STX7

gene
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Summary

STX7 (syntaxin 7, HGNC:11442) is a protein-coding gene on chromosome 6q23.2, encoding Syntaxin-7 (O15400). May be involved in protein trafficking from the plasma membrane to the early endosome (EE) as well as in homotypic fusion of endocytic organelles.

The protein encoded by this gene is a syntaxin family membrane receptor involved in vesicle transport. The encoded protein binds alpha-SNAP, an important regulator of transport vesicle fusion. Along with syntaxin 13, this protein plays a role in the ordered fusion of endosomes and lysosomes with the phagosome.

Source: NCBI Gene 8417 — RefSeq curated summary.

At a glance

  • GWAS associations: 17
  • Clinical variants (ClinVar): 48 total — 1 likely-pathogenic
  • MANE Select transcript: NM_003569

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:11442
Approved symbolSTX7
Namesyntaxin 7
Location6q23.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000079950
Ensembl biotypeprotein_coding
OMIM603217
Entrez8417

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000367937, ENST00000367941, ENST00000448348, ENST00000475879, ENST00000862289, ENST00000862290, ENST00000862291, ENST00000862292, ENST00000862293, ENST00000942368, ENST00000942369

RefSeq mRNA: 4 — MANE Select: NM_003569 NM_001326578, NM_001326579, NM_001326580, NM_003569

CCDS: CCDS5153, CCDS87441

Canonical transcript exons

ENST00000367941 — 10 exons

ExonStartEnd
ENSE00000798744132463993132464075
ENSE00000798746132469951132470047
ENSE00001445973132445867132460850
ENSE00001750391132468403132468475
ENSE00001856918132513007132513116
ENSE00003501102132503446132503588
ENSE00003698784132471463132471600
ENSE00003699060132472282132472375
ENSE00003699492132470574132470626
ENSE00003700055132475593132475662

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 97.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.2144 / max 647.2784, expressed in 1821 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
7559846.22671821
755970.9449463
755990.042718

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534397.99gold quality
endothelial cellCL:000011597.91gold quality
monocyteCL:000057696.69gold quality
mononuclear cellCL:000084296.48gold quality
tendon of biceps brachiiUBERON:000818896.42gold quality
calcaneal tendonUBERON:000370196.19gold quality
leukocyteCL:000073896.17gold quality
middle temporal gyrusUBERON:000277196.15gold quality
tendonUBERON:000004395.99gold quality
ganglionic eminenceUBERON:000402395.54gold quality
amniotic fluidUBERON:000017395.27gold quality
medial globus pallidusUBERON:000247794.92gold quality
renal glomerulusUBERON:000007494.78gold quality
secondary oocyteCL:000065594.71gold quality
metanephric glomerulusUBERON:000473694.58gold quality
corpus callosumUBERON:000233694.54gold quality
vermiform appendixUBERON:000115494.42gold quality
nephron tubuleUBERON:000123194.40gold quality
gall bladderUBERON:000211094.19gold quality
lymph nodeUBERON:000002993.86gold quality
deciduaUBERON:000245093.75gold quality
Brodmann (1909) area 23UBERON:001355493.51gold quality
globus pallidusUBERON:000187593.45gold quality
prefrontal cortexUBERON:000045193.37gold quality
tonsilUBERON:000237293.18gold quality
C1 segment of cervical spinal cordUBERON:000646993.18gold quality
esophagus squamous epitheliumUBERON:000692093.07gold quality
dorsal root ganglionUBERON:000004492.94gold quality
colonic epitheliumUBERON:000039792.92gold quality
frontal poleUBERON:000279592.65gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-CURD-122yes19.00
E-MTAB-6678yes4.47
E-MTAB-6075no365.62
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 8)

