GBF1

gene
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Also known as KIAA0248ARF1GEF

Summary

GBF1 (golgi brefeldin A resistant guanine nucleotide exchange factor 1, HGNC:4181) is a protein-coding gene on chromosome 10q24.32, encoding Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 (Q92538). Guanine-nucleotide exchange factor (GEF) for members of the Arf family of small GTPases involved in trafficking in the early secretory pathway; its GEF activity initiates the coating of nascent vesicles via the localized generation of activated ARFs through replacement of GDP wi…. It is a common-essential gene (DepMap: required in 98.4% of cancer cell lines).

This gene encodes a member of the Sec7 domain family. The encoded protein is a guanine nucleotide exchange factor that regulates the recruitment of proteins to membranes by mediating GDP to GTP exchange. The encoded protein is localized to the Golgi apparatus and plays a role in vesicular trafficking by activating ADP ribosylation factor 1. The encoded protein has also been identified as an important host factor for viral replication. Multiple transcript variants have been observed for this gene.

Source: NCBI Gene 8729 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Charcot-Marie-Tooth Disease, axonal, type 2GG (Strong, GenCC) — +1 more curated relationship
  • GWAS associations: 18
  • Clinical variants (ClinVar): 409 total — 2 pathogenic, 4 likely-pathogenic
  • Phenotypes (HPO): 23
  • Cancer dependency (DepMap): dependent in 98.4% of screened cell lines (common-essential)
  • MANE Select transcript: NM_001377137

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4181
Approved symbolGBF1
Namegolgi brefeldin A resistant guanine nucleotide exchange factor 1
Location10q24.32
Locus typegene with protein product
StatusApproved
AliasesKIAA0248, ARF1GEF
Ensembl geneENSG00000107862
Ensembl biotypeprotein_coding
OMIM603698
Entrez8729

Gene structure

Transcript identifiers

Ensembl transcripts: 126 — 48 protein_coding, 48 nonsense_mediated_decay, 18 protein_coding_CDS_not_defined, 12 retained_intron

ENST00000369983, ENST00000476019, ENST00000673650, ENST00000674034, ENST00000676474, ENST00000676482, ENST00000676513, ENST00000676558, ENST00000676560, ENST00000676561, ENST00000676606, ENST00000676673, ENST00000676682, ENST00000676735, ENST00000676802, ENST00000676807, ENST00000676854, ENST00000676861, ENST00000676877, ENST00000676900, ENST00000676927, ENST00000676934, ENST00000676939, ENST00000676985, ENST00000676993, ENST00000677017, ENST00000677098, ENST00000677100, ENST00000677235, ENST00000677240, ENST00000677247, ENST00000677269, ENST00000677431, ENST00000677439, ENST00000677461, ENST00000677487, ENST00000677491, ENST00000677504, ENST00000677506, ENST00000677522, ENST00000677607, ENST00000677618, ENST00000677627, ENST00000677629, ENST00000677642, ENST00000677655, ENST00000677662, ENST00000677683, ENST00000677719, ENST00000677776, ENST00000677797, ENST00000677811, ENST00000677838, ENST00000677842, ENST00000677852, ENST00000677871, ENST00000677917, ENST00000677947, ENST00000677956, ENST00000677975, ENST00000678007, ENST00000678014, ENST00000678036, ENST00000678126, ENST00000678127, ENST00000678157, ENST00000678215, ENST00000678222, ENST00000678268, ENST00000678292, ENST00000678293, ENST00000678319, ENST00000678344, ENST00000678351, ENST00000678401, ENST00000678417, ENST00000678426, ENST00000678453, ENST00000678476, ENST00000678486, ENST00000678504, ENST00000678514, ENST00000678527, ENST00000678530, ENST00000678558, ENST00000678571, ENST00000678575, ENST00000678585, ENST00000678604, ENST00000678665, ENST00000678666, ENST00000678722, ENST00000678742, ENST00000678767, ENST00000678806, ENST00000678826, ENST00000678840, ENST00000678923, ENST00000678924, ENST00000678941, ENST00000679003, ENST00000679013, ENST00000679040, ENST00000679080, ENST00000679084, ENST00000679087, ENST00000679093, ENST00000679139, ENST00000679155, ENST00000679186, ENST00000679203, ENST00000679238, ENST00000679253, ENST00000679280, ENST00000679288, ENST00000679298, ENST00000679305, ENST00000679317, ENST00000871604, ENST00000871605, ENST00000871606, ENST00000871607, ENST00000871608, ENST00000916344, ENST00000916345, ENST00000965494

RefSeq mRNA: 20 — MANE Select: NM_001377137 NM_001199378, NM_001199379, NM_001377137, NM_001377138, NM_001377139, NM_001377140, NM_001377141, NM_001391922, NM_001391923, NM_001391924, NM_001391925, NM_001391926, NM_001391927, NM_001391928, NM_001391929, NM_001391930, NM_001391931, NM_001411003, NM_001411027, NM_004193

