STXBP5L

gene
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Also known as KIAA1006LLGL4tomosyn-2

Summary

STXBP5L (syntaxin binding protein 5L, HGNC:30757) is a protein-coding gene on chromosome 3q13.33, encoding Syntaxin-binding protein 5-like (Q9Y2K9). Plays a role in vesicle trafficking and exocytosis inhibition.

The protein encoded by this gene is similar to syntaxin-binding protein 5 and contains ten N-terminal WD40 repeats, four variable region WD40 repeats, and a C-terminal R-SNARE domain. Studies of the orthologous proteins in mouse and rat have shown that the encoded protein may inhibit exocytosis in neurosecretory cells, and may negatively regulate the secretion of insulin. A missense variant in this gene is likely the cause of an infantile-onset neurodegenerative disorder diagnosed in two siblings of consanguineous parents.

Source: NCBI Gene 9515 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 177 total
  • MANE Select transcript: NM_001308330

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30757
Approved symbolSTXBP5L
Namesyntaxin binding protein 5L
Location3q13.33
Locus typegene with protein product
StatusApproved
AliasesKIAA1006, LLGL4, tomosyn-2
Ensembl geneENSG00000145087
Ensembl biotypeprotein_coding
OMIM609381
Entrez9515

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 nonsense_mediated_decay

ENST00000273666, ENST00000461772, ENST00000471262, ENST00000471454, ENST00000472879, ENST00000492541, ENST00000495504, ENST00000497029, ENST00000707001, ENST00000879204, ENST00000938469

RefSeq mRNA: 5 — MANE Select: NM_001308330 NM_001308330, NM_001348343, NM_001348344, NM_001348345, NM_014980

CCDS: CCDS43137, CCDS77799

Canonical transcript exons

ENST00000471454 — 27 exons

ExonStartEnd
ENSE00000968706121157504121157627
ENSE00000968707121205923121206001
ENSE00000968709121233616121233688
ENSE00000968710121238971121239118
ENSE00000968711121240440121240507
ENSE00000968712121250723121250763
ENSE00000968713121254895121255112
ENSE00000968714121257161121257333
ENSE00000968715121259043121259168
ENSE00000968716121279805121279956
ENSE00000968718121318475121318540
ENSE00000968723121223003121223157
ENSE00001012295121413158121413323
ENSE00001012297121381293121381532
ENSE00001012307121415857121415968
ENSE00001012310121378716121378886
ENSE00001012312121418337121418557
ENSE00001012313121407243121407603
ENSE00001078687120909571120909767
ENSE00001078688120954940120955037
ENSE00001137699121419056121424761
ENSE00001137704120908205120908334
ENSE00003472237121114925121115059
ENSE00003530309121045435121045535
ENSE00003604300121152477121152560
ENSE00003645823121041700121041781
ENSE00003653782121121641121121704

Expression profiles

Bgee: expression breadth ubiquitous, 145 present calls, max score 89.45.

FANTOM5 (CAGE): breadth broad, TPM avg 6.2174 / max 737.0575, expressed in 368 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
381816.0515363
381820.077644
381830.052731
381840.035627

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
Brodmann (1909) area 23UBERON:001355489.45gold quality
cerebellar cortexUBERON:000212989.40gold quality
cerebellar hemisphereUBERON:000224589.35gold quality
right hemisphere of cerebellumUBERON:001489089.10gold quality
cerebellumUBERON:000203788.57gold quality
buccal mucosa cellCL:000233687.44gold quality
endothelial cellCL:000011587.34gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.31gold quality
ponsUBERON:000098885.24gold quality
cerebellar vermisUBERON:000472084.67gold quality
primary visual cortexUBERON:000243683.83gold quality
Brodmann (1909) area 46UBERON:000648383.08gold quality
prefrontal cortexUBERON:000045183.04gold quality
occipital lobeUBERON:000202182.44gold quality
superior frontal gyrusUBERON:000266182.20gold quality
frontal cortexUBERON:000187081.40gold quality
postcentral gyrusUBERON:000258181.08gold quality
dorsolateral prefrontal cortexUBERON:000983481.07gold quality
parietal lobeUBERON:000187280.98gold quality
Brodmann (1909) area 9UBERON:001354080.95gold quality
middle temporal gyrusUBERON:000277180.76gold quality
CA1 field of hippocampusUBERON:000388180.75gold quality
right frontal lobeUBERON:000281080.29gold quality
entorhinal cortexUBERON:000272880.11gold quality
neocortexUBERON:000195079.93gold quality
cerebral cortexUBERON:000095679.30gold quality
orbitofrontal cortexUBERON:000416777.45gold quality
telencephalonUBERON:000189375.90gold quality
brainUBERON:000095575.77gold quality
Ammon’s hornUBERON:000195475.55gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 6.

