:0098978), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
synapse	2
cellular anatomical structure	2
transport	1
cellular process	1
calcium-ion regulated exocytosis	1
regulation of regulated secretory pathway	1
cellular developmental process	1
regulation of receptor internalization	1
regulation of biological quality	1
postsynaptic neurotransmitter receptor internalization	1
positive regulation of cell growth	1
positive regulation of developmental growth	1
dendrite extension	1
regulation of dendrite extension	1
protein binding	1
phospholipid binding	1
calcium ion binding	1
metal ion sensor activity	1
binding	1
Golgi apparatus subcompartment	1
membrane	1
cell periphery	1
transport vesicle	1
secretory vesicle	1

Protein interactions and networks

STRING

653 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SYT17	NT5DC3	Q86UY8	460
SYT17	AGBL4	Q5VU57	433
SYT17	ENTPD4	Q9Y227	425
SYT17	MRPL13	Q9BYD1	413
SYT17	GSG1L	Q6UXU4	401
SYT17	NTNG2	Q96CW9	393
SYT17	GPR26	Q8NDV2	389
SYT17	VGLL3	A8MV65	385
SYT17	CAMK2N2	Q96S95	383
SYT17	PLCB1	Q9NQ66	376
SYT17	SNTB2	Q13425	356
SYT17	SLC10A7	Q0GE19	350
SYT17	FAM81A	Q8TBF8	347
SYT17	TAF2	Q6P1X5	344
SYT17	STARD8	Q92502	344

IntAct

163 interactions, top by confidence:

A	B	Type	Score
SYT17	CHMP4A	psi-mi:“MI:0915”(physical association)	0.800
CHMP4A	SYT17	psi-mi:“MI:0915”(physical association)	0.800
SYT17	MID2	psi-mi:“MI:0915”(physical association)	0.780
MID2	SYT17	psi-mi:“MI:0915”(physical association)	0.780
TRAF2	SYT17	psi-mi:“MI:0915”(physical association)	0.720
SYT17	TRAF2	psi-mi:“MI:0915”(physical association)	0.720
SYT17	FAM9B	psi-mi:“MI:0915”(physical association)	0.670
FAM9B	SYT17	psi-mi:“MI:0915”(physical association)	0.670
SYT17	MEOX2	psi-mi:“MI:0915”(physical association)	0.560
MEOX1	SYT17	psi-mi:“MI:0915”(physical association)	0.560
IKZF1	SYT17	psi-mi:“MI:0915”(physical association)	0.560
FLJ13057	SYT17	psi-mi:“MI:0915”(physical association)	0.560
SYT17	RUNDC3A	psi-mi:“MI:0915”(physical association)	0.560
CEP70	SYT17	psi-mi:“MI:0915”(physical association)	0.560
SYT17	CEP63	psi-mi:“MI:0915”(physical association)	0.560
NIF3L1	SYT17	psi-mi:“MI:0915”(physical association)	0.560
SYT17	SSX2IP	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	SYT17	psi-mi:“MI:0915”(physical association)	0.560
SYT17	MEOX1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (65): SYT17 (Two-hybrid), SYT17 (Two-hybrid), SYT17 (Two-hybrid), SYT17 (Two-hybrid), SYT17 (Two-hybrid), SYT17 (Two-hybrid), SYT17 (Two-hybrid), NIF3L1 (Two-hybrid), GMCL1 (Two-hybrid), CEP63 (Two-hybrid), CEP70 (Two-hybrid), SSX2IP (Two-hybrid), FAM9B (Two-hybrid), TF (Affinity Capture-MS), MID2 (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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	66
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1821 predictions. Top by Δscore:

Variant	Effect	Δscore
16:19172707:A:AG	acceptor_gain	1.0000
16:19172708:A:G	acceptor_gain	1.0000
16:19180386:TATA:T	acceptor_loss	1.0000
16:19180387:ATAG:A	acceptor_gain	1.0000
16:19180388:TAGG:T	acceptor_loss	1.0000
16:19180389:A:AG	acceptor_gain	1.0000
16:19180389:AG:A	acceptor_gain	1.0000
16:19180389:AGGAT:A	acceptor_gain	1.0000
16:19180390:G:GC	acceptor_gain	1.0000
16:19180390:GG:G	acceptor_gain	1.0000
16:19180390:GGA:G	acceptor_gain	1.0000
16:19180390:GGAT:G	acceptor_gain	1.0000
16:19180390:GGATG:G	acceptor_gain	1.0000
16:19180535:TTCGA:T	donor_gain	1.0000
16:19180536:TCGA:T	donor_gain	1.0000
16:19180537:CGA:C	donor_gain	1.0000
16:19180538:GA:G	donor_gain	1.0000
16:19180538:GAG:G	donor_gain	1.0000
16:19180540:G:GG	donor_gain	1.0000
16:19180540:GTA:G	donor_loss	1.0000
16:19184041:A:G	donor_gain	1.0000
16:19184143:CTCAG:C	donor_loss	1.0000
16:19184144:TCAG:T	donor_loss	1.0000
16:19184145:CAGGT:C	donor_loss	1.0000
16:19184146:AGGTA:A	donor_loss	1.0000
16:19184147:GGTA:G	donor_loss	1.0000
16:19184148:G:T	donor_loss	1.0000
16:19184149:T:G	donor_loss	1.0000
16:19223040:TACA:T	acceptor_loss	1.0000
16:19223041:ACAG:A	acceptor_loss	1.0000

AlphaMissense

3109 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:19183818:G:C	A208P	1.000
16:19183888:T:A	V231D	1.000
16:19184067:G:T	G291W	1.000
16:19184068:G:A	G291E	1.000
16:19223060:G:T	G323W	1.000
16:19223067:T:C	L325P	1.000
16:19223075:T:C	S328P	1.000
16:19223106:T:C	L338P	1.000
16:19223112:T:A	V340D	1.000
16:19223127:C:A	A345D	1.000
16:19224704:T:C	L365P	1.000
16:19266918:G:A	G423R	1.000
16:19266918:G:C	G423R	1.000
16:19266918:G:T	G423W	1.000
16:19266919:G:A	G423E	1.000
16:19266933:G:C	G428R	1.000
16:19266934:G:T	G428V	1.000
16:19267011:T:A	W454R	1.000
16:19267011:T:C	W454R	1.000
16:19183759:T:C	L188P	0.999
16:19183798:T:C	L201P	0.999
16:19183804:T:A	V203E	0.999
16:19183828:T:C	L211P	0.999
16:19183882:C:G	P229R	0.999
16:19183884:T:G	Y230D	0.999
16:19183930:C:T	T245I	0.999
16:19183936:T:A	V247D	0.999
16:19183957:C:A	P254H	0.999
16:19183962:T:C	F256L	0.999
16:19183963:T:C	F256S	0.999

dbSNP variants (sampled 300 via entrez): RS1000039039 (16:19226266 A>T), RS1000126387 (16:19221593 G>A,T), RS1000164000 (16:19175357 CAA>C), RS1000196389 (16:19268158 C>G,T), RS1000198718 (16:19229278 C>T), RS1000220656 (16:19265115 T>C), RS1000224933 (16:19181725 C>T), RS1000235786 (16:19175519 T>TTG), RS1000255554 (16:19222450 C>T), RS1000265418 (16:19229460 G>C,T), RS1000290136 (16:19208554 C>T), RS1000306411 (16:19255659 C>T), RS1000325383 (16:19227257 C>A), RS1000331498 (16:19169467 G>A), RS1000371824 (16:19222675 T>G)

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

5 associations (top):

Study	Trait	p-value
GCST001211_1	Alcohol dependence	4.000000e-06
GCST003984_17	Parkinson’s disease	1.000000e-08
GCST009325_20	Parkinson’s disease or first degree relation to individual with Parkinson’s disease	3.000000e-11
GCST010136_51	Fruit consumption	3.000000e-09
GCST90000025_86	Appendicular lean mass	4.000000e-15

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression, increases methylation	7
trichostatin A	decreases expression	2
Acetaminophen	decreases expression	2
Nickel	decreases expression	2
Aflatoxin B1	decreases expression	2
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
terbufos	increases methylation	1
cypermethrin	decreases expression	1
sodium arsenite	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases expression, affects cotreatment	1
CGP 52608	affects binding, increases reaction	1
entinostat	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases expression, affects cotreatment	1
Aripiprazole	affects cotreatment, decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Coumestrol	decreases expression	1
Fonofos	increases methylation	1
Lead	affects expression	1
Lipopolysaccharides	affects cotreatment, decreases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Niclosamide	increases expression	1
Ozone	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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