CCDS: CCDS7533, CCDS91328, CCDS91329, CCDS91330, CCDS91331, CCDS91332, CCDS91333, CCDS91334, CCDS91335, CCDS91336

Canonical transcript exons

ENST00000369983 — 40 exons

ExonStartEnd
ENSE00000722583102344051102344182
ENSE00000722587102351843102351951
ENSE00000722599102358039102358186
ENSE00000722602102358506102358729
ENSE00000722612102360184102360395
ENSE00000722616102361022102361120
ENSE00000722619102361718102361912
ENSE00000722622102362475102362664
ENSE00000722626102363256102363396
ENSE00000722630102363710102363798
ENSE00000722634102365397102365599
ENSE00000722639102366383102366506
ENSE00000722644102367085102367210
ENSE00000722647102367478102367560
ENSE00000722651102368218102368454
ENSE00000722653102368739102368832
ENSE00000722654102369211102369387
ENSE00000722655102369711102369775
ENSE00000722657102369861102369984
ENSE00000722658102370174102370245
ENSE00000722659102370384102370478
ENSE00000722660102370707102370860
ENSE00000722662102375359102375584
ENSE00000722663102376272102376432
ENSE00000722665102376560102376800
ENSE00000722669102376935102377140
ENSE00000722673102379284102379434
ENSE00000722677102379521102379651
ENSE00000722682102379853102379954
ENSE00000722687102380249102380362
ENSE00000722690102380506102380686
ENSE00000722693102381127102381255
ENSE00000811504102351256102351374
ENSE00001026428102352458102352518
ENSE00001100976102260050102260116
ENSE00001136564102353600102353654
ENSE00001451422102258929102259034
ENSE00001451424102245532102245781
ENSE00003904487102359267102359435
ENSE00003936997102382056102382896

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 98.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 58.8629 / max 438.0609, expressed in 1823 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
10669458.65821823
1066950.204764

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
colonic epitheliumUBERON:000039798.95gold quality
ventricular zoneUBERON:000305398.17gold quality
adenohypophysisUBERON:000219698.04gold quality
sural nerveUBERON:001548897.76gold quality
stromal cell of endometriumCL:000225597.54gold quality
right lobe of thyroid glandUBERON:000111997.24gold quality
ganglionic eminenceUBERON:000402397.24gold quality
apex of heartUBERON:000209897.17gold quality
cortical plateUBERON:000534397.07gold quality
mucosa of transverse colonUBERON:000499196.91gold quality
right hemisphere of cerebellumUBERON:001489096.80gold quality
left lobe of thyroid glandUBERON:000112096.69gold quality
hindlimb stylopod muscleUBERON:000425296.64gold quality
pituitary glandUBERON:000000796.52gold quality
cerebellar hemisphereUBERON:000224596.42gold quality
adrenal tissueUBERON:001830396.35gold quality
cerebellar cortexUBERON:000212996.34gold quality
small intestine Peyer’s patchUBERON:000345496.24gold quality
metanephros cortexUBERON:001053396.14gold quality
right uterine tubeUBERON:000130296.07gold quality
right frontal lobeUBERON:000281096.07gold quality
transverse colonUBERON:000115796.02gold quality
granulocyteCL:000009496.01gold quality
muscle layer of sigmoid colonUBERON:003580595.83gold quality
right lobe of liverUBERON:000111495.80gold quality
left testisUBERON:000453395.77gold quality
minor salivary glandUBERON:000183095.75gold quality
lower esophagus mucosaUBERON:003583495.72gold quality
skin of legUBERON:000151195.71gold quality
skin of abdomenUBERON:000141695.70gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-GEOD-76312yes105.67
E-ANND-3yes9.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

49 targeting GBF1, 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-4795-3P100.0074.624024
HSA-MIR-4481100.0066.421669
HSA-MIR-1213699.9872.815713
HSA-MIR-7152-3P99.9767.47849
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-526B-3P99.8874.062587
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-519D-3P99.8873.972607
HSA-MIR-93-5P99.8873.982606
HSA-MIR-3617-5P99.7569.411968
HSA-MIR-64199.7569.351975
HSA-MIR-1212999.7267.451311
HSA-MIR-472999.6972.184233
HSA-MIR-64699.6867.841645
HSA-MIR-519A-3P99.6771.671868
HSA-MIR-519B-3P99.6771.671868
HSA-MIR-519C-3P99.6771.671870
HSA-MIR-58799.6470.862611
HSA-MIR-6751-5P99.5664.991145
HSA-MIR-608399.4768.732393
HSA-MIR-766-5P99.4767.912225
HSA-MIR-361299.4566.021333
HSA-MIR-65099.4565.771309
HSA-MIR-6507-3P99.3567.321059
HSA-MIR-130A-5P99.3370.262623

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.4% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 40)