ExperimentMarker?Max mean expression
E-HCAD-35yes2630.28
E-GEOD-180759yes2354.45
E-HCAD-25yes2234.64
E-GEOD-98556yes279.29
E-MTAB-5061yes10.94
E-ANND-3yes5.67
E-HCAD-30no1343.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

257 targeting STXBP5L, 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-6867-5P100.0082.213464
HSA-MIR-4425100.0067.591049
HSA-MIR-4283100.0066.422097
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3646100.0073.565283
HSA-MIR-450A-1-3P100.0069.331837
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-318599.9968.121959
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-511-3P99.9968.851467
HSA-MIR-548AW99.9972.573559
HSA-MIR-477599.9875.006394
HSA-MIR-548P99.9872.253784
HSA-MIR-4482-3P99.9872.503147
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-60799.9773.625593
HSA-MIR-493-5P99.9672.472382
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-590-3P99.9674.346478
HSA-MIR-302E99.9670.742669
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-551B-5P99.9671.283493
HSA-LET-7C-3P99.9573.422862
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-335-3P99.9373.364958

Literature-anchored findings (GeneRIF, showing 4)

  • In skin aging rs322458, was in linkage disequilibrium (LD) with intronic single nucleotide polymorphisms of the STXBP5L gene, which is expressed in the skin. (PMID:23223146)
  • A homozygous nonsynonymous mutation in STXBP5L (c.3127G>A, p.Val1043Ile [CCDS43137.1]) was implicated in an infantile-onset neurodegenerative disorder manifesting a predominant sensorimotor axonal neuropathy, optic atrophy and cognitive deficit. (PMID:25504045)
  • Homozygous mutation of STXBP5L is associated with autosomal recessive infantile-onset neurodegenerative disorder. (PMID:25504045)
  • Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women. (PMID:37054626)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriostxbp5lENSDARG00000006383
mus_musculusStxbp5lENSMUSG00000022829
rattus_norvegicusStxbp5lENSRNOG00000002496
drosophila_melanogasterTomosynFBGN0030412
caenorhabditis_eleganstom-1WBGENE00006594

Paralogs (3): LLGL2 (ENSG00000073350), LLGL1 (ENSG00000131899), STXBP5 (ENSG00000164506)

Protein

Protein identifiers

Syntaxin-binding protein 5-likeQ9Y2K9 (reviewed: Q9Y2K9)

Alternative names: Lethal(2) giant larvae protein homolog 4, Tomosyn-2

All UniProt accessions (7): C9JCY1, C9JPK3, C9JQS3, C9JUZ7, C9K0E4, E9PFI2, Q9Y2K9

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in vesicle trafficking and exocytosis inhibition. In pancreatic beta-cells, inhibits insulin secretion probably by interacting with and regulating STX1A and STX4, key t-SNARE proteins involved in the fusion of insulin granules to the plasma membrane. Also plays a role in neurotransmitter release by inhibiting basal acetylcholine release from axon terminals and by preventing synaptic fatigue upon repetitive stimulation. Promotes as well axonal outgrowth.

Subunit / interactions. Interacts with STX1A and STX4.

Subcellular location. Cytoplasm. Cell membrane. Membrane.

Tissue specificity. Detected in kidney, hippocampus and lung carcinoma.

