SYBU

Summary

SYBU (syntabulin, HGNC:26011) is a protein-coding gene on chromosome 8q23.2, encoding Syntabulin (Q9NX95). Part of a kinesin motor-adapter complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development.

Syntabulin/GOLSYN is part of a kinesin motor-adaptor complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development (Cai et al., 2007 [PubMed 17611281]).

Source: NCBI Gene 55638 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 119 total
• MANE Select transcript: NM_001099754

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26011
Approved symbol	SYBU
Name	syntabulin
Location	8q23.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20366, GOLSYN, KIAA1472, OCSYN, SNPHL
Ensembl gene	ENSG00000147642
Ensembl biotype	protein_coding
OMIM	611568
Entrez	55638

Gene structure

Transcript identifiers

Ensembl transcripts: 44 — 38 protein_coding, 3 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000276646, ENST00000399066, ENST00000408889, ENST00000408908, ENST00000422135, ENST00000424158, ENST00000433638, ENST00000440310, ENST00000446070, ENST00000524720, ENST00000526302, ENST00000526736, ENST00000527600, ENST00000527664, ENST00000527707, ENST00000528045, ENST00000528331, ENST00000528569, ENST00000528647, ENST00000528716, ENST00000528735, ENST00000529175, ENST00000529190, ENST00000529690, ENST00000530841, ENST00000531230, ENST00000531284, ENST00000532189, ENST00000532594, ENST00000532779, ENST00000533065, ENST00000533171, ENST00000533394, ENST00000533821, ENST00000533895, ENST00000534184, ENST00000534501, ENST00000534578, ENST00000894648, ENST00000894649, ENST00000938538, ENST00000958720, ENST00000958721, ENST00000958722

RefSeq mRNA: 17 — MANE Select: NM_001099754 NM_001099743, NM_001099744, NM_001099745, NM_001099746, NM_001099747, NM_001099748, NM_001099749, NM_001099750, NM_001099751, NM_001099752, NM_001099753, NM_001099754, NM_001099755, NM_001099756, NM_001330596, NM_001363032, NM_017786

CCDS: CCDS43763, CCDS43764, CCDS47912, CCDS55271, CCDS83315

Canonical transcript exons

ENST00000276646 — 7 exons

Exon	Start	End
ENSE00002147559	109573978	109576013
ENSE00003464606	109586060	109586162
ENSE00003490065	109577868	109578017
ENSE00003524301	109618842	109619039
ENSE00003560377	109644636	109644822
ENSE00003784948	109642728	109642932
ENSE00003785573	109579799	109580002

Expression profiles

Bgee: expression breadth ubiquitous, 263 present calls, max score 98.99.

FANTOM5 (CAGE): breadth broad, TPM avg 8.3117 / max 272.7187, expressed in 909 samples.

FANTOM5 promoters (19 alternative TSS)

Promoter ID	TPM avg	Samples expressed
94419	2.6258	740
94421	1.5676	97
94418	1.1305	464
94417	0.7817	366
94415	0.5244	146
94426	0.5121	188
94425	0.1736	80
94414	0.1647	81
94420	0.1642	68
94428	0.1457	53

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	98.99	gold quality
middle temporal gyrus	UBERON:0002771	98.91	gold quality
superior frontal gyrus	UBERON:0002661	97.10	gold quality
postcentral gyrus	UBERON:0002581	97.08	gold quality
Brodmann (1909) area 23	UBERON:0013554	97.07	gold quality
body of pancreas	UBERON:0001150	96.76	gold quality
cerebellum	UBERON:0002037	96.65	gold quality
entorhinal cortex	UBERON:0002728	96.62	gold quality
cerebellar cortex	UBERON:0002129	96.53	gold quality
cerebellar hemisphere	UBERON:0002245	96.49	gold quality
orbitofrontal cortex	UBERON:0004167	96.36	gold quality
parietal lobe	UBERON:0001872	96.31	gold quality
pons	UBERON:0000988	96.26	gold quality
primary visual cortex	UBERON:0002436	96.01	gold quality
lateral nuclear group of thalamus	UBERON:0002736	95.89	gold quality
dorsal root ganglion	UBERON:0000044	95.84	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.84	gold quality
cortical plate	UBERON:0005343	95.68	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	95.64	gold quality
substantia nigra pars compacta	UBERON:0001965	95.61	gold quality
Brodmann (1909) area 46	UBERON:0006483	95.61	gold quality
Brodmann (1909) area 9	UBERON:0013540	95.20	gold quality
frontal cortex	UBERON:0001870	95.10	gold quality
frontal lobe	UBERON:0016525	95.10	gold quality
prefrontal cortex	UBERON:0000451	94.99	gold quality
neocortex	UBERON:0001950	94.79	gold quality
cerebral cortex	UBERON:0000956	94.76	gold quality
occipital lobe	UBERON:0002021	94.71	gold quality
temporal lobe	UBERON:0001871	94.68	gold quality
hypothalamus	UBERON:0001898	94.68	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.49
E-GEOD-93593	yes	6.74