  • detailed subcellular localization to the cis-Golgi (PMID:12047556)
  • novel interaction between p115 and Golgi-specific brefeldin-A-resistant factor 1 (GBF1) (PMID:12634853)
  • characterization of alternatively spliced and truncated forms of GBF1 defines regions important for activity (PMID:12646181)
  • an Arf1-GBF1-Brefeldin A complex is formed and has a longer residence time on Golgi membranes than GBF1 or Arf1 alone (PMID:15616190)
  • A continuous cycle of recruitment and dissociation of GBF1 to membranes is required for sustained ARF activation and COP I recruitment that underlies ER-Golgi traffic. (PMID:15813748)
  • GBF1 is recruited to the endogenous IRF-9 promoter, and interacts with C/EBP-beta, IL-1, and IL-6 (PMID:16318580)
  • These observations strongly suggest that GBF1 regulates COPI membrane recruitment in the early secretory pathway. (PMID:16926190)
  • Two different poliovirus proteins independently recruit different Arf GEFs (GBF1 and BIG1/2) to membranes as part of cellular pathways utilized by the virus to form its membranous replication complex. (PMID:17079330)
  • analysis of the binding domain in GBF1 showed that the extreme N terminus, the dimerization/cyclophilin binding domain, and the homology upstream of Sec7 domain are required for the interaction with coxsackievirus protein 3A (PMID:17329336)
  • These data support a model where Rab1b-GTP induces GBF1 recruitment at the ERES interface and at the Golgi complex where it is required for COPII/COPI exchange or COPI vesicle formation, respectively. (PMID:17429068)
  • Required for GGA adaptor protein recruitment to Golgi membranes; plays a role in the proper processing and sorting of lysosomal cargo. (PMID:17666033)
  • These findings suggest that a secretory pathway capable of trafficking soluble proteins can be maintained in cells in which COPI recruitment is compromised by GBF1 depletion. (PMID:17956946)
  • COPII is the only coat required for sorting and export from the endoplasmic reticulum exit sites, whereas GBF1, but not BIGs, is required for COPI recruitment, Golgi subcompartmentalization, and cargo progression to the cell surface. (PMID:18003980)
  • GBF1 is a AMPK substrate and AMPK-mediated phosphorylation of GBF1 at Thr(1337) has a critical role, presumably by attenuating function of GBF1, in disassembly of the Golgi apparatus induced under stress conditions that lower the intracellular ATP (PMID:18063581)
  • Unfolded protein response and cell death after depletion of brefeldin A-inhibited guanine nucleotide-exchange protein GBF1. (PMID:18287014)
  • GDP-bound class II Arfs associate with the ER-Golgi intermediate compartment independently of GBF1 (PMID:18524849)
  • siRNAs demonstrate that GBF1-mediated ARF1 activation is required for efficient MHV RNA replication (PMID:18551169)
  • AG1478 inhibits GBF1, a large nucleotide exchange factor for the ADP-ribosylation factor, in a Sec7 domain-dependent manner and mimics the phenotype of a GBF1 mutant that has an inactive mutation (PMID:18799457)
  • GBF1 is responsible for the sensitivity of poliovirus infection to BFA, and is required for virus replication (PMID:19023417)
  • crucial for coxsackievirus B3 RNA replication (PMID:19740986)
  • GBF1 is a cellular factor required for HCV infection. (PMID:19906930)
  • The authors demonstrate that Rab1b-activated GBF1 and ARF1 are involved in Ebolavirus virion formation, suggesting that both the COPII and COPI transport systems play a role in Ebolavirus VP40-mediated particle formation. (PMID:20164217)
  • Data propose that the phosphorylation and membrane dissociation of GBF1 and the consequent reduction in ARF-GTP levels in mitosis are important for changes in Golgi dynamics (PMID:20175751)
  • The brefeldin A block of poliovirus replication is rescued by expression of only the N-terminal region of GBF1 lacking the Sec7 domain. (PMID:20497182)
  • Data suggest that Rab1 contributes to the specificity and timing of GBF1 recruitment by activating PI4KIIIalpha, and that the PtdIns(4)P produced then allows GBF1 to bind to Golgi membranes and activate Arf1. (PMID:20530568)
  • Both human and canine GBF1 can be inhibited by compound LG186, a small molecule derived from Exo2, a small molecule inhibitor of secretion and Shiga toxin cytotoxicity. (PMID:20854417)
  • The COG (conserved oligomeric Golgi) complex plays a role in the localization, but not membrane association of GBF1. (PMID:21722633)
  • GBF1 and ATGL interact directly and in cells, through multiple contact sites on each protein. (PMID:21789191)
  • We hypothesize that sphingomyelin acquired by CERT-dependent transport of ceramide and subsequent conversion to SM is necessary for C. trachomatis replication whereas SM acquired by GBF1-dependent pathway is essential for inclusion growth and stability. (PMID:21909260)
  • The GBF1 participated in delivery of adipose triglyceride lipase (ATGL) onto the lipid droplets(LD) surface (PMID:22185782)
  • the vesicular transport proteins ARF1 and GBF1 colocalized with PI4KIIIbeta and were both required for HCV replication (PMID:22359663)
  • A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration. (PMID:22360420)
  • GBF1-mediated Arf1 activation is necessary to unify cell polarity during chemotaxis (PMID:22573891)
  • an early acting GEF (GBF1) activates ARFs that mediate recruitment of late acting GEFs (BIG1/2) to coordinate coating events within the pre-Golgi/Golgi/TGN continuum. (PMID:23386609)
  • These data suggest that AMPK-GBF1-Arf1 signaling is involved in the regulation of Golgi fragmentation during mitosis. (PMID:23418352)
  • Study provides evidence that GBF-1 is required in endoplasmic reticulum structure and endosomal traffic. (PMID:23840591)
  • GBF1 causes increased Arf-GTP production at the Golgi, consistent with a feed-forward self-limiting mechanism of Arf activation. (PMID:24213530)
  • GBF1 plays a critical role early in dengue infection that is independent of its role in the maintenance of Golgi structure. (PMID:24855065)
  • Although human rhinovirus 3A protein was previously shown to interact with ACBD3, these data suggest that PI4KIIIbeta recruitment occurred independently of both GBF1 and ACBD3. (PMID:25410869)
  • The role of GBF1 in poliovirus replication is independent of its Arf activating function. (PMID:25653442)

