STX12

gene
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Also known as STX13STX14

Summary

STX12 (syntaxin 12, HGNC:11430) is a protein-coding gene on chromosome 1p35.3, encoding Syntaxin-12 (Q86Y82). SNARE promoting fusion of transport vesicles with target membranes.

Predicted to enable SNAP receptor activity and SNARE binding activity. Involved in autophagosome assembly; cholesterol efflux; and protein stabilization. Located in several cellular components, including BLOC-1 complex; phagocytic vesicle; and phagophore assembly site. Part of SNARE complex.

Source: NCBI Gene 23673 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 48 total
  • MANE Select transcript: NM_177424

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11430
Approved symbolSTX12
Namesyntaxin 12
Location1p35.3
Locus typegene with protein product
StatusApproved
AliasesSTX13, STX14
Ensembl geneENSG00000117758
Ensembl biotypeprotein_coding
OMIM606892
Entrez23673

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 7 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000373943, ENST00000440806, ENST00000468761, ENST00000472285, ENST00000481874, ENST00000893600, ENST00000893601, ENST00000961041, ENST00000961042, ENST00000961043

RefSeq mRNA: 1 — MANE Select: NM_177424 NM_177424

CCDS: CCDS310

Canonical transcript exons

ENST00000373943 — 9 exons

ExonStartEnd
ENSE000007617412781965027819732
ENSE000008667092780167827801815
ENSE000010374632781024627810289
ENSE000011536142777321927773425
ENSE000016517182781785127817923
ENSE000018142462782223127824443
ENSE000034831262778956227789631
ENSE000035714122779353327793632
ENSE000037877312781216327812268

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 97.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 58.6149 / max 399.7117, expressed in 1823 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
174658.61491823

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
middle temporal gyrusUBERON:000277197.54gold quality
corpus epididymisUBERON:000435997.47gold quality
Brodmann (1909) area 23UBERON:001355497.31gold quality
left lobe of thyroid glandUBERON:000112097.08gold quality
esophagus squamous epitheliumUBERON:000692097.03gold quality
right lobe of thyroid glandUBERON:000111996.88gold quality
thyroid glandUBERON:000204696.87gold quality
lower lobe of lungUBERON:000894996.53gold quality
cauda epididymisUBERON:000436096.46gold quality
superior frontal gyrusUBERON:000266196.42gold quality
substantia nigra pars reticulataUBERON:000196696.28gold quality
Brodmann (1909) area 46UBERON:000648396.25gold quality
epithelium of esophagusUBERON:000197696.24gold quality
postcentral gyrusUBERON:000258196.24gold quality
substantia nigra pars compactaUBERON:000196596.23gold quality
entorhinal cortexUBERON:000272896.18gold quality
orbitofrontal cortexUBERON:000416796.17gold quality
cortical plateUBERON:000534396.13gold quality
endothelial cellCL:000011596.07gold quality
parietal lobeUBERON:000187296.05gold quality
right lungUBERON:000216796.01gold quality
ponsUBERON:000098895.95gold quality
body of stomachUBERON:000116195.89gold quality
substantia nigraUBERON:000203895.78gold quality
squamous epitheliumUBERON:000691495.78gold quality
midbrainUBERON:000189195.74gold quality
C1 segment of cervical spinal cordUBERON:000646995.73gold quality
superior vestibular nucleusUBERON:000722795.72gold quality
spinal cordUBERON:000224095.63gold quality
subthalamic nucleusUBERON:000190695.62gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-HCAD-13yes23.71
E-MTAB-11011no221.72
E-MTAB-6678no3.20
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

112 targeting STX12, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5692A100.0074.406850
HSA-MIR-4425100.0067.591049
HSA-MIR-3646100.0073.565283
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-60799.9773.625593
HSA-MIR-426799.9666.532368
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-302E99.9670.742669
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-539-5P99.9370.302855
HSA-MIR-6744-5P99.9366.82748
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-338-5P99.9272.342951

Literature-anchored findings (GeneRIF, showing 7)

  • ABCA1 forms a complex with syntaxin 13 and flotillin-1, residing at the plasma membrane and in phagosomes that are partially located in raft microdomains (PMID:15469992)
  • the importance of syntaxin-13 in the trafficking of matrix metalloproteinases during degradation of extracellular matrix substrates and subsequent cellular invasion (PMID:19910495)
  • Data indicate that knockdown of syntaxin 13 (syx13) further increased the cellular toxicity caused by mutant CHMP2B (CHMP2BIntron5) expression. (PMID:24095276)
  • The association of Src, EGFR and beta1 integrin is dependent upon membrane traffic that is mediated by syntaxin13 (officially known as STX12) and SNAP23. (PMID:24496451)
  • STX13 acts as a fusion SNARE in melanosomal trafficking pathways. (PMID:26208634)
  • A BLOC-1-AP-3 super-complex sorts a cis-SNARE complex into endosome-derived tubular transport carriers. (PMID:33886957)
  • Syntaxin 12 and COMMD3 are new factors that function with VPS33B in the biogenesis of platelet alpha-granules. (PMID:34905616)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriostx12lENSDARG00000044605
danio_reriostx12ENSDARG00000098813
mus_musculusStx12ENSMUSG00000028879
rattus_norvegicusStx12ENSRNOG00000011804
drosophila_melanogasterSyx7FBGN0267849
caenorhabditis_eleganssyx-7WBGENE00009478

