STX10

Summary

STX10 (syntaxin 10, HGNC:11428) is a protein-coding gene on chromosome 19p13.13, encoding Syntaxin-10 (O60499). SNARE involved in vesicular transport from the late endosomes to the trans-Golgi network.

This gene belongs to the syntaxin family and encodes a soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE). The encoded protein is involved in docking and fusion events at the Golgi apparatus. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 8677 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_003765

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11428
Approved symbol	STX10
Name	syntaxin 10
Location	19p13.13
Locus type	gene with protein product
Status	Approved
Aliases	hsyn10, SYN10
Ensembl gene	ENSG00000104915
Ensembl biotype	protein_coding
OMIM	603765
Entrez	8677

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 13 protein_coding, 2 nonsense_mediated_decay

ENST00000242770, ENST00000343587, ENST00000440593, ENST00000587230, ENST00000587318, ENST00000588848, ENST00000589083, ENST00000591197, ENST00000591415, ENST00000591843, ENST00000593126, ENST00000964221, ENST00000964222, ENST00000964223, ENST00000964224

RefSeq mRNA: 4 — MANE Select: NM_003765 NM_001271609, NM_001271610, NM_001271611, NM_003765

CCDS: CCDS32922, CCDS62569, CCDS62570, CCDS62571

Canonical transcript exons

ENST00000587230 — 8 exons

Exon	Start	End
ENSE00001374244	13150139	13150375
ENSE00001504674	13149728	13149897
ENSE00003459927	13144577	13144671
ENSE00003475344	13144058	13144486
ENSE00003495479	13149029	13149091
ENSE00003524921	13145288	13145395
ENSE00003644296	13149499	13149593
ENSE00003668958	13144764	13144870

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 97.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.1387 / max 178.4977, expressed in 1814 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179472	7.6597	1770
179471	6.1329	1761
179473	4.1242	1699
179470	0.2219	108

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	97.65	gold quality
granulocyte	CL:0000094	97.52	gold quality
mononuclear cell	CL:0000842	97.37	gold quality
leukocyte	CL:0000738	97.23	gold quality
lower esophagus mucosa	UBERON:0035834	96.96	gold quality
mucosa of transverse colon	UBERON:0004991	96.22	gold quality
stromal cell of endometrium	CL:0002255	95.21	gold quality
blood	UBERON:0000178	95.12	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.83	gold quality
apex of heart	UBERON:0002098	94.77	gold quality
esophagus mucosa	UBERON:0002469	94.76	gold quality
endocervix	UBERON:0000458	94.74	gold quality
right lung	UBERON:0002167	94.56	gold quality
cerebellar hemisphere	UBERON:0002245	94.55	gold quality
body of stomach	UBERON:0001161	94.54	gold quality
skin of leg	UBERON:0001511	94.52	gold quality
skin of abdomen	UBERON:0001416	94.44	gold quality
cerebellar cortex	UBERON:0002129	94.37	gold quality
ectocervix	UBERON:0012249	94.35	gold quality
upper lobe of left lung	UBERON:0008952	94.32	gold quality
spleen	UBERON:0002106	94.29	gold quality
small intestine Peyer’s patch	UBERON:0003454	94.28	gold quality
right adrenal gland cortex	UBERON:0035827	94.28	gold quality
right adrenal gland	UBERON:0001233	94.27	gold quality
right lobe of thyroid gland	UBERON:0001119	94.23	gold quality
right uterine tube	UBERON:0001302	94.23	gold quality
metanephros cortex	UBERON:0010533	94.19	gold quality
transverse colon	UBERON:0001157	94.17	gold quality
left adrenal gland cortex	UBERON:0035825	94.09	gold quality
right lobe of liver	UBERON:0001114	94.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	14.08
E-MTAB-6075	no	242.31

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting STX10, 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-302E	99.96	70.74	2669
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-3929	98.32	65.58	1026
HSA-MIR-10398-5P	97.12	64.94	1051
HSA-MIR-6805-5P	95.79	64.86	670

Literature-anchored findings (GeneRIF, showing 2)

• May have a hitherto unrecognized function in the trans-Golgi network-endosome boundary. (PMID:16154903)
• Loss of syntaxin 10 leads to defects in normal chlamydial maturation including: variable inclusion size with fewer chlamydial organisms per inclusion, fewer infectious progeny, and delayed or halted reticulate body-elementary body differentiation. (PMID:26442221)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	Syx6	FBGN0037084
caenorhabditis_elegans		WBGENE00015789

Paralogs (2): STX6 (ENSG00000135823), STX8 (ENSG00000170310)

Protein

Protein identifiers

Syntaxin-10 — O60499 (reviewed: O60499)

All UniProt accessions (10): O60499, F6RTM7, K7EIY4, K7EJ05, K7EK75, K7ELY2, K7EPP9, K7EQ84, Q5U8S2, X6R2W0

UniProt curated annotations — full annotation on UniProt →

Function. SNARE involved in vesicular transport from the late endosomes to the trans-Golgi network.

