TBC1D10B

gene
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Also known as DKFZP434P1750Rab27A-GAPbetaFLJ13130EPI64B

Summary

TBC1D10B (TBC1 domain family member 10B, HGNC:24510) is a protein-coding gene on chromosome 16p11.2, encoding TBC1 domain family member 10B (Q4KMP7). Acts as a GTPase-activating protein for RAB3A, RAB22A, RAB27A, and RAB35.

Small G proteins of the RAB family (see MIM 179508) function in intracellular vesicle trafficking by switching from the GTP-bound state to the GDP-bound state with the assistance of guanine nucleotide exchange factors (GEFs; see MIM 609700) and GTPase-activating proteins (GAPs). TBC1D10B functions as a GAP for several proteins of the Rab family (Ishibashi et al., 2009 [PubMed 19077034]).

Source: NCBI Gene 26000 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 56 total
  • MANE Select transcript: NM_015527

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24510
Approved symbolTBC1D10B
NameTBC1 domain family member 10B
Location16p11.2
Locus typegene with protein product
StatusApproved
AliasesDKFZP434P1750, Rab27A-GAPbeta, FLJ13130, EPI64B
Ensembl geneENSG00000169221
Ensembl biotypeprotein_coding
OMIM613620
Entrez26000

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 6 protein_coding, 5 retained_intron

ENST00000409939, ENST00000464644, ENST00000475650, ENST00000475872, ENST00000478158, ENST00000490703, ENST00000566671, ENST00000936813, ENST00000936814, ENST00000955945, ENST00000955946

RefSeq mRNA: 1 — MANE Select: NM_015527 NM_015527

CCDS: CCDS10676

Canonical transcript exons

ENST00000409939 — 9 exons

ExonStartEnd
ENSE000011398933036549530365594
ENSE000019586153036922830370494
ENSE000035339653035953830359603
ENSE000035474183036510530365212
ENSE000035879083035917230359361
ENSE000035909533036490030365006
ENSE000036296763035972730359841
ENSE000036573943035710230358573
ENSE000036824543035866330358817

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 93.52.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.0333 / max 356.9954, expressed in 1797 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
15704014.03331797

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453393.52gold quality
right testisUBERON:000453493.30gold quality
mucosa of transverse colonUBERON:000499192.72gold quality
C1 segment of cervical spinal cordUBERON:000646992.66gold quality
granulocyteCL:000009491.84gold quality
apex of heartUBERON:000209891.72gold quality
right hemisphere of cerebellumUBERON:001489091.68gold quality
cerebellar hemisphereUBERON:000224591.63gold quality
cerebellar cortexUBERON:000212991.59gold quality
spinal cordUBERON:000224091.55gold quality
right frontal lobeUBERON:000281091.33gold quality
spermCL:000001990.97gold quality
prefrontal cortexUBERON:000045190.91gold quality
male germ cellCL:000001590.81gold quality
cingulate cortexUBERON:000302790.79gold quality
anterior cingulate cortexUBERON:000983590.79gold quality
gastrocnemiusUBERON:000138890.73gold quality
testisUBERON:000047390.58gold quality
right adrenal gland cortexUBERON:003582790.48gold quality
hindlimb stylopod muscleUBERON:000425290.47gold quality
lower esophagus mucosaUBERON:003583490.43gold quality
ileal mucosaUBERON:000033190.36gold quality
cerebellumUBERON:000203790.35gold quality
stromal cell of endometriumCL:000225590.17gold quality
sural nerveUBERON:001548890.11gold quality
ganglionic eminenceUBERON:000402390.03gold quality
right adrenal glandUBERON:000123389.97gold quality
muscle of legUBERON:000138389.90gold quality
Brodmann (1909) area 9UBERON:001354089.90gold quality
amygdalaUBERON:000187689.66gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting TBC1D10B, 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-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-5692A100.0074.406850
HSA-MIR-4533100.0069.482758
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-23B-5P99.9866.07587
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-23A-5P99.9465.39468
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-444799.8567.812900
HSA-MIR-449599.8272.083080
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-182599.7268.111089
HSA-MIR-320299.6667.702737
HSA-MIR-447299.5666.081478
HSA-MIR-4761-5P99.5166.69804
HSA-MIR-65799.4866.02848
HSA-MIR-330-3P99.4169.952521
HSA-MIR-1912-3P99.3267.40936
HSA-MIR-751599.3168.221795
HSA-MIR-504-3P99.3067.181745
HSA-MIR-465199.0667.572002
HSA-MIR-1295B-5P99.0367.50810
HSA-MIR-670-3P99.0368.882404

Literature-anchored findings (GeneRIF, showing 5)