Paralogs (12): STX7 (ENSG00000079950), STX1B (ENSG00000099365), STX4 (ENSG00000103496), STX1A (ENSG00000106089), STX2 (ENSG00000111450), STX16 (ENSG00000124222), STX11 (ENSG00000135604), STX17 (ENSG00000136874), STX5 (ENSG00000162236), STX3 (ENSG00000166900), TSNARE1 (ENSG00000171045), STX19 (ENSG00000178750)

Protein

Protein identifiers

Syntaxin-12Q86Y82 (reviewed: Q86Y82)

All UniProt accessions (2): B1AJQ6, Q86Y82

UniProt curated annotations — full annotation on UniProt →

Function. SNARE promoting fusion of transport vesicles with target membranes. Together with SNARE STX6, promotes movement of vesicles from endosomes to the cell membrane, and may therefore function in the endocytic recycling pathway. Through complex formation with GRIP1, GRIA2 and NSG1 controls the intracellular fate of AMPAR and the endosomal sorting of the GRIA2 subunit toward recycling and membrane targeting.

Subunit / interactions. Interacts with NAPA and SNAP23. Identified in a complex containing STX6, STX12, VAMP4 and VTI1A. Associates with the BLOC-1 complex. Interacts with BLOC1S6. Interacts with GRIPAP1. Forms a complex with GRIP1, GRIA2 and NSG1; controls the intracellular fate of AMPAR and the endosomal sorting of the GRIA2 subunit toward recycling and membrane targeting. Interacts with NSG1. Interacts with TPC1. Interacts (via N-terminus) with VPS13B.

Subcellular location. Endosome membrane. Golgi apparatus membrane. Endomembrane system. Early endosome membrane. Recycling endosome membrane.

Similarity. Belongs to the syntaxin family.

RefSeq proteins (1): NP_803173* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000727T_SNARE_domDomain
IPR006011Syntaxin_NDomain
IPR006012Syntaxin/epimorphin_CSConserved_site
IPR010989SNAREHomologous_superfamily
IPR045242SyntaxinFamily

Pfam: PF05739, PF14523

UniProt features (17 total): modified residue 5, helix 3, topological domain 2, initiator methionine 1, chain 1, sequence variant 1, strand 1, transmembrane region 1, domain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2DNXSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86Y82-F180.330.44

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 (5): 218, 225, 2, 139, 142

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 245 (showing top): GSE45365_NK_CELL_VS_BCELL_UP, GCM_MAP4K4, GOBP_VACUOLE_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_ORGANIZATION, TTTGTAG_MIR520D, GOBP_MEMBRANE_FUSION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, GGGTGGRR_PAX4_03, GOBP_MACROAUTOPHAGY, GOBP_MEMBRANE_DOCKING, GOBP_ORGANIC_HYDROXY_COMPOUND_TRANSPORT, GOBP_CHOLESTEROL_EFFLUX, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN

GO Biological Process (10): autophagosome assembly (GO:0000045), intracellular protein transport (GO:0006886), vesicle fusion (GO:0006906), endocytic recycling (GO:0032456), cholesterol efflux (GO:0033344), obsolete vesicle docking (GO:0048278), protein stabilization (GO:0050821), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192), regulation of biological quality (GO:0065008)

GO Molecular Function (3): SNARE binding (GO:0000149), SNAP receptor activity (GO:0005484), protein binding (GO:0005515)

