BET1L

gene
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Also known as GS15GOLIM3

Summary

BET1L (Bet1 golgi vesicular membrane trafficking protein like, HGNC:19348) is a protein-coding gene on chromosome 11p15.5, encoding BET1-like protein (Q9NYM9). Vesicle SNARE required for targeting and fusion of retrograde transport vesicles with the Golgi complex.

Enables SNAP receptor activity. Involved in regulation of retrograde vesicle-mediated transport, Golgi to ER and retrograde transport, endosome to Golgi. Located in Golgi apparatus and endosome. Implicated in uterine fibroid. Biomarker of endometrial adenocarcinoma.

Source: NCBI Gene 51272 — RefSeq curated summary.

At a glance

  • GWAS associations: 25
  • Clinical variants (ClinVar): 36 total
  • MANE Select transcript: NM_001098787

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19348
Approved symbolBET1L
NameBet1 golgi vesicular membrane trafficking protein like
Location11p15.5
Locus typegene with protein product
StatusApproved
AliasesGS15, GOLIM3
Ensembl geneENSG00000177951
Ensembl biotypeprotein_coding
OMIM615417
Entrez51272

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000325147, ENST00000332865, ENST00000382762, ENST00000410108, ENST00000479463, ENST00000486280, ENST00000529614, ENST00000851020

RefSeq mRNA: 2 — MANE Select: NM_001098787 NM_001098787, NM_016526

CCDS: CCDS41582, CCDS7689

Canonical transcript exons

ENST00000382762 — 4 exons

ExonStartEnd
ENSE00001747069205611205667
ENSE00001784479202924205469
ENSE00003531019205952206043
ENSE00004283420207303207399

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 95.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.3718 / max 150.6083, expressed in 1819 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
11771924.07791817
1177160.4122189
1177150.4005172
1177170.3213139
1177180.160068

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
body of pancreasUBERON:000115095.82gold quality
adenohypophysisUBERON:000219694.97gold quality
pituitary glandUBERON:000000793.90gold quality
left ovaryUBERON:000211993.70gold quality
right coronary arteryUBERON:000162593.60gold quality
descending thoracic aortaUBERON:000234593.56gold quality
body of stomachUBERON:000116193.34gold quality
mucosa of stomachUBERON:000119993.34gold quality
endocervixUBERON:000045893.25gold quality
thoracic aortaUBERON:000151593.20gold quality
ascending aortaUBERON:000149693.15gold quality
stromal cell of endometriumCL:000225593.13gold quality
popliteal arteryUBERON:000225093.13gold quality
tibial arteryUBERON:000761093.12gold quality
aortaUBERON:000094793.08gold quality
right ovaryUBERON:000211892.83gold quality
right lungUBERON:000216792.65gold quality
left uterine tubeUBERON:000130392.63gold quality
left coronary arteryUBERON:000162692.57gold quality
granulocyteCL:000009492.47gold quality
pancreasUBERON:000126492.34gold quality
small intestine Peyer’s patchUBERON:000345492.27gold quality
minor salivary glandUBERON:000183092.25gold quality
body of uterusUBERON:000985392.13gold quality
coronary arteryUBERON:000162192.10gold quality
left lobe of thyroid glandUBERON:000112092.08gold quality
transverse colonUBERON:000115792.01gold quality
right lobe of liverUBERON:000111491.99gold quality
left adrenal gland cortexUBERON:003582591.96gold quality
right lobe of thyroid glandUBERON:000111991.92gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes14.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

96 targeting BET1L, 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-453499.9966.581907
HSA-MIR-318599.9968.121959
HSA-MIR-223-3P99.9970.141140
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-426799.9666.532368
HSA-MIR-808299.9567.271170
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-545-3P99.9570.742783
HSA-MIR-185-3P99.9567.011743
HSA-MIR-452599.9464.38675
HSA-MIR-5010-5P99.9464.11705
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-449399.9066.48977
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-797899.8666.90856
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-808099.8267.521342
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-149-3P99.7268.223963
HSA-MIR-119799.7067.751027
HSA-MIR-518A-5P99.7069.012209