  • syntaxin 7 has a role in the intracellular vacuolation induced by VacA (PMID:12730232)
  • Results report that syntaxin 7, syntaxin 8, vti1b and VAMP8 physically and functionally interact with CFTR. (PMID:18570918)
  • Palmitoylation-defective syntaxin 7 is selectively retained on the plasma membrane, suggesting that palmitoylation is important for intercompartmental transport of syntaxin 7. (PMID:18980942)
  • The expression level of STX7 protein was inversely correlated to tumor stage, suggesting that decreased expression of STX7 is associated with more aggressive tumors. (PMID:19714869)
  • data reveal the presence of syntaxin 7 in the membranes of exocytosis-prone granules and phagocytosis-related granules in human neutrophils, and therefore it might play a role in both exocytosis and phagocytosis in human neutrophils (PMID:20170677)
  • Data suggest that accumulation of recycling T cell receptors at the immunological synapse is SNARE-dependent and that Stx7-mediated processing of recycling TCRs through endosomes is a prerequisite for the cytolytic function of cytotoxic T lymphocytes. (PMID:21438968)
  • Syntaxin 7 contributes to breast cancer cell invasion by promoting invadopodia formation. (PMID:35762511)
  • Syntaxin 7 modulates seizure activity in epilepsy. (PMID:37031804)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriostx7lENSDARG00000069208
mus_musculusStx7ENSMUSG00000019998
rattus_norvegicusStx7ENSRNOG00000015670
drosophila_melanogasterSyx7FBGN0267849
caenorhabditis_eleganssyx-7WBGENE00009478

Paralogs (12): STX1B (ENSG00000099365), STX4 (ENSG00000103496), STX1A (ENSG00000106089), STX2 (ENSG00000111450), STX12 (ENSG00000117758), STX16 (ENSG00000124222), STX11 (ENSG00000135604), STX17 (ENSG00000136874), STX5 (ENSG00000162236), STX3 (ENSG00000166900), TSNARE1 (ENSG00000171045), STX19 (ENSG00000178750)

Protein

Protein identifiers

Syntaxin-7O15400 (reviewed: O15400)

All UniProt accessions (2): O15400, B4DWC2

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in protein trafficking from the plasma membrane to the early endosome (EE) as well as in homotypic fusion of endocytic organelles. Mediates the endocytic trafficking from early endosomes to late endosomes and lysosomes.

Subunit / interactions. Forms a SNARE complex with VTI1B, STX8 and VAMP8 which functions in the homotypic fusion of late endosomes. Component of the SNARE complex composed of STX7, STX8, VAMP7 and VTI1B that is required for heterotypic fusion of late endosomes with lysosomes. Interacts with VPS11, VPS16 and VPS18. Interacts with VPS33A. Interacts with TPC1.

Subcellular location. Early endosome membrane.

Tissue specificity. Highest expression is found in placenta followed by heart, skeletal muscle, kidney and brain. Low expression is found in pancreas, lung and liver.

Similarity. Belongs to the syntaxin family.

Isoforms (2)

UniProt IDNamesCanonical?
O15400-11yes
O15400-22

RefSeq proteins (4): NP_001313507, NP_001313508, NP_001313509, NP_003560* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000727T_SNARE_domDomain
IPR006011Syntaxin_NDomain
IPR006012Syntaxin/epimorphin_CSConserved_site
IPR010989SNAREHomologous_superfamily
IPR045242SyntaxinFamily

Pfam: PF05739, PF14523

UniProt features (19 total): modified residue 9, topological domain 2, initiator methionine 1, chain 1, splice variant 1, sequence conflict 1, transmembrane region 1, domain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15400-F178.960.45

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 (9): 45, 75, 79, 125, 126, 129, 205, 2, 4

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 291 (showing top): LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP, GOBP_POSITIVE_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, GOBP_REGULATION_OF_ADAPTIVE_IMMUNE_RESPONSE, GOBP_VESICLE_ORGANIZATION, GOBP_MEMBRANE_FUSION, GOBP_LEUKOCYTE_MEDIATED_CYTOTOXICITY, GOBP_VESICLE_MEDIATED_TRANSPORT, LHX3_01, CHX10_01, GOBP_LEUKOCYTE_MEDIATED_IMMUNITY, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_MEMBRANE_DOCKING