Post-translational modifications. Phosphorylated, leading to STXBP5L increased turnover and subsequent de-repression of insulin secretion. Phosphorylated on serine residues in response to glucose or phorbol esters. Ubiquitinated by the E3 ligase SYVN1, leading to STXBP5L proteasomal degradation.

Similarity. Belongs to the WD repeat L(2)GL family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9Y2K9-11yes
Q9Y2K9-22

RefSeq proteins (5): NP_001295259, NP_001335272, NP_001335273, NP_001335274, NP_055795 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000664Lethal2_giantFamily
IPR001680WD40_rptRepeat
IPR013577LLGL2Domain
IPR013905Lgl_C_domDomain
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019775WD40_repeat_CSConserved_site
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR042855V_SNARE_CCDomain

Pfam: PF00400, PF08366, PF08596

UniProt features (46 total): modified residue 20, repeat 14, sequence variant 3, region of interest 2, compositionally biased region 2, splice variant 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y2K9-F177.380.56

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 (20): 1, 568, 574, 589, 593, 596, 599, 709, 763, 765, 766, 771, 772, 793, 800, 812, 820, 822, 823, 1093

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 130 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_EXOCYTOSIS, GOBP_GOLGI_TO_PLASMA_MEMBRANE_TRANSPORT, MORF_IL4, GOBP_SECRETION, GOBP_LOCALIZATION_WITHIN_MEMBRANE, BLALOCK_ALZHEIMERS_DISEASE_DN, GOMF_SYNTAXIN_BINDING, ZHENG_IL22_SIGNALING_UP, GOBP_GOLGI_VESICLE_TRANSPORT, MORF_PAX7, GOMF_ENZYME_ACTIVATOR_ACTIVITY, GOMF_CYTOSKELETAL_PROTEIN_BINDING, GOMF_NUCLEOSIDE_TRIPHOSPHATASE_REGULATOR_ACTIVITY, GOMF_ENZYME_REGULATOR_ACTIVITY

GO Biological Process (7): exocytosis (GO:0006887), Golgi to plasma membrane transport (GO:0006893), protein transport (GO:0015031), regulation of exocytosis (GO:0017157), glucose homeostasis (GO:0042593), negative regulation of insulin secretion (GO:0046676), regulation of synaptic vesicle exocytosis (GO:2000300)

GO Molecular Function (4): GTPase activator activity (GO:0005096), syntaxin binding (GO:0019905), myosin II binding (GO:0045159), protein binding (GO:0005515)

GO Cellular Component (6): cytoplasm (GO:0005737), plasma membrane (GO:0005886), SNARE complex (GO:0031201), membrane (GO:0016020), neuromuscular junction (GO:0031594), neuronal dense core vesicle (GO:0098992)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
vesicle-mediated transport1
secretion by cell1
vesicle fusion to plasma membrane1
post-Golgi vesicle-mediated transport1
vesicle-mediated transport to the plasma membrane1
transport1
intracellular protein localization1
establishment of protein localization1
exocytosis1
regulation of vesicle-mediated transport1
regulation of secretion by cell1
carbohydrate homeostasis1
insulin secretion1
negative regulation of protein secretion1
regulation of insulin secretion1
negative regulation of peptide hormone secretion1
synaptic vesicle exocytosis1
regulation of neurotransmitter secretion1
regulation of regulated secretory pathway1
GTPase activity1
enzyme activator activity1
GTPase regulator activity1
SNARE binding1
myosin binding1
binding1
intracellular anatomical structure1
membrane1
cell periphery1
cytoplasm1
membrane protein complex1
synapse1
dense core granule1

Protein interactions and networks

STRING

1266 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
STXBP5LSNAP23O00161701
STXBP5LSTX4Q12846637
STXBP5LSTX1AQ16623627
STXBP5LSTX11O75558574
STXBP5LSTX19Q8N4C7566
STXBP5LAP3S2P59780474
STXBP5LSCGNO76038455
STXBP5LSNAP25P13795412
STXBP5LSYNPO2Q9UMS6410
STXBP5LSTXBP1P61764407
STXBP5LAZIN1O14977399
STXBP5LSDR39U1Q9NRG7390
STXBP5LNSG2Q9Y328384
STXBP5LC9orf153Q5TBE3369
STXBP5LSTXBP3O00186360

