TBC1D2

gene
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Also known as PARIS1TBC1D2AArmus

Summary

TBC1D2 (TBC1 domain family member 2, HGNC:18026) is a protein-coding gene on chromosome 9q22.33, encoding TBC1 domain family member 2A (Q9BYX2). Acts as a GTPase-activating protein for RAB7A.

Enables GTPase activator activity and cadherin binding activity. Involved in positive regulation of GTPase activity. Located in several cellular components, including cytoplasmic vesicle; cytosol; and nucleoplasm.

Source: NCBI Gene 55357 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 165 total
  • MANE Select transcript: NM_001267571

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18026
Approved symbolTBC1D2
NameTBC1 domain family member 2
Location9q22.33
Locus typegene with protein product
StatusApproved
AliasesPARIS1, TBC1D2A, Armus
Ensembl geneENSG00000095383
Ensembl biotypeprotein_coding
OMIM609871
Entrez55357

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000342112, ENST00000375063, ENST00000375064, ENST00000375066, ENST00000465784, ENST00000493589

RefSeq mRNA: 4 — MANE Select: NM_001267571 NM_001267571, NM_001267572, NM_001410988, NM_018421

CCDS: CCDS35080, CCDS59137, CCDS75865, CCDS94445

Canonical transcript exons

ENST00000465784 — 13 exons

ExonStartEnd
ENSE000018500339825517398255649
ENSE000035836419824399498244129
ENSE000037517709819901198199588
ENSE000038887549825178598251926
ENSE000038891389821310898213218
ENSE000038892469820025398200374
ENSE000038894129822895298229148
ENSE000038921629822083398221228
ENSE000038928479820866898209144
ENSE000038931179820328898203408
ENSE000038944529821065698210843
ENSE000038954429820147998201664
ENSE000038962189823341698233549

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 91.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.8033 / max 180.9976, expressed in 1712 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1016795.16001388
1016783.4847878
1016803.44971267
1016763.1698688
1016770.5391324

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
monocyteCL:000057691.11gold quality
upper lobe of left lungUBERON:000895291.05gold quality
mononuclear cellCL:000084290.89gold quality
leukocyteCL:000073890.63gold quality
upper lobe of lungUBERON:000894890.45gold quality
esophagus mucosaUBERON:000246989.93gold quality
granulocyteCL:000009488.66gold quality
right lungUBERON:000216788.27gold quality
gingival epitheliumUBERON:000194988.00gold quality
C1 segment of cervical spinal cordUBERON:000646987.27gold quality
mucosa of transverse colonUBERON:000499187.22gold quality
stromal cell of endometriumCL:000225587.12gold quality
lower esophagus mucosaUBERON:003583486.98gold quality
skin of legUBERON:000151186.53gold quality
gingivaUBERON:000182886.01gold quality
skin of abdomenUBERON:000141685.89gold quality
bloodUBERON:000017885.47gold quality
spinal cordUBERON:000224084.86gold quality
olfactory segment of nasal mucosaUBERON:000538684.34gold quality
zone of skinUBERON:000001483.90gold quality
lungUBERON:000204883.75gold quality
right lobe of liverUBERON:000111483.35gold quality
minor salivary glandUBERON:000183082.12gold quality
deciduaUBERON:000245082.05gold quality
esophagusUBERON:000104382.04gold quality
mouth mucosaUBERON:000372982.04gold quality
vaginaUBERON:000099681.64gold quality
tibial nerveUBERON:000132380.21gold quality
saliva-secreting glandUBERON:000104480.10gold quality
epithelium of esophagusUBERON:000197679.68gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.85
E-MTAB-6075no11.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

47 targeting TBC1D2, 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-302E99.9670.742669
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-146A-5P99.9668.93988
HSA-MIR-146B-5P99.9669.13977
HSA-MIR-7153-5P99.9468.891006
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-302A-3P99.8971.231777
HSA-MIR-302B-3P99.8971.231777
HSA-MIR-302C-3P99.8971.201778
HSA-MIR-302D-3P99.8971.251777
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-373-3P99.8470.681668
HSA-MIR-520E-3P99.8470.551698
HSA-MIR-372-3P99.8370.581691
HSA-MIR-520A-3P99.8370.591687
HSA-MIR-520B-3P99.8370.561699
HSA-MIR-520C-3P99.8370.561699
HSA-MIR-520D-3P99.8370.781676
HSA-MIR-370-5P99.7866.81706
HSA-MIR-452-5P99.6569.631762
HSA-MIR-4676-3P99.6569.311733
HSA-MIR-892C-3P99.6569.381745
HSA-MIR-312399.4767.152693
HSA-MIR-425199.4069.193363