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

87 targeting SYBU, 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-4789-3P	99.99	70.75	2484
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4648	99.91	67.00	710
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4671-3P	99.88	72.46	1045

Literature-anchored findings (GeneRIF, showing 3)

• Functional characterization of the mouse Golsyn/Syntabulin ortholog. (PMID:16750881)
• syntabulin could be a novel effector of Epac2 and play a critical role in cAMP-enhanced insulin secretion (PMID:22975310)
• syntabulin forms a complex with PICK1 and ASICs, regulates ASIC protein expression in neurons, and participates in ASIC-induced acidotoxicity. (PMID:26868290)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	sybu	ENSDARG00000060112
mus_musculus	Sybu	ENSMUSG00000022340
rattus_norvegicus	Sybu	ENSRNOG00000004200

Paralogs (1): SNPH (ENSG00000101298)

Protein

Protein identifiers

Syntabulin — Q9NX95 (reviewed: Q9NX95)

Alternative names: Golgi-localized syntaphilin-related protein, Syntaxin-1-binding protein

All UniProt accessions (18): Q9NX95, A0A0C4DG86, B3KRD1, B7Z4D2, E9PI48, E9PJ11, E9PK96, E9PL50, E9PL66, E9PLB9, E9PN31, E9PNN9, E9PPC2, E9PPS4, E9PQE2, E9PQG2, E9PRH8, E9PRT7

UniProt curated annotations — full annotation on UniProt →

Function. Part of a kinesin motor-adapter complex that is critical for the anterograde axonal transport of active zone components and contributes to activity-dependent presynaptic assembly during neuronal development.

Subunit / interactions. Interacts with STX1A and KIF5B.

Subcellular location. Cytoplasm. Cytoskeleton. Cytoplasmic vesicle Golgi apparatus membrane Golgi apparatus membrane Golgi apparatus membrane.

Tissue specificity. Isoform 3, isoform 4 and isoform 5 are expressed in HeLa cell line (at protein level). Isoform 3 is expressed in fetal and adult brain. Isoform 4 is expressed in numerous fetal tissues (brain, kidney, liver, lung, and thymus) and in adult brain, kidney, liver, lung, pancreas, colon, prostate, small intestine, testis and thymus. Isoform 5 is expressed in fetal brain, brain and small intestine.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9NX95-1	1	yes
Q9NX95-2	2
Q9NX95-3	3, GOLSYN A
Q9NX95-4	4, GOLSYN C
Q9NX95-5	5, GOLSYN B

RefSeq proteins (17): NP_001093213, NP_001093214, NP_001093215, NP_001093216, NP_001093217, NP_001093218, NP_001093219, NP_001093220, NP_001093221, NP_001093222, NP_001093223, NP_001093224, NP_001093225, NP_001093226, NP_001317525, NP_001349961, NP_060256 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028197	Syntaphilin/Syntabulin	Family

Pfam: PF15290

UniProt features (24 total): compositionally biased region 5, splice variant 5, modified residue 4, region of interest 4, sequence conflict 3, chain 1, transmembrane region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NX95-F1	56.28	0.18

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 (4): 50, 107, 396, 555

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 196 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GOBP_AXO_DENDRITIC_TRANSPORT, TGCACTT_MIR519C_MIR519B_MIR519A, TATTATA_MIR374, GOBP_ORGANELLE_TRANSPORT_ALONG_MICROTUBULE, USF_C, GOBP_CELL_JUNCTION_ORGANIZATION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, SMID_BREAST_CANCER_LUMINAL_B_UP, MASSARWEH_RESPONSE_TO_ESTRADIOL, GOCC_NEURON_PROJECTION