  • Data suggest that EPI64A and B, which are ubiquitously expressed members of the EPI64 subfamily, inactivate Ras and certain Rabs at the periphery of cells. (PMID:23248241)
  • Regulation of VEGFR2 trafficking and signaling by Rab GTPase-activating proteins. (PMID:31527750)
  • STAT4-mediated down-regulation of miR-3619-5p facilitates stomach adenocarcinoma by modulating TBC1D10B. (PMID:32397798)
  • The RabGAPs EPI64A and EPI64B regulate the apical structure of epithelial cells (dagger). (PMID:34757852)
  • TBC1D10B promotes tumor progression in colon cancer via PAK4-mediated promotion of the PI3K/AKT/mTOR pathway. (PMID:38824479)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotbc1d10bENSDARG00000078604
mus_musculusTbc1d10bENSMUSG00000042492
rattus_norvegicusTbc1d10bENSRNOG00000017349

Paralogs (45): RABGAP1 (ENSG00000011454), TBC1D22A (ENSG00000054611), TBC1D22B (ENSG00000065491), TBC1D1 (ENSG00000065882), EVI5 (ENSG00000067208), TBC1D25 (ENSG00000068354), TBC1D2 (ENSG00000095383), 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), 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 10BQ4KMP7 (reviewed: Q4KMP7)

Alternative names: Rab27A-GAP-beta

All UniProt accessions (2): Q4KMP7, H3BSE1

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a GTPase-activating protein for RAB3A, RAB22A, RAB27A, and RAB35. Does not act on RAB2A and RAB6A.

Subcellular location. Cytoplasm. Cell membrane.

Isoforms (2)

UniProt IDNamesCanonical?
Q4KMP7-11yes
Q4KMP7-22

RefSeq proteins (1): NP_056342* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000195Rab-GAP-TBC_domDomain
IPR035969Rab-GAP_TBC_sfHomologous_superfamily
IPR050302Rab_GAP_TBC_domainFamily

Pfam: PF00566

UniProt features (33 total): compositionally biased region 11, modified residue 8, sequence conflict 5, region of interest 4, chain 1, domain 1, splice variant 1, mutagenesis site 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q4KMP7-F169.940.45

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 (8): 22, 141, 152, 186, 658, 661, 678, 687

Mutagenesis-validated functional residues (1):

PositionPhenotype
409loss of gap activity. unable to exclude rab3a from the dense-core vesicles, when tested in a pheochromocytoma cell line.

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: 154 (showing top): GCM_MAP4K4, GCM_GSPT1, GOBP_REGULATION_OF_GTPASE_ACTIVITY, RACCACAR_AML_Q6, GOBP_VESICLE_MEDIATED_TRANSPORT, AP2_Q3, REACTOME_MEMBRANE_TRAFFICKING, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GCGCTTT_MIR518B_MIR518C_MIR518D, CEBPB_01, CATRRAGC_UNKNOWN, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, TGCTGAY_UNKNOWN, GOBP_CILIUM_ORGANIZATION

GO Biological Process (2): retrograde transport, endosome to Golgi (GO:0042147), regulation of GTPase activity (GO:0043087)

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

GO Cellular Component (4): cytosol (GO:0005829), plasma membrane (GO:0005886), cytoplasm (GO:0005737), membrane (GO:0016020)

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 structure3
GTPase activity2
intercellular transport1
endosomal transport1
cytosolic transport1
regulation of hydrolase activity1
enzyme activator activity1
GTPase regulator activity1
binding1
cytoplasm1
membrane1
cell periphery1
intracellular anatomical structure1

Protein interactions and networks

STRING

998 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TBC1D10BRAB35Q15286877
TBC1D10BRAB27AP51159851
TBC1D10BRAB22AQ9UL26823
TBC1D10BCDC16Q13042774
TBC1D10BRAB6AP20340667
TBC1D10BRAB2AP08886666
TBC1D10BARF6P26438664
TBC1D10BEIF3KQ9UBQ5644
TBC1D10BRAB3AP20336643
TBC1D10BTBC1D22BQ9NU19607
TBC1D10BTBC1D13Q9NVG8584
TBC1D10BNRDE2Q9H7Z3571
TBC1D10BTBC1D19Q8N5T2517
TBC1D10BTMUB2Q71RG4511
TBC1D10BTBC1D21Q8IYX1508

IntAct

45 interactions, top by confidence:

ABTypeScore
RIOK1PRMT5psi-mi:“MI:0914”(association)0.710
TBC1D10BCCDC70psi-mi:“MI:0915”(physical association)0.560
ZYXTBC1D10Bpsi-mi:“MI:0914”(association)0.530
GALNSCLGNpsi-mi:“MI:0914”(association)0.530
TipinNEMFpsi-mi:“MI:0914”(association)0.350
Kif20bSHTN1psi-mi:“MI:0914”(association)0.350
SYNCRIPARHGAP32psi-mi:“MI:0914”(association)0.350
ORF73ECI2psi-mi:“MI:0914”(association)0.350
RYBPPIPSLpsi-mi:“MI:0914”(association)0.350
HLA-Cpsi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350
EAF1C1orf226psi-mi:“MI:0914”(association)0.350
KCMF1CITpsi-mi:“MI:0914”(association)0.350
RNPS1WWP2psi-mi:“MI:0914”(association)0.350
RPS19ZNF316psi-mi:“MI:0914”(association)0.350
RRP7AMAGEB2psi-mi:“MI:0914”(association)0.350
UTP4POLR3Apsi-mi:“MI:0914”(association)0.350
ZCCHC10ARHGAP10psi-mi:“MI:0914”(association)0.350
ZNF692U2SURPpsi-mi:“MI:0914”(association)0.350
CDH1ESYT2psi-mi:“MI:2364”(proximity)0.270
CTDSPLESYT2psi-mi:“MI:2364”(proximity)0.270
EPHA7PIK3R2psi-mi:“MI:2364”(proximity)0.270
EPHB2ARHGAP32psi-mi:“MI:2364”(proximity)0.270
FGFR1BLTP3Bpsi-mi:“MI:2364”(proximity)0.270
NTRK1C1orf226psi-mi:“MI:2364”(proximity)0.270
NTRK3C1orf226psi-mi:“MI:2364”(proximity)0.270
ROR2SH3PXD2Bpsi-mi:“MI:2364”(proximity)0.270

BioGRID (120): TBC1D10B (Affinity Capture-MS), TBC1D10B (Affinity Capture-MS), TBC1D10B (Affinity Capture-MS), TBC1D10B (Affinity Capture-MS), TBC1D10B (Affinity Capture-MS), TBC1D10B (Affinity Capture-MS), TBC1D10B (Proximity Label-MS), TBC1D10B (Proximity Label-MS), TBC1D10B (Affinity Capture-MS), TBC1D10B (Affinity Capture-MS), TBC1D10B (Affinity Capture-MS), TBC1D10B (Affinity Capture-MS), TBC1D10B (Proximity Label-MS), TBC1D10B (Affinity Capture-MS), TBC1D10B (Affinity Capture-MS)

ESM2 similar proteins: A1L1I3, A5PKW4, O08919, O70405, O75385, O75420, O75553, P16554, P42128, P49757, P53814, P85037, P97318, P98081, Q04637, Q2LC84, Q3UCQ1, Q4KMP7, Q5DTT2, Q5I1X5, Q5RBR0, Q5VZ18, Q69ZH9, Q69ZI1, Q7TN02, Q7Z6J0, Q80VC9, Q80XI3, Q80Z38, Q86V15, Q8BGT6, Q8BHL3, Q8BSD5, Q8C120, Q8CI12, Q8IY33, Q8K4J6, Q8N3F8, Q8TEH3, Q8TEJ3

Diamond homologs: A0A087WVF3, A0A087WXS9, A0A087X179, A0A087X1G2, A2AWA9, A3KGB4, A6H6A9, A6NDS4, A6NER0, A6QP29, B0R0W9, B7ZAP0, B9A6J9, H2KZZ6, O60343, O60447, O95759, O97790, P0C7X1, P35125, P58802, P97366, Q0IIM8, Q10496, Q12317, Q12344, Q28CB1, Q3UYK3, Q4KMP7, Q5R372, Q5RAN1, Q5RCW6, Q5SVR0, Q5TC63, Q5ZJ17, Q60949, Q66K14, Q6DHY5, Q6IPX1, Q6ZT07

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 64 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
SARS-CoV-1-host interactions622.4×4e-05
SARS-CoV-1 Infection618.2×1e-04
Apoptosis517.9×6e-04
Programmed Cell Death515.6×9e-04
mRNA Splicing614.0×3e-04
SARS-CoV-2-host interactions512.7×1e-03
Metabolism of RNA1210.6×3e-07
Processing of Capped Intron-Containing Pre-mRNA610.5×9e-04

GO biological processes:

GO termPartnersFoldFDR
ribosomal small subunit biogenesis520.3×2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance52
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1432 predictions. Top by Δscore:

VariantEffectΔscore
16:30358569:GTCAC:Gacceptor_gain1.0000
16:30358570:TCAC:Tacceptor_gain1.0000
16:30358571:CAC:Cacceptor_gain1.0000
16:30358571:CACC:Cacceptor_gain1.0000
16:30358572:AC:Aacceptor_gain1.0000
16:30358573:CC:Cacceptor_gain1.0000
16:30358574:C:CCacceptor_gain1.0000
16:30358575:T:Cacceptor_loss1.0000
16:30358577:C:CTacceptor_gain1.0000
16:30358659:CTACC:Cdonor_loss1.0000
16:30358660:TACCT:Tdonor_loss1.0000
16:30358662:C:Adonor_loss1.0000
16:30358682:T:TAdonor_gain1.0000
16:30358813:AACGC:Aacceptor_gain1.0000
16:30358814:ACGC:Aacceptor_gain1.0000
16:30358815:CGC:Cacceptor_gain1.0000
16:30358815:CGCC:Cacceptor_gain1.0000
16:30358816:GC:Gacceptor_gain1.0000
16:30358817:CC:Cacceptor_gain1.0000
16:30358818:C:CCacceptor_gain1.0000
16:30358818:CT:Cacceptor_loss1.0000
16:30358821:C:CTacceptor_gain1.0000
16:30358822:A:Tacceptor_gain1.0000
16:30358826:G:Cacceptor_gain1.0000
16:30358826:G:GCacceptor_gain1.0000
16:30359722:CTGA:Cdonor_loss1.0000
16:30359723:TGACC:Tdonor_loss1.0000
16:30359726:C:Adonor_loss1.0000
16:30359726:CCT:Cdonor_gain1.0000
16:30359728:T:TAdonor_gain1.0000

AlphaMissense

5087 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:30358712:A:GL583P1.000
16:30359172:C:GG548R1.000
16:30359189:T:AD542V1.000
16:30359189:T:GD542A1.000
16:30359190:C:AD542Y1.000
16:30359190:C:GD542H1.000
16:30359193:A:GW541R1.000
16:30359193:A:TW541R1.000
16:30359214:A:GW534R1.000
16:30359214:A:TW534R1.000
16:30359219:A:GL532P1.000
16:30359236:G:CC526W1.000
16:30359237:C:TC526Y1.000
16:30359238:A:GC526R1.000
16:30359245:C:AW523C1.000
16:30359245:C:GW523C1.000
16:30359247:A:GW523R1.000
16:30359247:A:TW523R1.000
16:30359288:A:GL509P1.000
16:30359321:A:GL498P1.000
16:30359343:C:AG491W1.000
16:30359343:C:GG491R1.000
16:30359343:C:TG491R1.000
16:30359345:T:AD490V1.000
16:30359348:A:GL489P1.000
16:30359354:A:TI487N1.000
16:30359539:A:GL484P1.000
16:30359563:A:GL476P1.000
16:30359587:A:GL468P1.000
16:30359595:A:CF465L1.000

dbSNP variants (sampled 300 via entrez): RS1000062567 (16:30364676 C>T), RS1000240179 (16:30370832 TAA>T), RS1000653113 (16:30369674 C>A,G), RS1000808286 (16:30362849 C>T), RS1000947587 (16:30366666 G>T), RS1001062444 (16:30366374 A>G), RS1001274748 (16:30372325 G>A), RS1001310302 (16:30371885 C>T), RS1001619879 (16:30370491 T>A,C), RS1001773677 (16:30369942 G>C,T), RS1001890416 (16:30356707 C>A,G), RS1002090171 (16:30357050 C>T), RS1002187004 (16:30367053 G>A,C), RS1002382708 (16:30363234 T>C), RS1002410126 (16:30360068 C>G)

Disease associations

OMIM: gene MIM:613620 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST010703_269Brain morphology (MOSTest)4.000000e-13
GCST010796_3833Electrocardiogram morphology (amplitude at temporal datapoints)9.000000e-09
GCST010796_3834Electrocardiogram morphology (amplitude at temporal datapoints)3.000000e-08

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement
EFO:0004327electrocardiography

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 arseniteincreases expression, decreases expression2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
beta-lapachonedecreases expression1
perfluorooctanoic aciddecreases expression1
coumarinaffects phosphorylation1
nutlin 3affects cotreatment, increases secretion1
ICG 001decreases 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
Sunitinibincreases expression1
Air Pollutantsaffects expression, increases abundance1
Aspirinincreases expression1
Benzo(a)pyrenedecreases methylation1
Caffeineaffects phosphorylation1
Dactinomycinincreases secretion, affects cotreatment1
Diazinonincreases methylation1
Doxorubicindecreases expression1
Ivermectindecreases expression1
Ozoneaffects expression, increases abundance1
Quercetinincreases phosphorylation1
Smokedecreases expression1
Sulindacincreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutionaffects expression1
Tretinoinincreases expression1
Aflatoxin B1increases 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.