Literature-anchored findings (GeneRIF, showing 9)

  • Data suggest that GS15 exists in a distinct SNARE complex that contains syntaxin5, GS28, and Ykt6, and may be involved in both ER-to-Golgi and intra-Golgi transport. (PMID:12388752)
  • single nucleotide polymorphisms in the BET1L gene is associated with uterine fibroid. (PMID:23604678)
  • Meta-analysis showed a strong association at blocked early in transport 1 homolog (BET1L) rs2280543 for intramural uterine fibroid type in european americans. (PMID:23892540)
  • COG sub-complexes are spatially separated on the Golgi with lobe A preferential localization on Golgi stacks and the presence of lobe B on vesicle-like structures, where it physically interacts with v-SNARE GS15. (PMID:27385402)
  • both BET1L and TNRC6B contributed to the risk of UL in Chinese women (PMID:29743541)
  • BET1L rs2280543 polymorphisms are associated with an increased risk of intracranial aneurysm. (PMID:31275455)
  • Transcriptome analysis using patient iPSC-derived skeletal myocytes: Bet1L as a new molecule possibly linked to neuromuscular junction degeneration in ALS. (PMID:34310943)
  • Risk of uterine leiomyoma based on BET1L rs2280543 single nucleotide polymorphism and vegetarian diet. (PMID:35477381)
  • Genetic Modulation of BET1L Confers Colorectal Cancer Susceptibility by Reducing miRNA Binding and m6A Modification. (PMID:37115853)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusBet1lENSMUSG00000025484
rattus_norvegicusBet1lENSRNOG00000013165

Protein

Protein identifiers

BET1-like proteinQ9NYM9 (reviewed: Q9NYM9)

Alternative names: Golgi SNARE with a size of 15 kDa, Vesicle transport protein GOS15

All UniProt accessions (6): A0A0C4DH16, B8ZZS0, E9PHY4, E9PQJ6, Q9NYM9, H7BXT7

UniProt curated annotations — full annotation on UniProt →

Function. Vesicle SNARE required for targeting and fusion of retrograde transport vesicles with the Golgi complex. Required for the integrity of the Golgi complex.

Subunit / interactions. Component of a SNARE complex consisting of STX5, YKT6, GOSR1 and BET1L. Interacts with STX5.

Subcellular location. Golgi apparatus membrane. Golgi apparatus. trans-Golgi network membrane.

RefSeq proteins (2): NP_001092257, NP_057610 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000727T_SNARE_domDomain
IPR039899BET1_SNAREDomain

UniProt features (7 total): topological domain 2, modified residue 2, chain 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NYM9-F189.020.72

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 (2): 9, 37

Function

Pathways and Gene Ontology

Reactome pathways

10 pathways

IDPathway
R-HSA-6807878COPI-mediated anterograde transport
R-HSA-6811438Intra-Golgi traffic
R-HSA-199977ER to Golgi Anterograde Transport
R-HSA-199991Membrane Trafficking
R-HSA-392499Metabolism of proteins
R-HSA-446203Asparagine N-linked glycosylation
R-HSA-5653656Vesicle-mediated transport
R-HSA-597592Post-translational protein modification
R-HSA-6811442Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-948021Transport to the Golgi and subsequent modification

MSigDB gene sets: 142 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, MODULE_97, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_MEMBRANE_FUSION, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, LANG_MYB_FAMILY_TARGETS, MODULE_182, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, AGCGCTT_MIR518F_MIR518E_MIR518A, MODULE_480, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, GOBP_MEMBRANE_ORGANIZATION

GO Biological Process (4): protein transport (GO:0015031), retrograde transport, endosome to Golgi (GO:0042147), regulation of retrograde vesicle-mediated transport, Golgi to ER (GO:2000156), membrane fusion (GO:0061025)

GO Molecular Function (2): SNAP receptor activity (GO:0005484), protein binding (GO:0005515)