Cross-species orthologs

9 orthologs

OrganismSymbolGene ID
danio_reriogbf1ENSDARG00000027016
mus_musculusGbf1ENSMUSG00000025224
rattus_norvegicusGbf1ENSRNOG00000026048
drosophila_melanogastersizFBGN0026179
drosophila_melanogasterSec71FBGN0028538
drosophila_melanogastergarzFBGN0264560
caenorhabditis_elegansWBGENE00007703
caenorhabditis_elegansWBGENE00008685
caenorhabditis_elegansagef-1WBGENE00012386

Paralogs (15): CYTH3 (ENSG00000008256), PSD (ENSG00000059915), MON2 (ENSG00000061987), ARFGEF1 (ENSG00000066777), CYTH4 (ENSG00000100055), CYTH2 (ENSG00000105443), CYTH1 (ENSG00000108669), IQSEC3 (ENSG00000120645), ARFGEF2 (ENSG00000124198), IQSEC2 (ENSG00000124313), PSD4 (ENSG00000125637), IQSEC1 (ENSG00000144711), PSD2 (ENSG00000146005), PSD3 (ENSG00000156011), FBXO8 (ENSG00000164117)

Protein

Protein identifiers

Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1Q92538 (reviewed: Q92538)

All UniProt accessions (84): Q92538, A0A669KB10, A0A669KBG8, A0A7I2V2F8, A0A7I2V2G6, A0A7I2V2I0, A0A7I2V2L1, A0A7I2V2L4, A0A7I2V2L5, A0A7I2V2Q1, A0A7I2V2Q5, A0A7I2V2Q6, A0A7I2V2U1, A0A7I2V2Y7, A0A7I2V2Z8, A0A7I2V300, A0A7I2V305, A0A7I2V306, A0A7I2V329, A0A7I2V336, A0A7I2V338, A0A7I2V342, A0A7I2V350, A0A7I2V3A8, A0A7I2V3B1, A0A7I2V3E5, A0A7I2V3H2, A0A7I2V3J0, A0A7I2V3Q4, A0A7I2V3R2, A0A7I2V3S0, A0A7I2V3Y5, A0A7I2V3Y7, A0A7I2V452, A0A7I2V470, A0A7I2V489, A0A7I2V4E0, A0A7I2V4F1, A0A7I2V4F9, A0A7I2V4H1, A0A7I2V4K2, A0A7I2V4L8, A0A7I2V4M3, A0A7I2V4M6, A0A7I2V4N5, A0A7I2V4N7, A0A7I2V4Q7, A0A7I2V4V3, A0A7I2V4V8, A0A7I2V4W6, A0A7I2V4X4, A0A7I2V4Z4, A0A7I2V514, A0A7I2V528, A0A7I2V529, A0A7I2V541, A0A7I2V578, A0A7I2V5C9, A0A7I2V5I9, A0A7I2V5S3, A0A7I2V5T8, A0A7I2V5V9, A0A7I2V5W2, A0A7I2V5Z1, A0A7I2V5Z2, A0A7I2V622, A0A7I2V662, A0A7I2V6D0, A0A7I2V6G3, A0A7I2YQ62, A0A7I2YQ65, A0A7I2YQ79, A0A7I2YQA6, A0A7I2YQB8, A0A7I2YQC3, A0A7I2YQC6, A0A7I2YQD3, A0A7I2YQE0, A0A7I2YQJ5, A0A7I2YQM0, A0A7I2YQM2, A0A7I2YQN3, A0A7I2YQN6, A0A7I2YQP6

UniProt curated annotations — full annotation on UniProt →

Function. Guanine-nucleotide exchange factor (GEF) for members of the Arf family of small GTPases involved in trafficking in the early secretory pathway; its GEF activity initiates the coating of nascent vesicles via the localized generation of activated ARFs through replacement of GDP with GTP. Recruitment to cis-Golgi membranes requires membrane association of Arf-GDP and can be regulated by ARF1, ARF3, ARF4 and ARF5. Involved in the recruitment of the COPI coat complex to the endoplasmic reticulum exit sites (ERES), and the endoplasmic reticulum-Golgi intermediate (ERGIC) and cis-Golgi compartments which implicates ARF1 activation. Involved in COPI vesicle-dependent retrograde transport from the ERGIC and cis-Golgi compartments to the endoplasmic reticulum (ER). Involved in the trans-Golgi network recruitment of GGA1, GGA2, GGA3, BIG1, BIG2, and the AP-1 adaptor protein complex related to chlathrin-dependent transport; the function requires its GEF activity (probably at least in part on ARF4 and ARF5). Has GEF activity towards ARF1. Has in vitro GEF activity towards ARF5. Involved in the processing of PSAP. Required for the assembly of the Golgi apparatus. The AMPK-phosphorylated form is involved in Golgi disassembly during mitotis and under stress conditions. May be involved in the COPI vesicle-dependent recruitment of PNPLA2 to lipid droplets; however, this function is under debate. In neutrophils, involved in G protein-coupled receptor (GPCR)-mediated chemotaxis und superoxide production. Proposed to be recruited by phosphatidylinositol-phosphates generated upon GPCR stimulation to the leading edge where it recruits and activates ARF1, and is involved in recruitment of GIT2 and the NADPH oxidase complex. Plays a role in maintaining mitochondrial morphology.

Subunit / interactions. Can form homodimers and probably homotetramers. Interacts with COPG1; the interaction is independent of ARF1 activation. Interacts with ARF1, ARF3, ARF4 and ARF5. Interacts with RAB1B (GTP-bound form); required for GBF1 membrane association. Interacts with GGA1, GGA2 and GGA3. Interacts with USO1. Interacts (via SEC7 domain) with PNPLA2 (via C-terminus); the interaction is direct. Interacts with ARMH3. (Microbial infection) Interacts with poliovirus protein 3A.

