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Atlas / Gene / TBC1D17

TBC1D17

gene
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Also known as FLJ12168

Summary

TBC1D17 (TBC1 domain family member 17, HGNC:25699) is a protein-coding gene on chromosome 19q13.33, encoding TBC1 domain family member 17 (Q9HA65). Probable RAB GTPase-activating protein that inhibits RAB8A/B function.

Predicted to enable GTPase activator activity. Involved in retrograde transport, endosome to Golgi. Located in cytosol.

Source: NCBI Gene 79735 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 148 total
  • MANE Select transcript: NM_024682

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25699
Approved symbolTBC1D17
NameTBC1 domain family member 17
Location19q13.33
Locus typegene with protein product
StatusApproved
AliasesFLJ12168
Ensembl geneENSG00000104946
Ensembl biotypeprotein_coding
OMIM616659
Entrez79735

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 13 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000221543, ENST00000535102, ENST00000594984, ENST00000594996, ENST00000596243, ENST00000598789, ENST00000599049, ENST00000600354, ENST00000867139, ENST00000867140, ENST00000867141, ENST00000867142, ENST00000867143, ENST00000867144, ENST00000913307, ENST00000913308, ENST00000913309, ENST00000954148

RefSeq mRNA: 2 — MANE Select: NM_024682 NM_001168222, NM_024682

CCDS: CCDS12785, CCDS54294

Canonical transcript exons

ENST00000221543 — 17 exons

ExonStartEnd
ENSE000011261554987814349878241
ENSE000031898874987770249877744
ENSE000032161974988842449888750
ENSE000034728784988747649887573
ENSE000034737594988126849881475
ENSE000034987234988276449882892
ENSE000035098254988465949884758
ENSE000035153194988771849887834
ENSE000035283654988027949880402
ENSE000035367134988204149882152
ENSE000035446834988365149883745
ENSE000035829454988445949884559
ENSE000035946854988224249882400
ENSE000036009594988823149888317
ENSE000036292184988297349883076
ENSE000036393554987849849878572
ENSE000036615794988425349884369

Expression profiles

Bgee: expression breadth ubiquitous, 142 present calls, max score 97.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.7358 / max 116.9606, expressed in 1804 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
17709110.98941754
1770908.20101757
1770883.23281525
1770891.3125929

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
gastrocnemiusUBERON:000138897.19gold quality
right hemisphere of cerebellumUBERON:001489096.63gold quality
hindlimb stylopod muscleUBERON:000425296.61gold quality
cerebellar hemisphereUBERON:000224596.29gold quality
cerebellumUBERON:000203796.26gold quality
cerebellar cortexUBERON:000212996.26gold quality
muscle of legUBERON:000138396.21gold quality
skin of legUBERON:000151196.21gold quality
left ovaryUBERON:000211996.21gold quality
muscle organUBERON:000163096.18gold quality
skeletal muscle organUBERON:001489296.18gold quality
right ovaryUBERON:000211896.12gold quality
apex of heartUBERON:000209896.10gold quality
zone of skinUBERON:000001496.00gold quality
skin of abdomenUBERON:000141695.98gold quality
mucosa of stomachUBERON:000119995.95gold quality
right lobe of thyroid glandUBERON:000111995.94gold quality
body of uterusUBERON:000985395.91gold quality
popliteal arteryUBERON:000225095.88gold quality
tibial nerveUBERON:000132395.87gold quality
tibial arteryUBERON:000761095.87gold quality
lower esophagus muscularis layerUBERON:003583395.87gold quality
lower esophagusUBERON:001347395.86gold quality
esophagogastric junction muscularis propriaUBERON:003584195.85gold quality
right frontal lobeUBERON:000281095.77gold quality
endocervixUBERON:000045895.75gold quality
left lobe of thyroid glandUBERON:000112095.67gold quality
fundus of stomachUBERON:000116095.65gold quality
right adrenal gland cortexUBERON:003582795.62gold quality
skeletal muscle tissueUBERON:000113495.58gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.71
E-MTAB-6678yes5.83