IntAct

12 interactions, top by confidence:

ABTypeScore
STXBP5LGPSM3psi-mi:“MI:0915”(physical association)0.560
STX12STXBP5Lpsi-mi:“MI:0915”(physical association)0.560
STX2STXBP5Lpsi-mi:“MI:0915”(physical association)0.560
SNAP23STXBP5Lpsi-mi:“MI:0915”(physical association)0.370
STX19SULT1A2psi-mi:“MI:0914”(association)0.350
STX19SNAP23psi-mi:“MI:0914”(association)0.350
GPSM3STXBP5Lpsi-mi:“MI:0915”(physical association)0.000
STX12STXBP5Lpsi-mi:“MI:0915”(physical association)0.000
STX2STXBP5Lpsi-mi:“MI:0915”(physical association)0.000

BioGRID (256): STXBP5L (Affinity Capture-MS), STXBP5L (Affinity Capture-MS), STXBP5L (Affinity Capture-RNA), STXBP5L (Synthetic Lethality), STXBP5L (Two-hybrid), STXBP5L (Two-hybrid), GPSM3 (Two-hybrid), STXBP5L (Affinity Capture-MS), STXBP5L (Affinity Capture-MS), ANXA6 (Cross-Linking-MS (XL-MS)), STXBP5L (Affinity Capture-MS), SYVN1 (Affinity Capture-Western), Stxbp5l (Affinity Capture-MS), Dnaja1 (Affinity Capture-MS), Sncb (Affinity Capture-MS)

ESM2 similar proteins: A2AC93, B2RY71, E7F6H7, E9PYY5, E9Q5M6, O14576, O43815, O55106, O88485, O88487, P27766, P36872, P70483, Q0III3, Q13409, Q13610, Q16959, Q16960, Q29RQ3, Q2HJ56, Q32KS2, Q32LP9, Q4QR00, Q4V8G4, Q5DQR4, Q5NVM2, Q5SQE2, Q5VTH9, Q5XIL8, Q5ZLK1, Q62871, Q63100, Q66HC9, Q6GPB9, Q8BPM2, Q8C0M8, Q8C0P5, Q8IVH8, Q8IWG1, Q92828

Diamond homologs: Q2YDL1, Q5DQR4, Q5SQE2, Q5T5C0, Q8K400, Q8NFX7, Q8R3T5, Q9WU70, Q9Y2K9, Q8R3S6, Q9NV70

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance147
Likely benign12
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

5829 predictions. Top by Δscore:

VariantEffectΔscore
3:120909569:A:AGacceptor_gain1.0000
3:120909570:G:GGacceptor_gain1.0000
3:120909570:GT:Gacceptor_gain1.0000
3:120909763:GCAAG:Gdonor_gain1.0000
3:120909765:AAGGT:Adonor_loss1.0000
3:120909766:AGG:Adonor_loss1.0000
3:120909767:GGTA:Gdonor_loss1.0000
3:120909768:G:GAdonor_loss1.0000
3:120954939:GACA:Gacceptor_gain1.0000
3:121045429:TTCTA:Tacceptor_loss1.0000
3:121045430:TCTA:Tacceptor_loss1.0000
3:121045431:CTAG:Cacceptor_loss1.0000
3:121045432:TAG:Tacceptor_loss1.0000
3:121045433:A:AGacceptor_gain1.0000
3:121045433:A:Cacceptor_loss1.0000
3:121045433:AG:Aacceptor_gain1.0000
3:121045434:G:GCacceptor_loss1.0000
3:121045434:G:GGacceptor_gain1.0000
3:121045434:GG:Gacceptor_gain1.0000
3:121045434:GGGT:Gacceptor_gain1.0000
3:121045532:AACGG:Adonor_loss1.0000
3:121045533:ACGG:Adonor_loss1.0000
3:121045535:GGTA:Gdonor_loss1.0000
3:121045536:GTA:Gdonor_loss1.0000
3:121045537:T:Adonor_loss1.0000
3:121114924:GA:Gacceptor_gain1.0000
3:121114924:GAATT:Gacceptor_gain1.0000
3:121115055:GAACT:Gdonor_gain1.0000
3:121115058:CT:Cdonor_gain1.0000
3:121115060:G:GGdonor_gain1.0000