Subcellular location. Golgi apparatus. cis-Golgi network. Endoplasmic reticulum-Golgi intermediate compartment. trans-Golgi network. Cytoplasm. Lipid droplet. Membrane.

Tissue specificity. Ubiquitous.

Post-translational modifications. AMPK-mediated phosphorylation at Thr-1338 is induced by 2-deoxyglucose (2-DG) and AICA ribonucleotide, and occurs during mitosis leading to membrane disassociation and inactivation of ARF1 during mitosis.

Disease relevance. Charcot-Marie-Tooth disease, axonal, type 2GG (CMT2GG) [MIM:606483] An axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot-Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal degeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. CMT2GG is an autosomal dominant form characterized by slowly progressive distal muscle weakness and atrophy primarily affecting the lower limbs and causing difficulty walking. Some individuals may also have involvement of the hands. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Inhibited by brefeldin A (BFA). Inhibited by golgicide A (GCA).

Domain organisation. The DCB (dimerization and cyclophilin-binding) and HUS (homology upstream of Sec7) domains are necessary for dimerization. The DCB domain is proposed to support constitutive homodimerization; the HUS domain interacts with the DCB domain which may occur intramolecular or intermolecular.

Isoforms (4)

UniProt IDNamesCanonical?
Q92538-41yes
Q92538-14
Q92538-22
Q92538-33

RefSeq proteins (20): NP_001186307, NP_001186308, NP_001364066, NP_001364067, NP_001364068, NP_001364069, NP_001364070, NP_001378851, NP_001378852, NP_001378853, NP_001378854, NP_001378855, NP_001378856, NP_001378857, NP_001378858, NP_001378859, NP_001378860, NP_001397932, NP_001397956, NP_004184 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000904Sec7_domDomain
IPR016024ARM-type_foldHomologous_superfamily
IPR023394Sec7_C_sfHomologous_superfamily
IPR032691Mon2/Sec7/BIG1-like_HUSDomain
IPR035999Sec7_dom_sfHomologous_superfamily
IPR056604GBF1-like_TPRDomain

Pfam: PF01369, PF12783, PF23325

UniProt features (52 total): modified residue 13, region of interest 11, compositionally biased region 10, sequence variant 5, mutagenesis site 5, sequence conflict 4, splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q92538-F171.420.37

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 (13): 350, 353, 508, 663, 1299, 1317, 1319, 1321, 1336, 1338, 1476, 1774, 1785

Mutagenesis-validated functional residues (5):

PositionPhenotype
544increases interaction with copg1 and pnpla2.
795inhibits golgi membrane recruitment of gga1, gga2 and gga3; generates misprocessing of psap.
795arrests retrograde ergic/cis-golgi-to-er transport at an early step and causes disassembly of the golgi and disassociati
833confers bfa tolerance.
1338prevents 2-dg-induced golgi disassembly.

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-199992trans-Golgi Network Vesicle Budding
R-HSA-5620916VxPx cargo-targeting to cilium
R-HSA-6807878COPI-mediated anterograde transport
R-HSA-6811434COPI-dependent Golgi-to-ER retrograde traffic
R-HSA-9918476Assembly and Release of Dengue Virus Virions
R-HSA-9918481Dengue Virus-Host Interactions

MSigDB gene sets: 312 (showing top): GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_MONOPOLAR_CELL_POLARITY, GOBP_CELLULAR_RESPONSE_TO_VIRUS, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, GOBP_MYELOID_LEUKOCYTE_MIGRATION, GOBP_CELL_CHEMOTAXIS, GOBP_VESICLE_LOCALIZATION, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_VESICLE_ORGANIZATION, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_VESICLE_TARGETING, TGACCTY_ERR1_Q2, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, YY1_Q6, EFC_Q6

GO Biological Process (25): cell activation involved in immune response (GO:0002263), endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890), post-Golgi vesicle-mediated transport (GO:0006892), Golgi to endosome transport (GO:0006895), Golgi organization (GO:0007030), regulation of mitotic cell cycle (GO:0007346), protein transport (GO:0015031), neutrophil chemotaxis (GO:0030593), regulation of ARF protein signal transduction (GO:0032012), protein localization to Golgi apparatus (GO:0034067), retrograde transport, endosome to Golgi (GO:0042147), COPI coating of Golgi vesicle (GO:0048205), cilium assembly (GO:0060271), establishment of monopolar cell polarity (GO:0061162), protein localization to endoplasmic reticulum exit site (GO:0070973), Golgi disassembly (GO:0090166), endoplasmic reticulum-Golgi intermediate compartment organization (GO:0097111), cellular response to virus (GO:0098586), reactive oxygen species biosynthetic process (GO:1903409), protein localization to endoplasmic reticulum tubular network (GO:1903420), regulation of protein localization to cell surface (GO:2000008), endomembrane system organization (GO:0010256), vesicle-mediated transport (GO:0016192), endosomal transport (GO:0016197)