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting TBC1D17, 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-223-3P99.9970.141140
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-17-5P99.8973.832665
HSA-MIR-106B-5P99.8874.722795
HSA-MIR-20A-5P99.8874.762769
HSA-MIR-20B-5P99.8874.012621
HSA-MIR-93-5P99.8873.982606
HSA-MIR-4786-3P99.3668.351390
HSA-MIR-33B-3P97.9267.39529
HSA-MIR-515-3P97.9267.98506
HSA-MIR-519E-3P97.9268.25508
HSA-MIR-3944-3P91.0162.2744

Literature-anchored findings (GeneRIF, showing 3)

  • Optineurin acts as an adaptor to bring together Rab8 and its GTPase-activating protein TBC1D17. (PMID:22854040)
  • Demonstrate that TBC1D15 and TBC1D17 mediate proper autophagic encapsulation of mitochondria by regulating Rab7 activity at the interface between mitochondria and isolation membranes. (PMID:24569479)
  • AMPK-mediated phosphorylation enhances the auto-inhibition of TBC1D17 to promote Rab5-dependent glucose uptake. (PMID:34045668)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotbc1d17ENSDARG00000005927
mus_musculusTbc1d17ENSMUSG00000038520
rattus_norvegicusTbc1d17ENSRNOG00000020191

Paralogs (45): RABGAP1 (ENSG00000011454), TBC1D22A (ENSG00000054611), TBC1D22B (ENSG00000065491), TBC1D1 (ENSG00000065882), EVI5 (ENSG00000067208), TBC1D25 (ENSG00000068354), TBC1D2 (ENSG00000095383), TBC1D10A (ENSG00000099992), SGSM3 (ENSG00000100359), TBC1D13 (ENSG00000107021), TBC1D12 (ENSG00000108239), TBC1D9 (ENSG00000109436), TBC1D30 (ENSG00000111490), TBC1D15 (ENSG00000121749), TBC1D5 (ENSG00000131374), TBC1D14 (ENSG00000132405), TBC1D8B (ENSG00000133138), TBC1D4 (ENSG00000136111), GRTP1 (ENSG00000139835), SGSM2 (ENSG00000141258), EVI5L (ENSG00000142459), TBCK (ENSG00000145348), USP6NL (ENSG00000148429), RABGAP1L (ENSG00000152061), SGSM1 (ENSG00000167037), TBC1D21 (ENSG00000167139), TBC1D2B (ENSG00000167202), TBC1D16 (ENSG00000167291), TBC1D10B (ENSG00000169221), TBC1D10C (ENSG00000175463), TBC1D28 (ENSG00000189375), TBC1D9B (ENSG00000197226), TBC1D8 (ENSG00000204634), TBC1D26 (ENSG00000214946), TBC1D3G (ENSG00000260287), TBC1D3K (ENSG00000273513), TBC1D3H (ENSG00000274226), TBC1D3D (ENSG00000274419), TBC1D3L (ENSG00000274512), TBC1D3 (ENSG00000274611)

Protein

Protein identifiers

TBC1 domain family member 17 — Q9HA65 (reviewed: Q9HA65)

All UniProt accessions (4): Q9HA65, M0QXA2, M0QYC9, M0R2L2

UniProt curated annotations — full annotation on UniProt →

Function. Probable RAB GTPase-activating protein that inhibits RAB8A/B function. Reduces Rab8 recruitment to tubules emanating from the endocytic recycling compartment (ERC) and inhibits Rab8-mediated endocytic trafficking, such as that of transferrin receptor (TfR). Involved in regulation of autophagy.

Subunit / interactions. Interacts with OPTN; this interaction mediates TBC1D17 transient association with Rab8.

Subcellular location. Cytoplasmic vesicle. Autophagosome. Cytoplasm. Recycling endosome.

