SYT15B

Summary

SYT15B (synaptotagmin 15B, HGNC:51487) is a protein-coding gene on chromosome 10q11.22, encoding Synaptotagmin-15B (X6R8R1).

Predicted to enable SNARE binding activity; calcium ion sensor activity; and calcium-dependent phospholipid binding activity. Predicted to be involved in regulation of calcium ion-dependent exocytosis and vesicle-mediated transport. Predicted to be located in membrane. Predicted to be active in exocytic vesicle and plasma membrane.

Source: NCBI Gene 102724488 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001370184

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:51487
Approved symbol	SYT15B
Name	synaptotagmin 15B
Location	10q11.22
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000277758
Ensembl biotype	protein_coding
Entrez	102724488

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000615923, ENST00000622861, ENST00000623662, ENST00000887377, ENST00000887378

RefSeq mRNA: 5 — MANE Select: NM_001370184 NM_001370182, NM_001370183, NM_001370184, NM_001370185, NM_001370186

CCDS: CCDS91239, CCDS91240

Canonical transcript exons

ENST00000615923 — 8 exons

Exon	Start	End
ENSE00003717230	47761441	47761645
ENSE00003725157	47757208	47757328
ENSE00003731014	47756043	47756222
ENSE00003736611	47759632	47759927
ENSE00003750789	47757921	47758091
ENSE00003754154	47760787	47760929
ENSE00003756108	47762634	47763592
ENSE00003917181	47744717	47754314

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 79.29.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
anterior cingulate cortex	UBERON:0009835	79.29	gold quality
prefrontal cortex	UBERON:0000451	79.23	gold quality
frontal cortex	UBERON:0001870	78.79	gold quality
right frontal lobe	UBERON:0002810	78.75	gold quality
cerebral cortex	UBERON:0000956	77.61	gold quality
right lung	UBERON:0002167	77.20	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	76.96	gold quality
temporal lobe	UBERON:0001871	76.89	gold quality
amygdala	UBERON:0001876	76.86	gold quality
Ammon’s horn	UBERON:0001954	76.54	gold quality
superior frontal gyrus	UBERON:0002661	76.51	gold quality
upper lobe of left lung	UBERON:0008952	75.65	gold quality
lung	UBERON:0002048	74.76	gold quality
Brodmann (1909) area 9	UBERON:0013540	74.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.15	gold quality
nucleus accumbens	UBERON:0001882	73.02	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	72.99	gold quality
primary visual cortex	UBERON:0002436	71.99	gold quality
putamen	UBERON:0001874	71.30	gold quality
brain	UBERON:0000955	71.11	gold quality
body of pancreas	UBERON:0001150	71.08	gold quality
caudate nucleus	UBERON:0001873	70.96	gold quality
placenta	UBERON:0001987	70.17	gold quality
lymph node	UBERON:0000029	70.09	gold quality
stromal cell of endometrium	CL:0002255	69.89	gold quality
hypothalamus	UBERON:0001898	69.88	gold quality
substantia nigra	UBERON:0002038	69.17	gold quality
apex of heart	UBERON:0002098	69.17	gold quality
right hemisphere of cerebellum	UBERON:0014890	68.78	gold quality
cerebellum	UBERON:0002037	67.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.93

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	syt15	ENSDARG00000079926
mus_musculus	Syt15	ENSMUSG00000041479
rattus_norvegicus	Syt15	ENSRNOG00000051688

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), 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)

Protein

Protein identifiers

Synaptotagmin-15B — X6R8R1 (reviewed: X6R8R1)

All UniProt accessions (2): A0A096LNH4, X6R8R1

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the synaptotagmin family.

RefSeq proteins (5): NP_001357111, NP_001357112, NP_001357113, NP_001357114, NP_001357115 (=MANE)

Domains & families (InterPro)

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

Pfam: PF00168

UniProt features (6 total): domain 2, region of interest 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-X6R8R1-F1	73.02	0.47

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): GENES_CORRELATED_WITH_PTPN11_DELETION, chr10q11

GO Biological Process (2): vesicle-mediated transport (GO:0016192), regulation of calcium ion-dependent exocytosis (GO:0017158)

GO Molecular Function (3): SNARE binding (GO:0000149), calcium-dependent phospholipid binding (GO:0005544), calcium ion sensor activity (GO:0061891)

GO Cellular Component (3): plasma membrane (GO:0005886), exocytic vesicle (GO:0070382), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	1
cellular process	1
calcium-ion regulated exocytosis	1
regulation of regulated secretory pathway	1
protein binding	1
phospholipid binding	1
calcium ion binding	1
metal ion sensor activity	1
membrane	1
cell periphery	1
transport vesicle	1
secretory vesicle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

BioGRID (15): SYT15 (Affinity Capture-MS), SYT15 (Two-hybrid), LOC102724488 (Two-hybrid), SYT15 (Two-hybrid), LOC102724488 (Two-hybrid), SYT15 (Two-hybrid), LOC102724488 (Two-hybrid), SYT15 (Two-hybrid), LOC102724488 (Two-hybrid), SYT15 (Two-hybrid), LOC102724488 (Two-hybrid), SYT15 (Affinity Capture-MS), SYT15 (Affinity Capture-MS), C6orf211 (Cross-Linking-MS (XL-MS)), SYT15 (Affinity Capture-RNA)

ESM2 similar proteins: A4Q9F4, A6QLH5, D3Z7P3, D3ZVU9, E9PV86, M0R7T9, O35652, O43414, O54804, O60242, O60347, O70512, O94925, P08887, P0C7M8, P13264, P35790, P85298, Q01134, Q08DW9, Q13202, Q13505, Q2HJ53, Q2TBM7, Q3UGX3, Q4R766, Q4R7M4, Q58DH2, Q5XI70, Q62225, Q6AYT7, Q6DN14, Q80T74, Q80UW0, Q80ZF8, Q86W50, Q8C460, Q8N2K0, Q8NBA8, Q8NHH1

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS10545241 (10:46594606 AGAC>A), RS10588658 (10:46580719 CGTGTGTGT>C,CGT,CGTGT,CGTGTGT,CGTGTGTGTGT), RS10588659 (10:46580680 CTGTGTGTGTGTGTGTGTGTGTGTGTG>C,CTG,CTGTG,CTGTGTGTG,CTGTGTGTGTGTG,CTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG,CTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG), RS10712659 (10:46586841 CAAAAA>C,CAA,CAAA,CAAAA,CAAAAAA,CAAAAAAAAA), RS111273873 (10:46578735 A>G), RS111596780 (10:46586805 A>C,G), RS111625798 (10:46579453 C>A,T), RS111852046 (10:46584752 C>T), RS111926928 (10:46579627 G>T), RS112001859 (10:46578821 C>T), RS112045292 (10:46576692 G>A), RS11204657 (10:46592826 C>G), RS112255958 (10:46589134 G>A), RS112965082 (10:46583722 TC>T,TCC,TCCC), RS113324281 (10:46584716 A>C)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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