GO Molecular Function (5): guanyl-nucleotide exchange factor activity (GO:0005085), phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547), phosphatidylinositol-3,5-bisphosphate binding (GO:0080025), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (15): Golgi membrane (GO:0000139), peroxisome (GO:0005777), endoplasmic reticulum lumen (GO:0005788), endoplasmic reticulum-Golgi intermediate compartment (GO:0005793), Golgi apparatus (GO:0005794), Golgi stack (GO:0005795), cis-Golgi network (GO:0005801), trans-Golgi network (GO:0005802), lipid droplet (GO:0005811), cytosol (GO:0005829), membrane (GO:0016020), cell leading edge (GO:0031252), cytoplasm (GO:0005737), endomembrane system (GO:0012505), Golgi apparatus subcompartment (GO:0098791)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Dengue Virus Infection2
Membrane Trafficking1
Cargo trafficking to the periciliary membrane1
ER to Golgi Anterograde Transport1
Golgi-to-ER retrograde transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
cytoplasm4
intercellular transport3
Golgi vesicle transport3
Golgi apparatus3
intracellular membrane-bounded organelle3
cytosolic transport2
organelle organization2
phosphatidylinositol phosphate binding2
binding2
Golgi apparatus subcompartment2
cell activation1
immune effector process1
immune response1
intracellular transport1
post-Golgi vesicle-mediated transport1
endomembrane system organization1
mitotic cell cycle1
regulation of cell cycle1
transport1
intracellular protein localization1
establishment of protein localization1
granulocyte chemotaxis1
neutrophil migration1
ARF protein signal transduction1
regulation of small GTPase mediated signal transduction1
protein localization to organelle1
endosomal transport1
COPI-coated vesicle budding1
Golgi transport vesicle coating1
axoneme assembly1
intraciliary transport involved in cilium assembly1
cilium organization1
protein localization to cilium1
organelle assembly1
trans-Golgi to periciliary membrane compartment transport1
plasma membrane bounded cell projection assembly1
ciliary transition zone assembly1
establishment of cell polarity1
establishment or maintenance of monopolar cell polarity1

Protein interactions and networks

STRING

1711 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GBF1ARF1P10947796
GBF1ARF6P26438739
GBF1PI4KBP78405691
GBF1RABIFP47224667
GBF1CDKN2AP42771635
GBF1RAB6AP20340614
GBF1COPB1P53618562
GBF1CIAO1O76071542
GBF1RSAD2Q8WXG1535
GBF1ARFGAP1Q8N6T3531
GBF1ACBD3Q9H3P7529
GBF1ARF4P18085520
GBF1RAB1BQ9H0U4507
GBF1ARFRP1Q13795490
GBF1ARFGAP3Q9NP61488

IntAct

183 interactions, top by confidence:

ABTypeScore
HRASRAF1psi-mi:“MI:0914”(association)0.980
YWHAGGBF1psi-mi:“MI:0915”(physical association)0.820
YWHABWDR62psi-mi:“MI:0914”(association)0.770
MILR1INPPL1psi-mi:“MI:0914”(association)0.640
YWHAGBLTP3Bpsi-mi:“MI:2364”(proximity)0.640
IRS4PIK3R2psi-mi:“MI:0914”(association)0.640
RAB8AWDR91psi-mi:“MI:0914”(association)0.600
YWHAHBLTP3Bpsi-mi:“MI:2364”(proximity)0.570
YWHAGSHTN1psi-mi:“MI:0914”(association)0.560
NPY2RRTL8Cpsi-mi:“MI:0914”(association)0.530
EPHA1EXOC5psi-mi:“MI:0914”(association)0.530
SPACA1GOLIM4psi-mi:“MI:0914”(association)0.530
YWHAZBLTP3Bpsi-mi:“MI:0914”(association)0.530
CD70METTL15psi-mi:“MI:0914”(association)0.530
CHRM3PLD2psi-mi:“MI:0914”(association)0.530
TMEM9ESYT2psi-mi:“MI:0914”(association)0.530
FAM174ABLTP3Bpsi-mi:“MI:0914”(association)0.530
STK16UNC119Bpsi-mi:“MI:0914”(association)0.530
CD40EXOC5psi-mi:“MI:0914”(association)0.530
EVA1CSTK25psi-mi:“MI:0914”(association)0.530
ILVBLSLC33A1psi-mi:“MI:0914”(association)0.530
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
GBF1psi-mi:“MI:0914”(association)0.500
GBF1psi-mi:“MI:0915”(physical association)0.500

BioGRID (542): GBF1 (Affinity Capture-MS), GBF1 (Affinity Capture-MS), GBF1 (Affinity Capture-MS), GBF1 (Affinity Capture-MS), GBF1 (Affinity Capture-MS), GBF1 (Affinity Capture-MS), GBF1 (Affinity Capture-MS), GBF1 (Co-fractionation), PUS7 (Co-fractionation), RBM26 (Co-fractionation), VARS (Co-fractionation), GBF1 (Affinity Capture-MS), GBF1 (Proximity Label-MS), GBF1 (Biochemical Activity), GBF1 (Affinity Capture-MS)

ESM2 similar proteins: A1A5G2, A2AFR3, A7MBL8, B9EJ86, E1C1R4, E1C3P4, F1LXF1, O94806, O94967, P0C6S7, P0CAX5, P11274, P22682, Q0V9G5, Q14161, Q14CM0, Q15139, Q16513, Q1RMU2, Q3KR37, Q3LAC4, Q3UGM2, Q5RED8, Q5T6S3, Q5U252, Q62101, Q66H62, Q6DFZ1, Q6P5G6, Q6PAJ1, Q70Z35, Q7Z6G8, Q80TI0, Q80TQ2, Q80YA9, Q8BIZ1, Q8BWW9, Q8BY87, Q8K1Y2, Q8NEL9

Diamond homologs: A0A0G2JUG7, A2A5R2, A5PKW4, D4A631, E1JIT7, F1MUS9, F4IXW2, F4JN05, F4JSZ5, F4K2K3, G3X9K3, G5EET6, O08967, O13690, O13817, O43739, O46382, P11075, P34512, P39993, P47102, P63034, P63035, P97694, P97696, Q10491, Q15438, Q2KI41, Q2PFD7, Q3TES0, Q42510, Q54KA7, Q5DTT2, Q5DU25, Q5E9G6, Q5JU85, Q6DFZ1, Q6DN90, Q6P1I6, Q76M68

SIGNOR signaling

6 interactions.