GO Biological Process (5): axonal transport of mitochondrion (GO:0019896), positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774), regulation of synaptic activity (GO:0060025), synapse maturation (GO:0060074), anterograde neuronal dense core vesicle transport (GO:1990048)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (11): Golgi membrane (GO:0000139), mitochondrion (GO:0005739), cytoplasmic microtubule (GO:0005881), cytoplasmic vesicle (GO:0031410), axon cytoplasm (GO:1904115), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), cytoskeleton (GO:0005856), microtubule (GO:0005874), membrane (GO:0016020), vesicle (GO:0031982)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
intracellular membrane-bounded organelle	2
cellular anatomical structure	2
mitochondrion transport along microtubule	1
axonal transport	1
axon cytoplasm	1
positive regulation of insulin secretion	1
insulin secretion involved in cellular response to glucose stimulus	1
regulation of insulin secretion involved in cellular response to glucose stimulus	1
regulation of synapse structure or activity	1
modulation of chemical synaptic transmission	1
nervous system development	1
developmental maturation	1
synapse organization	1
anterograde axonal transport	1
vesicle transport along microtubule	1
dense core granule cytoskeletal transport	1
binding	1
Golgi apparatus	1
bounding membrane of organelle	1
microtubule	1
intracellular vesicle	1
axon	1
neuron projection cytoplasm	1
intracellular anatomical structure	1
endomembrane system	1
intracellular membraneless organelle	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
membrane-bounded organelle	1

Protein interactions and networks

STRING

1226 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SYBU	KIF5B	P33176	964
SYBU	STXBP5	Q5T5C0	873
SYBU	BSN	Q9UPA5	831
SYBU	STX1A	Q16623	774
SYBU	NAPA	P54920	686
SYBU	RHOT1	Q8IXI2	682
SYBU	SNAP25	P13795	667
SYBU	STX1B	P61266	647
SYBU	TRAK1	Q9UPV9	645
SYBU	FEZ1	Q99689	613
SYBU	TRAK2	O60296	599
SYBU	KLC1	Q07866	539
SYBU	RHOT2	Q8IXI1	507
SYBU	RANBP2	P49792	490
SYBU	MFF	Q9GZY8	475

IntAct

20 interactions, top by confidence:

A	B	Type	Score
MIS18A	DCTN6	psi-mi:“MI:0914”(association)	0.640
steC	SCD	psi-mi:“MI:0914”(association)	0.460
SYBU		psi-mi:“MI:0915”(physical association)	0.370
HCN1	POTEF	psi-mi:“MI:0914”(association)	0.350
MAPRE1	SCAMP1	psi-mi:“MI:0914”(association)	0.350
POLR1D	BDP1	psi-mi:“MI:0914”(association)	0.350
DTNBP1	AP3B1	psi-mi:“MI:0914”(association)	0.350
SYBU	SNPH	psi-mi:“MI:0914”(association)	0.350
ASB14	TOMM40	psi-mi:“MI:0914”(association)	0.350
DTNBP1	DUSP14	psi-mi:“MI:0914”(association)	0.350
AFG2A	ESYT2	psi-mi:“MI:0914”(association)	0.350
FHIP2A	MED19	psi-mi:“MI:2364”(proximity)	0.270
SYBU	DTNBP1	psi-mi:“MI:0915”(physical association)	0.000
DISC1	SYBU	psi-mi:“MI:0915”(physical association)	0.000
EXOC1	SYBU	psi-mi:“MI:0915”(physical association)	0.000
RPL29	SYBU	psi-mi:“MI:0915”(physical association)	0.000
ATXN1	SYBU	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (49): SYBU (Affinity Capture-MS), SYBU (Affinity Capture-MS), SYBU (Affinity Capture-MS), SYBU (Affinity Capture-MS), SYBU (Affinity Capture-MS), BICD1 (Affinity Capture-MS), CEP162 (Affinity Capture-MS), SYBU (Affinity Capture-MS), SNPH (Affinity Capture-MS), CLASP1 (Affinity Capture-MS), MARC2 (Affinity Capture-MS), SYBU (Affinity Capture-MS), BLOC1S2 (Affinity Capture-MS), TRAF7 (Affinity Capture-MS), SNAPIN (Affinity Capture-MS)

ESM2 similar proteins: A0A7P0TBJ1, A0A804C8T0, A2BE76, A2RRV3, A4IG66, A4IIE8, D4A4K3, O75182, P57095, P97578, Q02225, Q08AY9, Q09YG9, Q09YK4, Q1JPG0, Q28C41, Q2IBF8, Q2QL82, Q2QLF8, Q2QLG9, Q4QQM5, Q503U3, Q5BLE2, Q5M836, Q5XJS0, Q62141, Q62671, Q68EF0, Q6DFB7, Q6GR21, Q6NRB7, Q6P7D5, Q6PCG6, Q7L4E1, Q86YS3, Q8BG30, Q8BHS8, Q8BK03, Q8BQP8, Q8NAN2