GO Cellular Component (8): Golgi membrane (GO:0000139), endosome (GO:0005768), Golgi apparatus (GO:0005794), Golgi stack (GO:0005795), cytosol (GO:0005829), membrane (GO:0016020), SNARE complex (GO:0031201), endomembrane system (GO:0012505)

Reactome top-level categories

Rollup of top-8 pathways:

CategoryPathways
Membrane Trafficking2
ER to Golgi Anterograde Transport1
Intra-Golgi and retrograde Golgi-to-ER traffic1
Transport to the Golgi and subsequent modification1
Vesicle-mediated transport1
Post-translational protein modification1
Metabolism of proteins1
Asparagine N-linked glycosylation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm3
cellular anatomical structure3
endomembrane system2
transport1
intracellular protein localization1
establishment of protein localization1
intercellular transport1
endosomal transport1
cytosolic transport1
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum1
regulation of vesicle-mediated transport1
membrane organization1
protein-macromolecule adaptor activity1
membrane fusion1
fusogenic activity1
binding1
Golgi apparatus1
bounding membrane of organelle1
cytoplasmic vesicle1
intracellular membrane-bounded organelle1
Golgi apparatus subcompartment1
membrane protein complex1
vacuole1
plasma membrane1

Protein interactions and networks

STRING

1102 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BET1LVCPIP1Q96JH7769
BET1LGOSR1O95249755
BET1LGOSR2O14653747
BET1LSTX5Q13190739
BET1LGOLGA2Q08379701
BET1LYKT6O15498695
BET1LSEC22AQ96IW7691
BET1LTNRC6BQ9UPQ9663
BET1LVCPP55072605
BET1LFAM228BP0C875591
BET1LNPLOC4Q8TAT6589
BET1LPTPN3P26045545
BET1LSTX16O14662508
BET1LRIC8AQ9NPQ8506
BET1LUFD1Q92890497

IntAct

28 interactions, top by confidence:

ABTypeScore
GOSR2BET1psi-mi:“MI:0914”(association)0.810
STX18NBASpsi-mi:“MI:0914”(association)0.810
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
STX5GOSR2psi-mi:“MI:0914”(association)0.670
NAPANBASpsi-mi:“MI:0914”(association)0.530
VAMP5NBASpsi-mi:“MI:0914”(association)0.530
BET1LTRAPPC12psi-mi:“MI:0915”(physical association)0.400
GORABBET1Lpsi-mi:“MI:0915”(physical association)0.370
VAMP5ESYT2psi-mi:“MI:0914”(association)0.350
STX18NBASpsi-mi:“MI:0914”(association)0.350
BET1LGOSR1psi-mi:“MI:0914”(association)0.350
RAB18GDI2psi-mi:“MI:0914”(association)0.350
SCFD1NBASpsi-mi:“MI:0914”(association)0.350
NRSN1FAM171A2psi-mi:“MI:0914”(association)0.350
SEC22BNBASpsi-mi:“MI:0914”(association)0.350
SLC35F3TMEM223psi-mi:“MI:0914”(association)0.350
TMEM17ESYT2psi-mi:“MI:2364”(proximity)0.270
TMEM216GPR89Apsi-mi:“MI:2364”(proximity)0.270
TMEM216SNAP23psi-mi:“MI:2364”(proximity)0.270
BET1ESYT2psi-mi:“MI:2364”(proximity)0.270
TGOLN2BLTP3Bpsi-mi:“MI:2364”(proximity)0.270
FHIP2AMED19psi-mi:“MI:2364”(proximity)0.270

BioGRID (71): BET1L (Proximity Label-MS), BET1L (Proximity Label-MS), BET1L (Affinity Capture-MS), BET1L (Proximity Label-MS), BET1L (Proximity Label-MS), BET1L (Affinity Capture-MS), BET1L (Affinity Capture-MS), BET1L (Proximity Label-MS), BET1L (Proximity Label-MS), BET1L (Affinity Capture-Western), GOSR1 (Affinity Capture-Western), STX5 (Affinity Capture-Western), YKT6 (Affinity Capture-Western), BET1L (Affinity Capture-Western), BET1L (Proximity Label-MS)