GO Biological Process (9): positive regulation of T cell mediated cytotoxicity (GO:0001916), intracellular protein transport (GO:0006886), vesicle fusion (GO:0006906), obsolete vesicle docking (GO:0048278), organelle localization (GO:0051640), organelle assembly (GO:0070925), positive regulation of receptor localization to synapse (GO:1902685), regulation of protein localization to plasma membrane (GO:1903076), vesicle-mediated transport (GO:0016192)

GO Molecular Function (5): SNARE binding (GO:0000149), SNAP receptor activity (GO:0005484), chloride channel inhibitor activity (GO:0019869), syntaxin binding (GO:0019905), protein binding (GO:0005515)

GO Cellular Component (20): immunological synapse (GO:0001772), lysosome (GO:0005764), lysosomal membrane (GO:0005765), endosome (GO:0005768), early endosome (GO:0005769), late endosome (GO:0005770), plasma membrane (GO:0005886), synaptic vesicle (GO:0008021), endomembrane system (GO:0012505), endocytic vesicle (GO:0030139), SNARE complex (GO:0031201), early endosome membrane (GO:0031901), vesicle (GO:0031982), azurophil granule (GO:0042582), perinuclear region of cytoplasm (GO:0048471), recycling endosome (GO:0055037), extracellular exosome (GO:0070062), tertiary granule (GO:0070820), membrane (GO:0016020), secretory vesicle (GO:0099503)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
cytoplasmic vesicle3
endosome3
plasma membrane2
cytoplasm2
secretory granule2
positive regulation of leukocyte mediated cytotoxicity1
T cell mediated cytotoxicity1
regulation of T cell mediated cytotoxicity1
positive regulation of T cell mediated immunity1
intracellular protein localization1
protein transport1
intracellular transport1
vesicle organization1
vesicle-mediated transport1
organelle membrane fusion1
localization1
organelle organization1
cellular component assembly1
positive regulation of biological process1
receptor localization to synapse1
regulation of receptor localization to synapse1
protein localization to plasma membrane1
regulation of protein localization to cell periphery1
regulation of protein localization to membrane1
transport1
cellular process1
protein binding1
protein-macromolecule adaptor activity1
membrane fusion1
fusogenic activity1
chloride channel activity1
ion channel inhibitor activity1
chloride channel regulator activity1
SNARE binding1
binding1
lytic vacuole1
lysosome1
lytic vacuole membrane1
endomembrane system1

Protein interactions and networks

STRING

1814 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STX7STX8Q9UNK0999
STX7VAMP8Q9BV40998
STX7VAMP7P51809997
STX7VTI1BQ9UEU0997
STX7SNAP29O95721991
STX7YKT6O15498990
STX7STX6O43752949
STX7SNAP23O00161891
STX7MOXD1Q6UVY6859
STX7VPS33AQ96AX1836
STX7TAAR5O14804833
STX7VAMP3Q15836787
STX7STX17P56962766
STX7NAPAP54920760
STX7BET1O15155758

IntAct

269 interactions, top by confidence:

ABTypeScore
STX7STX4psi-mi:“MI:0915”(physical association)0.830
STX4STX7psi-mi:“MI:0915”(physical association)0.830
STX7LSMEM2psi-mi:“MI:0915”(physical association)0.740
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
VAMP8STX7psi-mi:“MI:0915”(physical association)0.670
TMPRSS2STX7psi-mi:“MI:0915”(physical association)0.600
STX7HSD17B13psi-mi:“MI:0915”(physical association)0.560
STX7REEP1psi-mi:“MI:0915”(physical association)0.560
STX7ELOVL5psi-mi:“MI:0915”(physical association)0.560
STX7AQP6psi-mi:“MI:0915”(physical association)0.560
STX7CYBRD1psi-mi:“MI:0915”(physical association)0.560
STX7JAGN1psi-mi:“MI:0915”(physical association)0.560
STX7EBPpsi-mi:“MI:0915”(physical association)0.560
STX7RETREG3psi-mi:“MI:0915”(physical association)0.560
STX7ANKS6psi-mi:“MI:0915”(physical association)0.560
STX7STX2psi-mi:“MI:0915”(physical association)0.560
STX7STX1Apsi-mi:“MI:0915”(physical association)0.560