Subunit / interactions. Interacts with VPS52.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Expressed at high levels in heart, skeletal muscle and pancreas.

Similarity. Belongs to the syntaxin family.

Isoforms (2)

UniProt ID	Names	Canonical?
O60499-1	1	yes
O60499-2	2

RefSeq proteins (4): NP_001258538, NP_001258539, NP_001258540, NP_003756* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000727	T_SNARE_dom	Domain
IPR006012	Syntaxin/epimorphin_CS	Conserved_site
IPR010989	SNARE	Homologous_superfamily
IPR015260	Syntaxin-6/10/61_N	Domain

Pfam: PF05739, PF09177

UniProt features (17 total): modified residue 6, helix 4, initiator methionine 1, chain 1, splice variant 1, topological domain 1, transmembrane region 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
4DND	X-RAY DIFFRACTION	1.4

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O60499-F1	81.12	0.36

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 (6): 140, 143, 2, 108, 110, 134

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-6811440	Retrograde transport at the Trans-Golgi-Network
R-HSA-199991	Membrane Trafficking
R-HSA-5653656	Vesicle-mediated transport
R-HSA-6811442	Intra-Golgi and retrograde Golgi-to-ER traffic

MSigDB gene sets: 137 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_ORGANIZATION, GOBP_MEMBRANE_FUSION, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, MODULE_16, YY1_Q6, GOBP_MEMBRANE_DOCKING, SRF_Q5_01, SRF_01, SRF_C, GOCC_TRANS_GOLGI_NETWORK, YY1_02, WCTCNATGGY_UNKNOWN

GO Biological Process (9): intracellular protein transport (GO:0006886), vesicle fusion (GO:0006906), regulation of protein localization (GO:0032880), retrograde transport, endosome to Golgi (GO:0042147), Golgi vesicle transport (GO:0048193), obsolete vesicle docking (GO:0048278), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192), membrane fusion (GO:0061025)

GO Molecular Function (4): SNARE binding (GO:0000149), SNAP receptor activity (GO:0005484), syntaxin binding (GO:0019905), protein binding (GO:0005515)

GO Cellular Component (13): Golgi membrane (GO:0000139), trans-Golgi network (GO:0005802), cytosol (GO:0005829), endomembrane system (GO:0012505), synaptic vesicle membrane (GO:0030672), SNARE complex (GO:0031201), vesicle (GO:0031982), trans-Golgi network membrane (GO:0032588), perinuclear region of cytoplasm (GO:0048471), Golgi apparatus (GO:0005794), membrane (GO:0016020), organelle membrane (GO:0031090), Golgi apparatus subcompartment (GO:0098791)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Intra-Golgi and retrograde Golgi-to-ER traffic	1
Vesicle-mediated transport	1
Membrane Trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	4
cellular anatomical structure	4
intracellular protein localization	3
vesicle-mediated transport	2
transport	2
Golgi apparatus	2
membrane-bounded organelle	2
protein transport	1
intracellular transport	1
vesicle organization	1
organelle membrane fusion	1
regulation of localization	1
intercellular transport	1
endosomal transport	1
cytosolic transport	1
establishment of protein localization	1
cellular process	1
membrane organization	1
protein binding	1
protein-macromolecule adaptor activity	1
membrane fusion	1
fusogenic activity	1
SNARE binding	1
binding	1
bounding membrane of organelle	1
Golgi apparatus subcompartment	1
vacuole	1
plasma membrane	1
synaptic vesicle	1
exocytic vesicle membrane	1
membrane protein complex	1
trans-Golgi network	1
organelle membrane	1
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane	1
organelle subcompartment	1

Protein interactions and networks

STRING

1190 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
STX10	STX16	O14662	986
STX10	VAMP3	Q15836	977
STX10	VTI1A	Q96AJ9	971
STX10	NAPA	P54920	819
STX10	VAMP4	O75379	760
STX10	VTI1B	Q9UEU0	724
STX10	GCC2	Q8IWJ2	667
STX10	STX5	Q13190	665
STX10	GOSR1	O95249	605
STX10	STX8	Q9UNK0	591
STX10	VPS52	Q8N1B4	591
STX10	STX12	Q86Y82	578
STX10	VPS54	Q9P1Q0	564
STX10	YKT6	O15498	558
STX10	VPS53	Q5VIR6	539