ESM2 similar proteins: A8XLW0, A8XP14, O13644, O14653, O35152, O35165, O35166, O65359, O89116, O94531, O94651, P25385, P32854, P38736, P41941, P59277, P78768, P93654, Q03322, Q04338, Q09835, Q12981, Q39233, Q54CK6, Q54IX6, Q6BVM4, Q6BZQ6, Q6CRX0, Q6FKA1, Q6QD59, Q75CY3, Q8L9S0, Q8VHI8, Q95ZW1, Q96AJ9, Q9FFK1, Q9FK28, Q9HGN3, Q9JI51, Q9LMP7

Diamond homologs: O13932, O15155, O35152, O35153, O35623, Q3MHP8, Q5RBX2, Q62896, Q68EL3, Q9M2J9, Q9NYM9, Q553P5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 28 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
COPII-mediated vesicle transport648.9×4e-08
ER to Golgi Anterograde Transport533.2×5e-06
Intra-Golgi and retrograde Golgi-to-ER traffic631.4×4e-07
COPI-mediated anterograde transport527.4×9e-06
Transport to the Golgi and subsequent modification525.7×1e-05
Membrane Trafficking916.7×4e-08
Vesicle-mediated transport915.7×4e-08
Asparagine N-linked glycosylation515.0×1e-04

GO biological processes:

GO termPartnersFoldFDR
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum570.2×7e-07
endoplasmic reticulum to Golgi vesicle-mediated transport634.0×8e-07
intracellular protein transport513.5×4e-04
protein transport712.8×2e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance25
Likely benign1
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

2258 predictions. Top by Δscore:

VariantEffectΔscore
11:193152:GCC:Gdonor_gain1.0000
11:193155:G:GGdonor_gain1.0000
11:197412:AGGT:Adonor_loss1.0000
11:197413:GGTA:Gdonor_loss1.0000
11:197414:G:GAdonor_loss1.0000
11:197414:G:GGdonor_gain1.0000
11:199516:G:GTdonor_gain1.0000
11:199517:A:Tdonor_gain1.0000
11:199527:C:Gdonor_gain1.0000
11:199531:GAGGG:Gdonor_gain1.0000
11:199533:GGG:Gdonor_gain1.0000
11:199534:GGG:Gdonor_gain1.0000
11:205664:CGAG:Cacceptor_gain1.0000
11:205668:C:CCacceptor_gain1.0000
11:205674:A:Tacceptor_gain1.0000
11:205948:TGACC:Tdonor_loss1.0000
11:205949:GAC:Gdonor_loss1.0000
11:205950:A:ACdonor_gain1.0000
11:205950:A:AGdonor_loss1.0000
11:205951:C:CAdonor_loss1.0000
11:205951:C:CCdonor_gain1.0000
11:206044:C:CCacceptor_gain1.0000
11:197410:ACAG:Adonor_gain0.9900
11:197555:CCACA:Cacceptor_loss0.9900
11:197556:CACA:Cacceptor_loss0.9900
11:197559:A:AGacceptor_gain0.9900
11:197559:AG:Aacceptor_gain0.9900
11:197559:AGG:Aacceptor_loss0.9900
11:197560:G:GGacceptor_gain0.9900
11:197560:G:GTacceptor_loss0.9900

AlphaMissense

730 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:205956:T:AK36I0.912
11:205428:G:CS70R0.909
11:205428:G:TS70R0.909
11:205430:T:GS70R0.909
11:205971:T:AK31I0.895
11:205955:T:AK36N0.881
11:205955:T:GK36N0.881
11:205959:A:GL35P0.880
11:205959:A:TL35H0.878
11:206000:G:CN21K0.878
11:206000:G:TN21K0.878
11:206001:T:AN21I0.871
11:205663:G:TA39D0.867
11:205664:C:GA39P0.867
11:205358:C:GG94R0.841
11:205416:A:CF74L0.841
11:205416:A:TF74L0.841
11:205418:A:GF74L0.841
11:206002:T:CN21D0.819
11:206001:T:GN21T0.817
11:205666:A:GL38P0.816
11:205990:C:GA25P0.808
11:205357:C:TG94D0.803
11:206002:T:AN21Y0.798
11:205968:A:TV32D0.797
11:206002:T:GN21H0.793
11:205643:C:GA46P0.782
11:205954:A:GS37P0.781
11:205980:A:GL28P0.770
11:205654:A:TI42N0.768