Domain organisation. The arginine and glutamine fingers are critical for the GTPase-activating mechanism, they pull out Rab’s ‘switch 2’ glutamine and insert in Rab’s active site.

Isoforms (3)

UniProt IDNamesCanonical?
Q9HA65-11yes
Q9HA65-22
Q9HA65-33

RefSeq proteins (2): NP_001161694, NP_078958* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000195Rab-GAP-TBC_domDomain
IPR021935SGSM1/2_RBDDomain
IPR035969Rab-GAP_TBC_sfHomologous_superfamily

Pfam: PF00566, PF12068

UniProt features (20 total): modified residue 5, region of interest 3, compositionally biased region 3, splice variant 2, sequence variant 2, site 2, chain 1, domain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
9SI7X-RAY DIFFRACTION3.34

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9HA65-F173.630.47

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 377 (arginine finger); 418 (glutamine finger)

Post-translational modifications (5): 602, 604, 606, 608, 615

Mutagenesis-validated functional residues (1):

PositionPhenotype
381strongly decreased inhibition of rab8-mediated transferrin receptor (tfr) endocytic trafficking; enhanced rab8 localizat

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-8854214TBC/RABGAPs
R-HSA-199991Membrane Trafficking
R-HSA-5653656Vesicle-mediated transport
R-HSA-9007101Rab regulation of trafficking

MSigDB gene sets: 180 (showing top): CREL_01, MULLIGHAN_NPM1_SIGNATURE_3_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, FOXO1_01, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GGAMTNNNNNTCCY_UNKNOWN, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, FREAC3_01, YY1_02, GOBP_CILIUM_ORGANIZATION, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, GOBP_ORGANELLE_ASSEMBLY

GO Biological Process (3): autophagy (GO:0006914), protein transport (GO:0015031), retrograde transport, endosome to Golgi (GO:0042147)

GO Molecular Function (2): GTPase activator activity (GO:0005096), protein binding (GO:0005515)

GO Cellular Component (6): autophagosome (GO:0005776), cytosol (GO:0005829), recycling endosome (GO:0055037), cytoplasm (GO:0005737), endosome (GO:0005768), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Rab regulation of trafficking1
Vesicle-mediated transport1
Membrane Trafficking1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm2
cellular anatomical structure2
catabolic process1
transmembrane transport1
process utilizing autophagic mechanism1
transport1
intracellular protein localization1
establishment of protein localization1
intercellular transport1
endosomal transport1
cytosolic transport1
GTPase activity1
enzyme activator activity1
GTPase regulator activity1
binding1
vacuole1
endosome1
intracellular anatomical structure1
endomembrane system1
cytoplasmic vesicle1
intracellular vesicle1

Protein interactions and networks

STRING

980 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TBC1D17FIS1Q9Y3D6962
TBC1D17TBC1D15Q8TC07804
TBC1D17GABARAPL2P60520711
TBC1D17F5GZY7F5GZY7709
TBC1D17TSC2P49815686
TBC1D17VAMP2P19065651
TBC1D17OPTNQ96CV9651
TBC1D17UBXN8O00124634
TBC1D17TBC1D14Q9P2M4599
TBC1D17RAB5AP20339576
TBC1D17TBC1D19Q8N5T2576
TBC1D17GABARAPO95166563
TBC1D17TBC1D20Q96BZ9519
TBC1D17RAB6AP20340507
TBC1D17TBC1D8O95759487

IntAct

62 interactions, top by confidence:

ABTypeScore
OPTNTBC1D17psi-mi:“MI:0915”(physical association)0.740
TBC1D17OPTNpsi-mi:“MI:0915”(physical association)0.740
OPTNTBC1D17psi-mi:“MI:0403”(colocalization)0.740
KLRG2GLRX3psi-mi:“MI:0914”(association)0.640
STX12SNAP23psi-mi:“MI:0914”(association)0.640
CCDC121SCRN1psi-mi:“MI:0914”(association)0.530
CXCR4TMEM120Bpsi-mi:“MI:0914”(association)0.530
TBC1D15MYO9Apsi-mi:“MI:0914”(association)0.530
TBC1D15UBXN8psi-mi:“MI:0914”(association)0.530
ANKRD22ESYT2psi-mi:“MI:0914”(association)0.530
TBC1D17RAB8Apsi-mi:“MI:0914”(association)0.430
TBC1D17RAB8Apsi-mi:“MI:0403”(colocalization)0.430
SLC25A31TBC1D17psi-mi:“MI:0915”(physical association)0.400
SLC25A5TBC1D17psi-mi:“MI:0915”(physical association)0.400
CDKN2DTBC1D17psi-mi:“MI:0915”(physical association)0.370
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
ESYT2psi-mi:“MI:0914”(association)0.350
CUL2ANXA2P2psi-mi:“MI:0914”(association)0.350
STX12NBASpsi-mi:“MI:0914”(association)0.350
TBC1D15UBXN8psi-mi:“MI:0914”(association)0.350
ZBBXZZEF1psi-mi:“MI:0914”(association)0.350
UBAC2SURF4psi-mi:“MI:0914”(association)0.350
HLA-Cpsi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350

BioGRID (66): TBC1D17 (Affinity Capture-MS), TBC1D17 (Affinity Capture-MS), TBC1D17 (Affinity Capture-MS), TBC1D17 (Two-hybrid), TBC1D17 (Two-hybrid), TBC1D17 (Affinity Capture-MS), UBXN8 (Affinity Capture-MS), TBC1D17 (Affinity Capture-MS), TBC1D17 (Affinity Capture-MS), TBC1D17 (Affinity Capture-MS), TBC1D17 (Affinity Capture-MS), TBC1D17 (Affinity Capture-MS), TBC1D17 (Affinity Capture-RNA), TBC1D17 (Two-hybrid), TBC1D17 (Two-hybrid)

ESM2 similar proteins: A1A4I4, A1A5B6, A4D2P6, B2DCZ9, B4F7F3, O00192, O08773, O08874, O08908, O35465, O43566, O62683, O75808, O95049, P70268, P97492, Q0QWG9, Q12851, Q14164, Q14318, Q16512, Q16513, Q3B7U9, Q3KR56, Q3MII6, Q3UFB7, Q5FVC2, Q60875, Q61161, Q63433, Q63788, Q6P5Z2, Q6PFQ7, Q6V7V2, Q6ZT62, Q7Z5H3, Q865S3, Q8BWW9, Q8IYK8, Q8K045

Diamond homologs: A1A5B6, O43147, P09379, P48365, Q2NKQ1, Q3MII6, Q6FWI1, Q80U12, Q8BPQ7, Q8BYH7, Q8TBP0, Q8TC07, Q94BY9, Q9CXF4, Q9HA65, Q9UUH7, I2HAA0, Q09830, Q6BU76, Q6GLZ0, Q28CB1, Q8R3D1, Q9NVG8, P48566, Q12344, O95759, O97790, Q5ZJ17, Q60949, Q86TI0, Q8BYJ6, Q9D9D3, Q9Z1A9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance124
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3264 predictions. Top by Δscore:

VariantEffectΔscore
19:49878569:GAAG:Gdonor_gain1.0000
19:49878571:AGG:Adonor_loss1.0000
19:49878573:GT:Gdonor_loss1.0000
19:49878574:T:Gdonor_loss1.0000
19:49880276:AAG:Aacceptor_gain1.0000
19:49880276:AAGG:Aacceptor_loss1.0000
19:49880277:A:Gacceptor_gain1.0000
19:49880278:G:GCacceptor_loss1.0000
19:49882149:GTCA:Gdonor_gain1.0000
19:49882153:G:GGdonor_gain1.0000
19:49882241:GC:Gacceptor_gain1.0000
19:49882241:GCGC:Gacceptor_gain1.0000
19:49882397:CTGT:Cdonor_gain1.0000
19:49882399:GT:Gdonor_gain1.0000
19:49882401:G:GGdonor_gain1.0000
19:49882403:GAGTA:Gdonor_gain1.0000
19:49882405:GTA:Gdonor_gain1.0000
19:49882408:G:GGdonor_gain1.0000
19:49882759:T:TAacceptor_gain1.0000
19:49882761:CAGGT:Cacceptor_loss1.0000
19:49882762:A:AGacceptor_gain1.0000
19:49882762:AG:Aacceptor_gain1.0000
19:49882762:AGGT:Aacceptor_gain1.0000
19:49882762:AGGTG:Aacceptor_gain1.0000
19:49882763:G:GAacceptor_gain1.0000
19:49882763:GG:Gacceptor_gain1.0000
19:49882763:GGT:Gacceptor_gain1.0000
19:49882763:GGTG:Gacceptor_gain1.0000
19:49882763:GGTGG:Gacceptor_gain1.0000
19:49882889:GGGG:Gdonor_gain1.0000

AlphaMissense

4208 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:49884480:A:CD422A1.000
19:49884480:A:GD422G1.000
19:49887534:G:CK501N1.000
19:49887534:G:TK501N1.000
19:49881334:T:AI129N0.999
19:49884258:G:CD378H0.999
19:49884259:A:CD378A0.999
19:49884259:A:GD378G0.999
19:49884259:A:TD378V0.999
19:49884260:T:AD378E0.999
19:49884260:T:GD378E0.999
19:49884267:C:AR381S0.999
19:49884268:G:CR381P0.999
19:49884461:T:CY416H0.999
19:49884469:G:CQ418H0.999
19:49884469:G:TQ418H0.999
19:49884470:G:CG419R0.999
19:49884476:A:CS421R0.999
19:49884478:T:AS421R0.999
19:49884478:T:GS421R0.999
19:49884479:G:CD422H0.999
19:49884480:A:TD422V0.999
19:49884483:T:CL423P0.999
19:49884668:T:CF452L0.999
19:49884670:T:AF452L0.999
19:49884670:T:GF452L0.999
19:49887508:T:CF493L0.999
19:49887510:C:AF493L0.999
19:49887510:C:GF493L0.999
19:49887514:T:AW495R0.999

dbSNP variants (sampled 300 via entrez): RS1000040277 (19:49885437 G>A,C,T), RS1000233165 (19:49880677 C>T), RS1000555472 (19:49888326 C>A,T), RS1000734337 (19:49883414 G>A,T), RS1000886414 (19:49889207 G>C), RS1001469063 (19:49879745 G>A,C), RS1001515127 (19:49887209 G>A,T), RS1001655362 (19:49884435 C>T), RS1001914913 (19:49877930 C>G,T), RS1002485292 (19:49886473 C>T), RS1002516331 (19:49886196 C>T), RS1002622302 (19:49883569 C>A,T), RS1002730449 (19:49878653 T>G), RS1002766272 (19:49881648 C>T), RS1002916728 (19:49877029 T>TCCCC)

Disease associations

OMIM: gene MIM:616659 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Fincreases expression, affects cotreatment2
Estradioldecreases expression, affects expression2
Ozonedecreases expression, affects expression, increases abundance2
aristolochic acid Iincreases expression1
GSK-J4increases expression1
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
beta-lapachoneincreases expression1
sodium arseniteincreases expression1
cobaltous chlorideincreases expression1
coumarinincreases phosphorylation1
exemestaneincreases expression1
abrineincreases expression1
jinfukangaffects cotreatment, increases expression1
Resveratrolaffects cotreatment, decreases expression1
Decitabinedecreases expression, affects reaction1
Air Pollutantsaffects expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Cisplatinaffects cotreatment, increases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Niclosamideincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Smokedecreases expression1
Dronabinolincreases expression1
Tobacco Smoke Pollutionincreases methylation1
Valproic Acidincreases methylation1

Clinical trials (associated diseases)

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

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

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

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