AEffectBMechanism
PRKAA1down-regulatesGBF1phosphorylation
AMPKdown-regulatesGBF1phosphorylation
CSNK2A1“down-regulates quantity by destabilization”GBF1phosphorylation
SCF-betaTRCP“down-regulates quantity by destabilization”GBF1ubiquitination
GBF1“up-regulates activity”ARF1“guanine nucleotide exchange factor”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 212 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
Activation of BAD and translocation to mitochondria738.1×5e-08
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex733.6×9e-08
SARS-CoV-1 targets host intracellular signalling and regulatory pathways733.6×9e-08
Activation of BH3-only proteins724.8×9e-07
RHO GTPases activate PKNs818.1×1e-06
Intrinsic Pathway for Apoptosis816.7×2e-06
Translocation of SLC2A4 (GLUT4) to the plasma membrane1213.2×3e-08
DAP12 signaling513.2×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic4
Uncertain significance288
Likely benign50
Benign19

Top pathogenic / likely-pathogenic (6)

Variant IDHGVSClassification
1456216NM_005029.4(PITX3):c.636_637dup (p.Gly213fs)Pathogenic
468353NM_005029.4(PITX3):c.640_656dup (p.Gly220fs)Pathogenic
1675431NM_001377137.1(GBF1):c.4384C>T (p.Arg1462Trp)Likely pathogenic
372897NM_005029.4(PITX3):c.646C>T (p.Gln216Ter)Likely pathogenic
620191NM_005029.4(PITX3):c.762C>A (p.Tyr254Ter)Likely pathogenic
6938NM_005029.4(PITX3):c.38G>A (p.Ser13Asn)Likely pathogenic

SpliceAI

6285 predictions. Top by Δscore:

VariantEffectΔscore
10:102258925:GTA:Gacceptor_loss1.0000
10:102258927:A:AGacceptor_gain1.0000
10:102258927:AG:Aacceptor_gain1.0000
10:102258928:G:GGacceptor_gain1.0000
10:102258928:GG:Gacceptor_gain1.0000
10:102258928:GGT:Gacceptor_gain1.0000
10:102258928:GGTT:Gacceptor_gain1.0000
10:102258928:GGTTT:Gacceptor_gain1.0000
10:102259031:ACTGG:Adonor_loss1.0000
10:102259032:CTGGT:Cdonor_loss1.0000
10:102259034:GGT:Gdonor_loss1.0000
10:102259035:G:GGdonor_gain1.0000
10:102259035:GTA:Gdonor_loss1.0000
10:102259036:T:Gdonor_loss1.0000
10:102260037:ATGT:Aacceptor_gain1.0000
10:102260038:T:Gacceptor_gain1.0000
10:102260038:T:TAacceptor_gain1.0000
10:102260040:T:TAacceptor_gain1.0000
10:102260045:TACA:Tacceptor_loss1.0000
10:102260046:A:AGacceptor_gain1.0000
10:102260046:ACAG:Aacceptor_gain1.0000
10:102260047:C:Gacceptor_gain1.0000
10:102260048:A:AGacceptor_gain1.0000
10:102260048:AG:Aacceptor_gain1.0000
10:102260049:G:GAacceptor_gain1.0000
10:102260049:GG:Gacceptor_gain1.0000
10:102260049:GGA:Gacceptor_gain1.0000
10:102260049:GGAT:Gacceptor_gain1.0000
10:102260095:G:GTdonor_gain1.0000
10:102260114:CAG:Cdonor_gain1.0000

AlphaMissense

12179 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:102344107:T:CS74P1.000
10:102344123:G:AG79D1.000
10:102344141:C:AA85E1.000
10:102344144:T:AL86H1.000
10:102344144:T:CL86P1.000
10:102344153:T:AV89D1.000
10:102351303:G:CA115P1.000
10:102351307:T:AV116D1.000
10:102351316:C:AA119D1.000
10:102351321:T:CF121L1.000
10:102351322:T:CF121S1.000
10:102351322:T:GF121C1.000
10:102351323:T:AF121L1.000
10:102351323:T:GF121L1.000
10:102351345:G:CD129H1.000
10:102351355:T:AV132D1.000
10:102351358:T:CL133P1.000
10:102351370:T:CL137P1.000
10:102351847:T:CL140P1.000
10:102351856:T:CL143P1.000
10:102351873:G:CG149R1.000
10:102351874:G:AG149D1.000
10:102351883:T:CL152P1.000
10:102351920:C:GC164W1.000
10:102351925:G:CR166P1.000
10:102352464:T:GL177W1.000
10:102352475:G:CA181P1.000
10:102352488:T:AL185H1.000
10:102352488:T:CL185P1.000
10:102359411:T:CF385L1.000

dbSNP variants (sampled 300 via entrez): RS1000018555 (10:102337050 A>T), RS1000030706 (10:102358921 A>G), RS1000059136 (10:102288635 C>T), RS1000066281 (10:102289293 C>A), RS1000073720 (10:102336300 AAAAAAAAAAAAAAAG>A), RS1000086738 (10:102329670 A>G), RS1000098013 (10:102354631 T>C), RS1000107592 (10:102346311 G>A), RS1000131849 (10:102281256 C>T), RS1000138388 (10:102233605 G>A,C), RS1000189662 (10:102245839 T>A), RS1000189797 (10:102260741 T>C), RS1000191412 (10:102322116 T>A), RS1000217600 (10:102380040 A>G), RS1000269003 (10:102357704 A>C,T)