Literature-anchored findings (GeneRIF, showing 3)

  • integration of Rac1 and Rab7 activities by Armus provides an important regulatory node for E-cadherin turnover and stability of cell-cell contacts (PMID:20116244)
  • TBC1D2/Armus, a GAP of Rab7 GTPase, is reported as a novel target of miR-17. (PMID:23285084)
  • Armus expression induces autophagosome accumulation in keratinocytes. (PMID:23562278)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotbc1d2ENSDARG00000071304
mus_musculusTbc1d2ENSMUSG00000039813
rattus_norvegicusTbc1d2ENSRNOG00000023348

Paralogs (45): RABGAP1 (ENSG00000011454), TBC1D22A (ENSG00000054611), TBC1D22B (ENSG00000065491), TBC1D1 (ENSG00000065882), EVI5 (ENSG00000067208), TBC1D25 (ENSG00000068354), TBC1D10A (ENSG00000099992), SGSM3 (ENSG00000100359), TBC1D17 (ENSG00000104946), 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 2AQ9BYX2 (reviewed: Q9BYX2)

Alternative names: Armus, Prostate antigen recognized and identified by SEREX 1

All UniProt accessions (1): Q9BYX2

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a GTPase-activating protein for RAB7A. Signal effector acting as a linker between RAC1 and RAB7A, leading to RAB7A inactivation and subsequent inhibition of cadherin degradation and reduced cell-cell adhesion.

Subunit / interactions. Interacts with activated RAC1 and CDH1.

Subcellular location. Cytoplasm. Cytoplasmic vesicle. Cell junction.

Tissue specificity. Expressed in a broad range of tissues, especially in kidney, liver, lung and placenta. Also expressed in keratinocytes and epithelia-containing organs. Isoform 2 is differentially expressed in prostate normal and cancer cells (at protein level).

Miscellaneous. ‘Armus’ means hinge, linker in Latin and ancient Greek.

Isoforms (6)

UniProt IDNamesCanonical?
Q9BYX2-11, A variant Cyes
Q9BYX2-22, PARIS-1
Q9BYX2-33, A
Q9BYX2-44
Q9BYX2-55
Q9BYX2-66

RefSeq proteins (4): NP_001254500, NP_001254501, NP_001397917, NP_060891 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000195Rab-GAP-TBC_domDomain
IPR001849PH_domainDomain
IPR011993PH-like_dom_sfHomologous_superfamily
IPR035969Rab-GAP_TBC_sfHomologous_superfamily
IPR050302Rab_GAP_TBC_domainFamily

Pfam: PF00169, PF00566

UniProt features (41 total): strand 9, sequence conflict 6, splice variant 5, modified residue 4, region of interest 4, sequence variant 3, helix 3, domain 2, coiled-coil region 2, chain 1, turn 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2DHKSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BYX2-F175.940.39

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 (4): 1, 436, 915, 920

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: 150 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOZGIT_ESR1_TARGETS_DN, GOBP_REGULATION_OF_GTPASE_ACTIVITY, REACTOME_MEMBRANE_TRAFFICKING, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, RICKMAN_METASTASIS_DN, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, KOYAMA_SEMA3B_TARGETS_UP, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_CILIUM_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN

GO Biological Process (1): positive regulation of GTPase activity (GO:0043547)

GO Molecular Function (3): GTPase activator activity (GO:0005096), cadherin binding (GO:0045296), protein binding (GO:0005515)

GO Cellular Component (7): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886), cell junction (GO:0030054), cytoplasmic vesicle (GO:0031410), anchoring junction (GO:0070161)

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
cellular anatomical structure4
GTPase activity2
cytoplasm2
regulation of GTPase activity1
positive regulation of hydrolase activity1
enzyme activator activity1
GTPase regulator activity1
cell adhesion molecule binding1
binding1
nuclear lumen1
intracellular anatomical structure1
membrane1
cell periphery1
intracellular vesicle1
cell junction1

Protein interactions and networks

STRING

1598 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TBC1D2TBC1D15Q8TC07696
TBC1D2TBC1D5Q92609642
TBC1D2VAMP7P51809551
TBC1D2TBC1D25Q3MII6550
TBC1D2CDC16Q13042526
TBC1D2LRRK1Q38SD2508
TBC1D2TBC1D20Q96BZ9486
TBC1D2TBC1D19Q8N5T2477
TBC1D2RAB5AP20339473
TBC1D2TBC1D21Q8IYX1466
TBC1D2TBC1D13Q9NVG8464
TBC1D2CCZ1BP86790454
TBC1D2MON1AQ86VX9432
TBC1D2PIK3C3Q8NEB9429
TBC1D2GABARAPO95166418