dbSNP variants (sampled 300 via entrez): RS1000026443 (11:209151 G>A), RS1000211245 (11:203704 G>C,T), RS1000463030 (11:208998 G>A,C,T), RS1000464743 (11:205470 C>G,T), RS1000586469 (11:206898 A>G), RS1000587197 (11:203921 T>C), RS1000980696 (11:207795 A>C), RS1001013272 (11:206637 T>G), RS1001192096 (11:202725 G>T), RS1001870999 (11:205754 AACAACTCTGCCAG>A), RS1002019134 (11:206392 G>A,T), RS1002359501 (11:206045 T>C,G), RS1002553365 (11:203933 G>C), RS1003025084 (11:205144 C>T), RS1003224912 (11:204087 G>A,T)

Disease associations

OMIM: gene MIM:615417 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

25 associations (top):

StudyTraitp-value
GCST000497_6Mean platelet volume1.000000e-14
GCST001027_3Uterine fibroids4.000000e-12
GCST001388_3Intracranial aneurysm3.000000e-06
GCST001482_25Lumbar spine bone mineral density2.000000e-06
GCST002186_8Platelet count5.000000e-12
GCST004607_122Plateletcrit3.000000e-24
GCST004621_19Red cell distribution width4.000000e-24
GCST005992_32Mean corpuscular hemoglobin concentration3.000000e-12
GCST005996_50Red blood cell count4.000000e-14
GCST006011_28Mean corpuscular volume3.000000e-13
GCST006462_50Uterine fibroids5.000000e-12
GCST007954_6Glycated hemoglobin levels2.000000e-10
GCST008423_8Uterine fibroids1.000000e-20
GCST009158_1Uterine fibroids2.000000e-14
GCST009822_3Gynecologic disease4.000000e-17
GCST009823_2Gynecologic disease (multivariate analysis)8.000000e-16
GCST009824_5Gynecologic disease3.000000e-16
GCST009833_2Uterine fibroids (MTAG)4.000000e-17
GCST009834_36Uterine fibroids1.000000e-21
GCST010867_73Coronary artery disease2.000000e-10
GCST90002395_43Mean platelet volume1.000000e-17
GCST90002400_625Plateletcrit9.000000e-52
GCST90002401_174Platelet distribution width1.000000e-37
GCST90002404_501Red cell distribution width1.000000e-21
GCST90014268_24Cataracts4.000000e-11

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0004309platelet count
EFO:0007985platelet crit
EFO:0009188Red cell distribution width
EFO:0004528mean corpuscular hemoglobin concentration
EFO:0004305erythrocyte count
EFO:0004541HbA1c measurement
EFO:0007984platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Tobacco Smoke Pollutionincreases expression2
Valproic Acidaffects expression, increases methylation2
Cyclosporinedecreases methylation, increases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359increases phosphorylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
sodium arseniteincreases expression1
butyraldehydeincreases expression1
coumarinincreases phosphorylation1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
Air Pollutantsincreases abundance, affects expression1
Caffeinedecreases phosphorylation1
Diazinonincreases methylation1
Bucladesineaffects cotreatment, increases expression1
Estradiolaffects cotreatment, increases expression1
Ivermectinincreases expression1
Niclosamideincreases expression1
Ozoneaffects expression, increases abundance1
Smokedecreases expression1
Tunicamycinincreases expression1
Medroxyprogesterone Acetateaffects cotreatment, increases expression1
Thapsigarginincreases expression1
Palmitic Aciddecreases phosphorylation1
Copper Sulfatedecreases expression1
Acrylamidedecreases expression1
Vitamin K 3affects expression1

Clinical trials (associated diseases)

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