BioGRID (954): STX7 (Two-hybrid), STX7 (Affinity Capture-MS), STX7 (Affinity Capture-Western), STX7 (Affinity Capture-Western), STX7 (Affinity Capture-Western), STX7 (Affinity Capture-Western), STX7 (Affinity Capture-MS), STX7 (Affinity Capture-MS), YKT6 (Affinity Capture-MS), GOLGA2 (Affinity Capture-MS), ZNF101 (Affinity Capture-MS), ZKSCAN1 (Affinity Capture-MS), VPS45 (Affinity Capture-MS), NAPA (Affinity Capture-MS), STX4 (Affinity Capture-MS)

ESM2 similar proteins: A8WVD0, O15400, O16000, O35526, O70257, O70439, P32850, P32851, P32856, P32867, P39926, P50279, P61264, P61265, P61266, P61267, P61268, P70452, Q00262, Q08849, Q08850, Q0VCI2, Q12846, Q13277, Q16623, Q16932, Q20024, Q24547, Q3SWZ3, Q3ZBT5, Q42374, Q59YF0, Q5R4L2, Q5R602, Q5TX47, Q64704, Q7XIE2, Q8N4C7, Q8R1Q0, Q8VZU2

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 98 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
trans-Golgi Network Vesicle Budding729.1×1e-06
Retrograde transport at the Trans-Golgi-Network518.0×4e-04
ER-Phagosome pathway510.6×1e-03
COPI-mediated anterograde transport59.0×2e-03
Membrane Trafficking84.9×2e-03
Vesicle-mediated transport84.6×2e-03
Neutrophil degranulation103.8×2e-03

GO biological processes:

GO termPartnersFoldFDR
exocytosis1018.7×7e-08
intracellular protein transport97.2×6e-04
protein transport105.4×9e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance32
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
218904NM_003569.3(STX7):c.159A>C (p.Gln53His)Likely pathogenic

SpliceAI

1864 predictions. Top by Δscore:

VariantEffectΔscore
6:132463990:TACCT:Tdonor_loss1.0000
6:132463991:A:ACdonor_gain1.0000
6:132463991:A:ATdonor_loss1.0000
6:132463992:C:Adonor_loss1.0000
6:132463992:C:CCdonor_gain1.0000
6:132464072:CTAT:Cacceptor_gain1.0000
6:132464073:TAT:Tacceptor_gain1.0000
6:132464074:AT:Aacceptor_gain1.0000
6:132464076:C:CCacceptor_gain1.0000
6:132464077:T:Cacceptor_loss1.0000
6:132464078:G:Cacceptor_gain1.0000
6:132464083:A:ACacceptor_gain1.0000
6:132464083:A:Cacceptor_gain1.0000
6:132469949:A:ACdonor_gain1.0000
6:132469950:C:CCdonor_gain1.0000
6:132469950:CTT:Cdonor_gain1.0000
6:132469952:T:TAdonor_gain1.0000
6:132469959:G:Adonor_gain1.0000
6:132470043:TTTGG:Tacceptor_gain1.0000
6:132470048:C:CCacceptor_gain1.0000
6:132471455:ATACT:Adonor_loss1.0000
6:132471456:TACTT:Tdonor_loss1.0000
6:132471460:TACAG:Tdonor_gain1.0000
6:132471461:A:ACdonor_gain1.0000
6:132471461:ACAGA:Adonor_gain1.0000
6:132471462:C:CCdonor_gain1.0000
6:132471462:CA:Cdonor_gain1.0000
6:132471462:CAG:Cdonor_gain1.0000
6:132471462:CAGA:Cdonor_gain1.0000
6:132471462:CAGAC:Cdonor_gain1.0000