IntAct

15 interactions, top by confidence:

ABTypeScore
TK2psi-mi:“MI:0915”(physical association)0.400
TBC1D2CDC42psi-mi:“MI:0915”(physical association)0.370
AURKATBC1D2psi-mi:“MI:0915”(physical association)0.370
BUB1TBC1D2psi-mi:“MI:0915”(physical association)0.370
TBC1D2CCND1psi-mi:“MI:0915”(physical association)0.370
DCCTBC1D2psi-mi:“MI:0915”(physical association)0.370
TBC1D2MLH3psi-mi:“MI:0915”(physical association)0.370
TBC1D2PDGFRLpsi-mi:“MI:0915”(physical association)0.370
KRT40ANKRD36psi-mi:“MI:0914”(association)0.350
TBC1D2HMMRpsi-mi:“MI:0914”(association)0.350
ZBTB43SPINDOCpsi-mi:“MI:0914”(association)0.350
KRT40NEURL1Bpsi-mi:“MI:0914”(association)0.350
RBBP4PHF20L1psi-mi:“MI:0914”(association)0.350

BioGRID (41): TBC1D2 (Affinity Capture-MS), TBC1D2 (Affinity Capture-MS), KCTD6 (Two-hybrid), TBC1D2 (Two-hybrid), TBC1D2 (Two-hybrid), TBC1D2 (Two-hybrid), TBC1D2 (Two-hybrid), TBC1D2 (Two-hybrid), TBC1D2 (Two-hybrid), TBC1D2 (Proximity Label-MS), TBC1D2 (Affinity Capture-MS), WBP5 (Affinity Capture-MS), SASS6 (Affinity Capture-MS), TBC1D2 (Affinity Capture-MS), FAM83D (Affinity Capture-MS)

ESM2 similar proteins: A0A8I3NFE2, A0FI79, B1AVH7, B5DFA1, D2H0G5, D7PF45, O00750, O15357, O70143, P29353, P97573, P98083, Q00IB7, Q0IIE2, Q15678, Q16825, Q17R13, Q2I6J0, Q2I6J1, Q2V2M9, Q5JV73, Q5M824, Q5R7W7, Q5U2X5, Q61120, Q62130, Q62136, Q62728, Q62925, Q69Z98, Q6P4S2, Q6P549, Q80TI1, Q8AY68, Q8BMC3, Q8BYW1, Q8IWQ3, Q8K245, Q92529, Q92835

Diamond homologs: A2AWA9, A3KGB4, A6H6A9, A6H8I2, A6QP29, B0R0W9, B1AVH7, B5DFA1, C8VDQ4, D2H0G5, F4HVW5, O60447, O95759, P53258, P58802, P87234, Q0IIM8, Q12317, Q28CB1, Q2KI13, Q3KR37, Q3KR56, Q3U0J8, Q3UYK3, Q4KMP7, Q4QQU7, Q5R372, Q5RAN1, Q5RCW6, Q5SVR0, Q5TC63, Q66K14, Q6C8M8, Q6GL87, Q6GLZ0, Q6P6R7, Q6PBU5, Q6ZT07, Q7T2D0, Q80TI0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance126
Likely benign13
Benign8

Top pathogenic / likely-pathogenic (0)

SpliceAI

2166 predictions. Top by Δscore:

VariantEffectΔscore
9:98199585:CTTC:Cacceptor_gain1.0000
9:98199586:TTCCT:Tacceptor_loss1.0000
9:98199587:TCCT:Tacceptor_loss1.0000
9:98199588:CCT:Cacceptor_loss1.0000
9:98199589:C:CCacceptor_gain1.0000
9:98199590:T:Aacceptor_loss1.0000
9:98200247:CCT:Cdonor_loss1.0000
9:98200248:CTCA:Cdonor_loss1.0000
9:98200249:TCACC:Tdonor_loss1.0000
9:98200250:CA:Cdonor_loss1.0000
9:98200251:A:ACdonor_gain1.0000
9:98200251:ACC:Adonor_loss1.0000
9:98200252:C:CCdonor_gain1.0000
9:98200252:C:Tdonor_loss1.0000
9:98200252:CCGG:Cdonor_gain1.0000
9:98200370:ACCAC:Aacceptor_gain1.0000
9:98200371:CCAC:Cacceptor_gain1.0000
9:98200371:CCACC:Cacceptor_gain1.0000
9:98200372:CAC:Cacceptor_gain1.0000
9:98200372:CACC:Cacceptor_gain1.0000
9:98200373:ACC:Aacceptor_loss1.0000
9:98200374:CCT:Cacceptor_loss1.0000
9:98200375:C:CCacceptor_gain1.0000
9:98200375:CTG:Cacceptor_loss1.0000
9:98200376:T:Aacceptor_loss1.0000
9:98201474:CCTA:Cdonor_loss1.0000
9:98201475:CTAC:Cdonor_loss1.0000
9:98201476:TA:Tdonor_loss1.0000
9:98201477:AC:Adonor_loss1.0000
9:98201478:CCTTC:Cdonor_loss1.0000