Diamond homologs: B5DF41, O15079, Q80U23, Q8BHS8, Q9NX95

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
KIF5B	“up-regulates activity”	SYBU	relocalization
SYBU	“up-regulates activity”	STX1A	relocalization

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	93
Likely benign	4
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

983 predictions. Top by Δscore:

Variant	Effect	Δscore
8:109577864:TCACC:T	donor_loss	1.0000
8:109577865:CA:C	donor_loss	1.0000
8:109577866:A:T	donor_loss	1.0000
8:109578015:CGC:C	acceptor_gain	1.0000
8:109578016:GCCT:G	acceptor_loss	1.0000
8:109578018:C:CC	acceptor_gain	1.0000
8:109578019:T:G	acceptor_loss	1.0000
8:109579794:CTCA:C	donor_loss	1.0000
8:109579795:TCA:T	donor_loss	1.0000
8:109579796:CAC:C	donor_loss	1.0000
8:109579798:CCT:C	donor_gain	1.0000
8:109579998:CTCGA:C	acceptor_gain	1.0000
8:109579999:TCGA:T	acceptor_gain	1.0000
8:109580000:CGA:C	acceptor_gain	1.0000
8:109580000:CGAC:C	acceptor_gain	1.0000
8:109580001:GA:G	acceptor_gain	1.0000
8:109580003:C:CC	acceptor_gain	1.0000
8:109580004:T:C	acceptor_loss	1.0000
8:109586058:A:AC	donor_gain	1.0000
8:109586059:C:CC	donor_gain	1.0000
8:109618837:CTGA:C	donor_loss	1.0000
8:109618838:TGAC:T	donor_loss	1.0000
8:109618839:GACCT:G	donor_loss	1.0000
8:109618840:A:C	donor_loss	1.0000
8:109618841:C:A	donor_loss	1.0000
8:109618897:T:TA	donor_gain	1.0000
8:109619040:C:CC	acceptor_gain	1.0000
8:109619040:CTA:C	acceptor_loss	1.0000
8:109644630:CCTTA:C	donor_loss	1.0000
8:109644631:CTTAC:C	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000035104 (8:109608493 G>T), RS1000133751 (8:109623028 C>T), RS1000139632 (8:109604676 G>A), RS1000155661 (8:109666586 C>T), RS1000164524 (8:109626998 T>C), RS1000175595 (8:109583043 T>C), RS1000258296 (8:109614926 T>C), RS1000283285 (8:109578858 G>A,C), RS1000377765 (8:109663407 T>C), RS1000396196 (8:109666753 A>G), RS1000400108 (8:109576211 C>T), RS1000420948 (8:109669269 G>T), RS1000436617 (8:109597959 T>C), RS1000451622 (8:109643541 T>C), RS1000507597 (8:109596895 G>A,T)

Disease associations

OMIM: gene MIM:611568 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST009141_1	Ankle-brachial index	2.000000e-08
GCST012311_33	Schizophrenia x sex interaction	6.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0003912	ankle brachial index
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Estradiol	increases expression, increases reaction, affects cotreatment, decreases expression, affects expression	8
Valproic Acid	increases expression, affects expression, decreases methylation, affects cotreatment	8
trichostatin A	affects cotreatment, increases expression	3
sodium arsenite	decreases expression	3
Progesterone	decreases expression, affects cotreatment, increases expression	3
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression, affects expression	3
mercuric bromide	increases expression, affects cotreatment	2
Air Pollutants	increases expression, decreases expression, increases abundance	2
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	2
Formaldehyde	decreases expression, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
methylmercuric chloride	decreases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	affects cotreatment, increases methylation	1
deoxynivalenol	decreases expression	1
beta-lapachone	increases expression	1
cupric chloride	decreases expression	1
hydroquinone	increases expression	1
beta-methylcholine	affects expression	1
avobenzone	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases response to substance, increases expression	1
bisphenol S	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Zoledronic Acid	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Arsenic	affects methylation	1

Cellosaurus cell lines

1 cell lines: 1 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A8MP	MRIi018-A	Induced pluripotent stem cell	Male

Clinical trials (associated diseases)

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