AlphaMissense

7638 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:120955012:G:TG88W1.000
3:121045445:T:AV127D1.000
3:121045447:A:CS128R1.000
3:121045449:T:AS128R1.000
3:121045449:T:GS128R1.000
3:121045469:T:CL135P1.000
3:121045477:T:AW138R1.000
3:121045477:T:CW138R1.000
3:121045517:T:CL151P1.000
3:121114959:T:AW169R1.000
3:121114959:T:CW169R1.000
3:121114963:T:CL170P1.000
3:121114969:T:AV172D1.000
3:121114971:G:AG173R1.000
3:121114971:G:CG173R1.000
3:121114972:G:AG173E1.000
3:121114983:G:AG177R1.000
3:121114983:G:CG177R1.000
3:121114984:G:AG177E1.000
3:121114984:G:TG177V1.000
3:121115040:T:AW196R1.000
3:121115040:T:CW196R1.000
3:121115041:G:CW196S1.000
3:121115042:G:CW196C1.000
3:121115042:G:TW196C1.000
3:121121667:T:AV211D1.000
3:121152478:T:CL224P1.000
3:121152487:G:AG227D1.000
3:121152499:G:TG231V1.000
3:121152513:T:AW236R1.000

dbSNP variants (sampled 300 via entrez): RS1000000198 (3:121311494 G>A,C), RS1000000604 (3:121083246 A>C,G), RS1000003965 (3:121224972 C>T), RS1000007809 (3:121003613 A>G,T), RS1000007839 (3:121112475 T>C), RS1000010975 (3:121155730 A>G,T), RS1000018756 (3:121401763 AGGGATAGCATT>A), RS1000019098 (3:121078645 T>C), RS1000025231 (3:121187170 G>A), RS1000030878 (3:121351473 C>T), RS1000037641 (3:121323016 C>A), RS1000037953 (3:121189653 C>A,T), RS1000038189 (3:121051847 T>A,G), RS1000038478 (3:121018456 G>A,T), RS1000042023 (3:121156080 C>G)

Disease associations

OMIM: gene MIM:609381 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST001767_1Aging (facial)2.000000e-08
GCST001767_2Aging (facial)6.000000e-09
GCST001767_3Aging (facial)4.000000e-09
GCST001767_4Aging (facial)1.000000e-09
GCST002366_11Response to anti-retroviral therapy (ddI/d4T) in HIV-1 infection (Grade 1 peripheral neuropathy)5.000000e-06
GCST006248_4Response to lurasidone in schizophrenia2.000000e-07
GCST006248_5Response to lurasidone in schizophrenia3.000000e-07
GCST009191_11Paracentral lobule volume3.000000e-06
GCST010396_268Gut microbiota (bacterial taxa, hurdle binary method)3.000000e-07

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0022597aging
EFO:0000180HIV-1 infection
EFO:0007874gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, affects cotreatment, increases expression6
Aflatoxin B1decreases methylation, increases methylation2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
testosterone undecanoateaffects cotreatment, increases expression1
sodium arsenitedecreases expression1
coumarindecreases phosphorylation1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment1
quinocetoneincreases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Saffects cotreatment, decreases expression1
Vorinostatincreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Dexamethasoneaffects cotreatment, decreases expression1
Indomethacinaffects cotreatment, decreases expression1
Silicon Dioxidedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
1-Methyl-3-isobutylxanthinedecreases expression, affects cotreatment1
Levonorgestrelaffects cotreatment, increases expression1
Okadaic Aciddecreases expression1
Magnetite Nanoparticlesincreases 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): peripheral neuropathy