AlphaMissense

6049 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:98251886:A:GL137P0.995
9:98251899:A:GW133R0.995
9:98251899:A:TW133R0.995
9:98255387:A:GL52S0.995
9:98255340:A:GW68R0.994
9:98255340:A:TW68R0.994
9:98255210:A:GF111S0.993
9:98255177:A:GL122P0.992
9:98255309:A:GL78P0.992
9:98255393:C:TG50E0.992
9:98251875:G:TR141S0.990
9:98251895:A:GL134P0.990
9:98201508:A:GW810R0.989
9:98201508:A:TW810R0.989
9:98251874:C:GR141P0.989
9:98251897:C:AW133C0.989
9:98251897:C:GW133C0.989
9:98255335:G:CF69L0.989
9:98255335:G:TF69L0.989
9:98255337:A:GF69L0.989
9:98255204:A:GI113T0.988
9:98255343:G:TR67S0.988
9:98208915:A:GW635R0.987
9:98208915:A:TW635R0.987
9:98243997:A:GI215T0.987
9:98220970:C:GA413P0.986
9:98255204:A:CI113S0.986
9:98255342:C:GR67P0.986
9:98255394:C:AG50W0.986
9:98255309:A:TL78Q0.985

dbSNP variants (sampled 300 via entrez): RS1000079747 (9:98222368 G>T), RS1000115465 (9:98236255 A>G), RS1000140464 (9:98252474 C>G), RS1000153676 (9:98216401 C>T), RS1000191799 (9:98207386 T>C), RS1000193805 (9:98231261 A>G), RS1000235418 (9:98236603 A>G), RS1000365772 (9:98212846 A>G), RS1000415364 (9:98200579 A>C,G), RS1000574539 (9:98230173 C>A), RS1000629048 (9:98223732 G>A), RS1000724151 (9:98254634 C>G,T), RS1000771987 (9:98225123 C>T), RS1000818231 (9:98249647 A>G), RS1000821216 (9:98213141 C>A)

Disease associations

OMIM: gene MIM:609871 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST002963_6Post-traumatic stress disorder1.000000e-06
GCST003123_22Severe influenza A (H1N1) infection4.000000e-08
GCST009391_1224Metabolite levels6.000000e-06
GCST009391_1234Metabolite levels2.000000e-06
GCST009557_13Rate of ventricular enlargement4.000000e-06
GCST012490_398Femur bone mineral density x serum urate levels interaction1.000000e-08

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:1001488influenza A (H1N1)
EFO:0010421triacylglycerol 54:3 measurement
EFO:0010422triacylglycerol 54:4 measurement
EFO:0010570ventricular enlargement measurement
EFO:0004531urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression4
Benzo(a)pyreneaffects methylation, decreases methylation, increases mutagenesis3
bisphenol Aaffects cotreatment, increases methylation, decreases methylation, increases expression2
sodium arseniteaffects cotreatment, decreases expression, increases abundance, increases expression2
Arsenicincreases expression, affects cotreatment, decreases expression, increases abundance2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tobacco Smoke Pollutiondecreases expression, increases expression2
Particulate Matterdecreases expression, increases abundance, affects cotreatment, increases expression2
aminomethylphosphonic acid (AMPA)decreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
glycidyl methacrylatedecreases expression1
sodium arsenateincreases abundance, increases expression1
2-methyl-4-isothiazolin-3-onedecreases expression1
ethyl-p-hydroxybenzoateincreases expression1
butyraldehydeincreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
potassium chromate(VI)affects cotreatment, decreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation1
epigallocatechin gallateaffects cotreatment, decreases expression1
avobenzoneincreases expression1
Am 580increases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
(+)-JQ1 compoundincreases expression1
Rosiglitazoneincreases expression1
Resveratrolincreases 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): post-traumatic stress disorder