AlphaMissense

1729 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:132464028:C:GA220P0.999
6:132464049:C:GA213P0.999
6:132464064:C:GA208P0.999
6:132469955:A:GL178P0.999
6:132471519:C:GA111P0.999
6:132471548:A:GL101P0.999
6:132464007:C:GA227P0.998
6:132464015:A:GL224P0.998
6:132464069:A:TI206K0.998
6:132468475:C:GA180P0.998
6:132471516:C:GA112P0.998
6:132472343:G:TA63D0.998
6:132468446:A:CF189L0.997
6:132468446:A:TF189L0.997
6:132468448:A:GF189L0.997
6:132464069:A:CI206R0.996
6:132471560:A:GF97S0.996
6:132471575:C:GR92P0.996
6:132472335:T:GT66P0.996
6:132472344:C:GA63P0.996
6:132472346:A:GL62P0.996
6:132468438:A:GL192S0.995
6:132468450:A:TI188K0.995
6:132472334:G:TT66K0.995
6:132464004:C:GA228P0.994
6:132471527:T:GQ108P0.994
6:132472334:G:CT66R0.994
6:132464036:A:TV217D0.993
6:132468405:A:TI203K0.993
6:132471536:T:GQ105P0.993

dbSNP variants (sampled 300 via entrez): RS1000006324 (6:132473023 G>A), RS1000006471 (6:132471108 C>G), RS1000153264 (6:132474222 T>C,G), RS1000154141 (6:132513051 C>T), RS1000174429 (6:132483118 G>A), RS1000181478 (6:132504444 G>C), RS1000205121 (6:132456419 G>A), RS1000306471 (6:132488695 G>C), RS1000359589 (6:132494705 C>G,T), RS1000422172 (6:132488966 C>T), RS1000428395 (6:132460160 T>C), RS1000492281 (6:132510806 G>A,T), RS1000497199 (6:132464497 G>T), RS1000604018 (6:132509041 C>A,G,T), RS1000642966 (6:132458035 A>T)

Disease associations

OMIM: gene MIM:603217 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

17 associations (top):

StudyTraitp-value
GCST004611_67High light scatter reticulocyte count7.000000e-10
GCST004612_26High light scatter reticulocyte percentage of red cells2.000000e-09
GCST004619_84Reticulocyte fraction of red cells3.000000e-09
GCST004621_106Red cell distribution width5.000000e-13
GCST004622_198Reticulocyte count2.000000e-09
GCST011739_3Cutaneous leishmaniasis6.000000e-06
GCST90002385_167High light scatter reticulocyte count5.000000e-30
GCST90002386_113High light scatter reticulocyte percentage of red cells5.000000e-29
GCST90002387_291Immature fraction of reticulocytes5.000000e-12
GCST90002397_481Mean spheric corpuscular volume8.000000e-12
GCST90002404_271Red cell distribution width1.000000e-23
GCST90002405_207Reticulocyte count1.000000e-28
GCST90002406_226Reticulocyte fraction of red cells5.000000e-27
GCST90020024_58A body shape index2.000000e-08
GCST90020025_533Waist-to-hip ratio adjusted for BMI2.000000e-08
GCST90020027_1052Waist-hip index7.000000e-09
GCST90020029_1445Waist circumference adjusted for body mass index3.000000e-09

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0007986reticulocyte count
EFO:0009188Red cell distribution width
EFO:0007789BMI-adjusted waist circumference
EFO:0007788BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases methylation, increases expression4
sodium arsenitedecreases expression, increases expression3
bisphenol Adecreases expression, increases expression2
GSK-J4increases expression1
FR900359affects phosphorylation1
bisphenol Fincreases expression1
dicrotophosdecreases expression1
decabromobiphenyl etherdecreases expression1
trichostatin Aaffects expression1
tetrabromobisphenol Adecreases expression1
perfluorooctanoic acidincreases expression1
manganese chlorideincreases abundance, increases expression1
ochratoxin Adecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
ciglitazoneaffects binding, increases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-oneaffects expression, affects reaction1
K 7174increases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
(+)-JQ1 compoundincreases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Air Pollutants, Occupationaldecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): cutaneous leishmaniasis