IntAct

108 interactions, top by confidence:

A	B	Type	Score
STX11	SNAP23	psi-mi:“MI:0914”(association)	0.900
STX18	NBAS	psi-mi:“MI:0914”(association)	0.810
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
STX6	GOSR2	psi-mi:“MI:0914”(association)	0.670
STX3	SNAP23	psi-mi:“MI:0914”(association)	0.660
STX7	SNAP23	psi-mi:“MI:0914”(association)	0.640
STX12	SNAP23	psi-mi:“MI:0914”(association)	0.640
NAPA	NBAS	psi-mi:“MI:0914”(association)	0.530
TMEM9	ESYT2	psi-mi:“MI:0914”(association)	0.530
VAMP5	NBAS	psi-mi:“MI:0914”(association)	0.530
FAM171B	FAM171A2	psi-mi:“MI:0914”(association)	0.530
STX11	EXOC5	psi-mi:“MI:0914”(association)	0.530
TEX29	TOR1A	psi-mi:“MI:0914”(association)	0.530
STX3	YKT6	psi-mi:“MI:0914”(association)	0.530
SLC39A4	TMEM120B	psi-mi:“MI:0914”(association)	0.530
STX12	FAM234B	psi-mi:“MI:0914”(association)	0.530
TMEM200A	STX6	psi-mi:“MI:0914”(association)	0.530
ANKH	FAM234B	psi-mi:“MI:0914”(association)	0.530
NRAS	ESYT2	psi-mi:“MI:2364”(proximity)	0.480
	ESYT2	psi-mi:“MI:0914”(association)	0.350
OCRL	MYO1C	psi-mi:“MI:0914”(association)	0.350
VAMP5	ESYT2	psi-mi:“MI:0914”(association)	0.350
NS3	C15orf61	psi-mi:“MI:0914”(association)	0.350

BioGRID (190): STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS), STX10 (Proximity Label-MS), STX10 (Proximity Label-MS), STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS), STX10 (Affinity Capture-MS)

ESM2 similar proteins: G3V7P1, O08522, O14662, O15400, O22151, O43752, O49377, O60499, O64791, O70257, O70439, O70480, O75379, O88384, O88630, O88983, O95249, P58200, Q08851, Q08DB5, Q13190, Q2KIU0, Q2TBU3, Q32L97, Q3T075, Q3ZBT5, Q5R602, Q5R6Q2, Q5RBL6, Q5RBW6, Q5RF94, Q5SRX1, Q5ZL19, Q62931, Q63635, Q86Y82, Q8BVI5, Q8K1E0, Q944A9, Q946Y7

Diamond homologs: O43752, O60499, P83528, Q5R6Q2, Q5ZL19, Q63635, Q9JKK1, O88983, Q3T075, Q54IX6, Q946Y7, Q9HGN3, Q9UNK0, Q9Z2Q7, Q553P5, Q9SA23, Q94KK7

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
STX10	“form complex”	“LE-TGN SNARE”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 112 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Intra-Golgi traffic	7	24.9×	2e-06
Retrograde transport at the Trans-Golgi-Network	7	21.1×	3e-06
RHOJ GTPase cycle	6	16.5×	1e-04
Golgi Associated Vesicle Biogenesis	5	13.7×	9e-04
COPII-mediated vesicle transport	6	13.4×	2e-04
Intra-Golgi and retrograde Golgi-to-ER traffic	9	12.9×	3e-06
RHOQ GTPase cycle	5	12.4×	1e-03
RAC3 GTPase cycle	7	11.4×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
obsolete vesicle docking	7	55.9×	4e-09
vesicle fusion	8	50.1×	1e-09
membrane fusion	7	45.5×	2e-08
obsolete vesicle docking involved in exocytosis	5	35.1×	3e-05
cellular response to type II interferon	5	10.8×	3e-03
retrograde transport, endosome to Golgi	5	10.7×	3e-03
intracellular protein transport	15	10.1×	4e-09
exocytosis	6	9.5×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1472 predictions. Top by Δscore:

Variant	Effect	Δscore
19:13144576:CCA:C	donor_gain	1.0000
19:13144607:T:TA	donor_gain	1.0000
19:13144667:GCATG:G	acceptor_gain	1.0000
19:13144668:CATG:C	acceptor_gain	1.0000
19:13144668:CATGC:C	acceptor_gain	1.0000
19:13144669:ATG:A	acceptor_gain	1.0000
19:13144670:TG:T	acceptor_gain	1.0000
19:13144672:C:CC	acceptor_gain	1.0000
19:13144673:T:C	acceptor_loss	1.0000
19:13144676:C:CT	acceptor_gain	1.0000
19:13144677:A:T	acceptor_gain	1.0000
19:13144752:T:TA	donor_gain	1.0000
19:13144762:A:AC	donor_gain	1.0000
19:13144763:C:CC	donor_gain	1.0000
19:13144763:CATG:C	donor_gain	1.0000
19:13144764:ATGC:A	donor_gain	1.0000
19:13144767:C:CA	donor_gain	1.0000
19:13144776:T:TA	donor_gain	1.0000
19:13144866:ATCAG:A	acceptor_gain	1.0000
19:13144867:TCAG:T	acceptor_gain	1.0000
19:13144868:CAG:C	acceptor_gain	1.0000
19:13144868:CAGC:C	acceptor_gain	1.0000
19:13144869:AG:A	acceptor_gain	1.0000
19:13144870:GCT:G	acceptor_loss	1.0000
19:13144871:C:CC	acceptor_gain	1.0000
19:13144871:CT:C	acceptor_loss	1.0000
19:13144872:T:A	acceptor_loss	1.0000
19:13144879:C:CT	acceptor_gain	1.0000
19:13144880:G:T	acceptor_gain	1.0000
19:13145392:GTAT:G	acceptor_gain	1.0000

AlphaMissense

1638 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:13149784:A:G	L50P	0.997
19:13149742:A:G	L64P	0.996
19:13149565:G:C	F78L	0.995
19:13149565:G:T	F78L	0.995
19:13149567:A:G	F78L	0.995
19:13149751:A:G	L61P	0.995
19:13150153:A:C	F7L	0.993
19:13150153:A:T	F7L	0.993
19:13150155:A:G	F7L	0.993
19:13149758:A:G	W59R	0.992
19:13149758:A:T	W59R	0.992
19:13149772:A:G	L54P	0.990
19:13149746:C:G	D63H	0.989
19:13149535:T:A	R88S	0.988
19:13149535:T:G	R88S	0.988
19:13149566:A:G	F78S	0.988
19:13149756:C:A	W59C	0.988
19:13149756:C:G	W59C	0.988
19:13149884:C:G	A17P	0.987
19:13150161:C:G	D5H	0.984
19:13144812:A:G	L177P	0.980
19:13149536:C:G	R88T	0.979
19:13149745:T:G	D63A	0.978
19:13150160:T:C	D5G	0.978
19:13149755:C:G	D60H	0.977
19:13149566:A:C	F78C	0.975
19:13149754:T:G	D60A	0.975
19:13149526:G:C	F91L	0.974
19:13149526:G:T	F91L	0.974
19:13149528:A:G	F91L	0.974

dbSNP variants (sampled 300 via entrez): RS1000264223 (19:13151707 G>A), RS1000633587 (19:13146938 C>T), RS1000698409 (19:13151415 G>T), RS1001727092 (19:13151822 C>T), RS1001913788 (19:13146226 G>A,C), RS1002056929 (19:13149465 T>C), RS1002512007 (19:13146601 T>C), RS1002799337 (19:13150068 G>A,C), RS1003179219 (19:13150261 C>G,T), RS1003773073 (19:13148841 C>T), RS1003948915 (19:13148372 G>A,T), RS1004556586 (19:13145016 T>C,G), RS1005245908 (19:13149348 G>A,T), RS1005899629 (19:13149708 G>A), RS1006001240 (19:13146129 G>A,T)

Disease associations

OMIM: gene MIM:603765 | 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
GCST009030_25	Venous thromboembolism	2.000000e-09
GCST90000025_557	Appendicular lean mass	2.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
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

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	3
cobaltous chloride	decreases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
Arsenic	affects methylation, decreases expression, increases abundance	2
triphenyl phosphate	affects expression	1
bisphenol A	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	increases expression	1
K 7174	decreases expression	1
ICG 001	increases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Cadmium	increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Cisplatin	affects cotreatment, increases expression	1
Copper	decreases expression, affects binding	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Ivermectin	decreases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases methylation	1
Cyclosporine	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3IL	Abcam HEK293T STX10 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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