Disease associations

OMIM: gene MIM:603698 | disease phenotypes: MIM:107250, MIM:606483, MIM:610623, MIM:620378

GenCC curated gene-disease

DiseaseClassificationInheritance
Charcot-Marie-Tooth Disease, axonal, type 2GGStrongAutosomal dominant
axonal neuropathyStrongAutosomal dominant

Mondo (5): anterior segment dysgenesis 1 (MONDO:0007138), Charcot-Marie-Tooth Disease, axonal, type 2GG (MONDO:0011675), cataract 11 multiple types (MONDO:0012527), Charcot-Marie-Tooth disease, dominant intermediate A (MONDO:0957273), axonal neuropathy (MONDO:0004183)

Orphanet (2): Autosomal dominant intermediate Charcot-Marie-Tooth disease type A (Orphanet:100043), Early onset non-syndromic cataract (Orphanet:91492)

HPO phenotypes

23 total (23 of 23 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0001260Dysarthria
HP:0001265Hyporeflexia
HP:0001270Motor delay
HP:0001284Areflexia
HP:0001288Gait disturbance
HP:0001761Pes cavus
HP:0001765Hammertoe
HP:0002460Distal muscle weakness
HP:0002936Distal sensory impairment
HP:0003376Steppage gait
HP:0003378Axonal degeneration/regeneration
HP:0003383Onion bulb formation
HP:0003393Thenar muscle atrophy
HP:0003394Muscle spasm
HP:0003445EMG: neuropathic changes
HP:0003481Segmental peripheral demyelination/remyelination
HP:0003596Middle age onset
HP:0003693Distal amyotrophy
HP:0007107Segmental peripheral demyelination
HP:0009027Foot dorsiflexor weakness
HP:0011462Young adult onset
HP:0011463Childhood onset

GWAS associations

18 associations (top):

StudyTraitp-value
GCST002500_66QT interval3.000000e-08
GCST005235_18Hand grip strength1.000000e-09
GCST005316_346Intelligence (MTAG)4.000000e-09
GCST005316_352Intelligence (MTAG)9.000000e-10
GCST005316_74Intelligence (MTAG)2.000000e-13
GCST005956_50Waist-to-hip ratio adjusted for BMI8.000000e-06
GCST005958_15Waist-to-hip ratio adjusted for BMI (age >50)4.000000e-06
GCST005962_36Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)6.000000e-07
GCST006269_323General cognitive ability2.000000e-11
GCST008810_89Smoking initiation (ever regular vs never regular)2.000000e-08
GCST009325_2Parkinson’s disease or first degree relation to individual with Parkinson’s disease1.000000e-09
GCST009524_145Household income (MTAG)1.000000e-12
GCST009524_82Household income (MTAG)2.000000e-08
GCST010002_298Refractive error3.000000e-22
GCST010173_177Triglyceride levels1.000000e-08
GCST010988_449Adult body size4.000000e-10
GCST90002388_574Lymphocyte count9.000000e-10
GCST90002389_454Lymphocyte percentage of white cells2.000000e-09

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0004682QT interval
EFO:0006941grip strength measurement
EFO:0004337intelligence
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0008007age at assessment
EFO:0008343sex interaction measurement
EFO:0005670smoking initiation
EFO:0009695household income
EFO:0004530triglyceride measurement
EFO:0004587lymphocyte count
EFO:0007993lymphocyte percentage of leukocytes

MeSH disease descriptors (2)

DescriptorNameTree numbers
C535344Cataract, posterior polar, 4 (supp.)
C564702Charcot-Marie-Tooth Disease, Dominant Intermediate A (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases abundance, increases expression3
Quercetinincreases expression, increases phosphorylation2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
dicrotophosincreases expression1
bisphenol Adecreases expression1
arseniteaffects binding, decreases reaction1
methylparabenincreases expression1
coumarinaffects phosphorylation1
cupric oxideincreases phosphorylation1
ICG 001decreases expression1
abrineincreases expression1
pentabrominated diphenyl ether 100increases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Arsenicdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Cadmiumdecreases expression, increases abundance1
Caffeineaffects phosphorylation1
Cisplatindecreases expression1
Ivermectindecreases expression1
Dronabinolincreases expression1
Thiramincreases expression1
Tretinoindecreases expression1
Urethaneincreases expression1
Cyclosporineincreases expression1
Aflatoxin B1increases methylation1
Cadmium Chloridedecreases expression, increases abundance1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT01847937Not specifiedCOMPLETEDMagnetic Resonance Diagnostics of Diabetic Peripheral Neuropathy
NCT05641103Not specifiedCOMPLETEDPREDIGA 2: Spanish Acronym of Educational and Diagnostic Project for Gaucher and ASMD