GO Cellular Component (20): Golgi membrane (GO:0000139), phagophore assembly site (GO:0000407), nucleoplasm (GO:0005654), Golgi apparatus (GO:0005794), synaptic vesicle (GO:0008021), endomembrane system (GO:0012505), synaptic vesicle membrane (GO:0030672), SNARE complex (GO:0031201), early endosome membrane (GO:0031901), vesicle (GO:0031982), membrane raft (GO:0045121), phagocytic vesicle (GO:0045335), recycling endosome (GO:0055037), recycling endosome membrane (GO:0055038), postsynaptic recycling endosome (GO:0098837), endosome (GO:0005768), endosome membrane (GO:0010008), membrane (GO:0016020), BLOC-1 complex (GO:0031083), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm4
cellular anatomical structure4
intracellular protein localization2
transport2
bounding membrane of organelle2
endomembrane system2
endosome membrane2
endosome2
recycling endosome2
Atg12 activating enzyme activity1
protein-phosphatidylethanolamide deconjugating activity1
Atg12 conjugating enzyme activity1
Atg12 ligase activity1
organelle assembly1
Atg1/ULK1 kinase complex assembly1
autophagosome organization1
protein transport1
intracellular transport1
vesicle organization1
vesicle-mediated transport1
organelle membrane fusion1
endosomal transport1
vesicle-mediated transport to the plasma membrane1
cholesterol transport1
regulation of protein stability1
establishment of protein localization1
cellular process1
biological regulation1
protein binding1
protein-macromolecule adaptor activity1
membrane fusion1
fusogenic activity1
binding1
Golgi apparatus1
nuclear lumen1
intracellular membrane-bounded organelle1
exocytic vesicle1
presynapse1
vacuole1
plasma membrane1

Protein interactions and networks

STRING

1712 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STX12STX8Q9UNK0936
STX12BLOC1S6Q9UL45858
STX12STX6O43752821
STX12VPS33AQ96AX1814
STX12VPS33BQ9H267792
STX12VTI1AQ96AJ9792
STX12VAMP4O75379781
STX12VIPAS39Q9H9C1773
STX12VAMP7P51809769
STX12SNAP23O00161758
STX12VAMP8Q9BV40751
STX12VAMP3Q15836738
STX12RAB11AP24410677
STX12VAMP2P19065671
STX12STX11O75558641

IntAct

269 interactions, top by confidence:

ABTypeScore
STX12SNAP29psi-mi:“MI:0915”(physical association)0.880
SNAP29STX12psi-mi:“MI:0915”(physical association)0.880
STX12STX4psi-mi:“MI:0915”(physical association)0.870
STX4STX12psi-mi:“MI:0915”(physical association)0.870
STX12DTX2psi-mi:“MI:0915”(physical association)0.780
DTX2STX12psi-mi:“MI:0915”(physical association)0.780
NAPASNAP23psi-mi:“MI:0914”(association)0.780
STX12SNAP47psi-mi:“MI:0915”(physical association)0.740
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
TRDNTMEM223psi-mi:“MI:0914”(association)0.640
STX12TIMMDC1psi-mi:“MI:0915”(physical association)0.560
STX12TMEM14Bpsi-mi:“MI:0915”(physical association)0.560
STX12PLPPR2psi-mi:“MI:0915”(physical association)0.560
STX12BCL2L13psi-mi:“MI:0915”(physical association)0.560
STX1ASTX12psi-mi:“MI:0915”(physical association)0.560
STX12KASH5psi-mi:“MI:0915”(physical association)0.560
STX2STX12psi-mi:“MI:0915”(physical association)0.560
STX12psi-mi:“MI:0915”(physical association)0.560

BioGRID (469): STX12 (Two-hybrid), STX12 (Two-hybrid), DTX2 (Two-hybrid), STX12 (Affinity Capture-RNA), STX12 (Affinity Capture-MS), STX12 (Affinity Capture-MS), STX12 (Affinity Capture-MS), EIF2B5 (Affinity Capture-MS), RNF13 (Affinity Capture-MS), KIAA1467 (Affinity Capture-MS), YKT6 (Affinity Capture-MS), EIF2B1 (Affinity Capture-MS), BNIP1 (Affinity Capture-MS), EIF2B4 (Affinity Capture-MS), GOLGA2 (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: A8WVD0, G3V7P1, O14662, O15400, O16000, O35526, O64791, O65359, O70257, O70439, O94651, P32850, P32851, P32854, P32856, P50279, P61264, P61265, P61266, P61267, P61268, P70452, P91409, Q00262, Q08144, Q08849, Q08850, Q12846, Q13277, Q16623, Q16932, Q24547, Q3SWZ3, Q3ZBT5, Q42374, Q54JY7, Q54X86, Q5R4L2, Q5R602, Q5RBW6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 128 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:

PathwayPartnersFoldFDR
Retrograde transport at the Trans-Golgi-Network1127.8×5e-11
Intra-Golgi traffic617.9×5e-05
trans-Golgi Network Vesicle Budding617.5×5e-05
NCAM signaling for neurite out-growth515.6×5e-04
Golgi Associated Vesicle Biogenesis511.5×1e-03
COPII-mediated vesicle transport611.2×5e-04
Intra-Golgi and retrograde Golgi-to-ER traffic910.8×1e-05
ER-Phagosome pathway68.9×1e-03

GO biological processes:

GO termPartnersFoldFDR
obsolete vesicle docking745.8×2e-08
vesicle fusion841.1×5e-09
synaptic vesicle priming534.3×2e-05
membrane fusion526.7×8e-05
exocytosis1418.2×3e-11
mitophagy616.3×1e-04
autophagosome maturation515.0×1e-03
retrograde transport, endosome to Golgi814.1×1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance33
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1262 predictions. Top by Δscore:

VariantEffectΔscore
1:27773422:GCCA:Gdonor_gain1.0000
1:27773426:G:GGdonor_gain1.0000
1:27789560:A:AGacceptor_gain1.0000
1:27789561:G:GGacceptor_gain1.0000
1:27789632:G:GGdonor_gain1.0000
1:27801675:TA:Tacceptor_loss1.0000
1:27801676:A:AGacceptor_gain1.0000
1:27801677:G:GGacceptor_gain1.0000
1:27801677:GC:Gacceptor_gain1.0000
1:27801778:A:Tdonor_gain1.0000
1:27801816:G:GGdonor_gain1.0000
1:27812161:A:AGacceptor_gain1.0000
1:27812162:G:GAacceptor_gain1.0000
1:27812162:GCC:Gacceptor_gain1.0000
1:27812162:GCCAT:Gacceptor_gain1.0000
1:27812267:AG:Adonor_loss1.0000
1:27812270:T:Adonor_loss1.0000
1:27817845:CCTTA:Cacceptor_loss1.0000
1:27817847:TTA:Tacceptor_loss1.0000
1:27817848:TA:Tacceptor_loss1.0000
1:27817849:A:AGacceptor_gain1.0000
1:27817850:G:GAacceptor_gain1.0000
1:27817850:GGCT:Gacceptor_gain1.0000
1:27817924:G:GGdonor_gain1.0000
1:27819645:TGCA:Tacceptor_loss1.0000
1:27819646:GCA:Gacceptor_loss1.0000
1:27819647:CAG:Cacceptor_loss1.0000
1:27819648:A:AGacceptor_gain1.0000
1:27819648:AG:Aacceptor_loss1.0000
1:27819649:G:GCacceptor_gain1.0000

AlphaMissense

1821 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:27812264:T:CL191P1.000
1:27801706:T:CL106P0.999
1:27817851:G:CA193P0.999
1:27817876:T:AI201K0.999
1:27817878:T:CF202L0.999
1:27817880:T:AF202L0.999
1:27817880:T:GF202L0.999
1:27817890:G:CA206P0.999
1:27819661:G:CA221P0.999
1:27819697:G:CA233P0.999
1:27819718:G:CA240P0.999
1:27793565:C:AA74D0.998
1:27793586:T:CL81P0.998
1:27801726:G:CA113P0.998
1:27817888:T:CL205S0.998
1:27819656:T:AI219K0.998
1:27789631:T:CL63P0.997
1:27793564:G:CA74P0.997
1:27793573:A:CT77P0.997
1:27801703:G:CR105P0.997
1:27801751:A:CQ121P0.997
1:27812251:G:CA187P0.997
1:27817867:T:AV198D0.997
1:27817876:T:CI201T0.997
1:27819676:T:CS226P0.997
1:27801718:T:CF110S0.996
1:27812243:G:TR184I0.996
1:27817876:T:GI201R0.996
1:27817888:T:GL205W0.996
1:27817911:G:TG213C0.996

dbSNP variants (sampled 300 via entrez): RS1000021133 (1:27777212 C>T), RS1000058975 (1:27776086 A>C), RS1000191154 (1:27816034 C>G,T), RS1000216018 (1:27795394 C>T), RS1000419991 (1:27790951 A>C), RS1000502832 (1:27794254 T>A), RS1000534042 (1:27794012 T>A), RS1000586540 (1:27824824 TCAC>T), RS1000658186 (1:27794586 T>C), RS1000662812 (1:27787908 A>G), RS1000680076 (1:27824576 TAGAG>T), RS1000708187 (1:27804547 C>G,T), RS1000815761 (1:27807597 A>G), RS1000866450 (1:27807809 A>G), RS1000882438 (1:27786091 A>G)

Disease associations

OMIM: gene MIM:606892 | 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

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases abundance, affects methylation3
Arsenicaffects methylation, decreases expression, increases abundance2
Tobacco Smoke Pollutionaffects expression, increases expression2
aristolochic acid Iincreases expression1
FR900359increases phosphorylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects cotreatment, increases expression1
methylselenic acidincreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, increases expression1
trichostatin Aaffects expression1
potassium chromate(VI)decreases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
K 7174increases expression1
ICG 001decreases expression1
bisphenol Bincreases expression1
ON 01910increases expression1
jinfukangdecreases expression1
bisphenol AFincreases expression1
Bortezomibincreases expression1
Acetaminophenincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Atrazinedecreases expression1
Benzo(a)pyreneaffects methylation1
Caffeinedecreases phosphorylation1
Demecolcineincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Dimethyl Sulfoxideincreases expression1
Ethyl Methanesulfonateincreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.