TBC1D10C

gene
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Also known as FLJ00332CarabinEPI64C

Summary

TBC1D10C (TBC1 domain family member 10C, HGNC:24702) is a protein-coding gene on chromosome 11q13.2, encoding Carabin (Q8IV04). Inhibits the Ras signaling pathway through its intrinsic Ras GTPase-activating protein (GAP) activity.

The protein encoded by this gene has an N-terminal Rab-GTPase domain and a binding site at the C-terminus for calcineurin, and is an inhibitor of both the Ras signaling pathway and calcineurin, a phosphatase regulated by calcium and calmodulin. Genes encoding similar proteins are located on chromosomes 16 and 22. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 374403 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 87 total
  • MANE Select transcript: NM_001369496

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24702
Approved symbolTBC1D10C
NameTBC1 domain family member 10C
Location11q13.2
Locus typegene with protein product
StatusApproved
AliasesFLJ00332, Carabin, EPI64C
Ensembl geneENSG00000175463
Ensembl biotypeprotein_coding
OMIM610831
Entrez374403

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 15 protein_coding, 5 retained_intron, 1 nonsense_mediated_decay

ENST00000312390, ENST00000524662, ENST00000526387, ENST00000526474, ENST00000529132, ENST00000529635, ENST00000530967, ENST00000533745, ENST00000542590, ENST00000868931, ENST00000868932, ENST00000868933, ENST00000868934, ENST00000868935, ENST00000868936, ENST00000946007, ENST00000946008, ENST00000946009, ENST00000946010, ENST00000946011, ENST00000946012

RefSeq mRNA: 8 — MANE Select: NM_001369496 NM_001256508, NM_001369492, NM_001369494, NM_001369495, NM_001369496, NM_001369497, NM_001369498, NM_198517

CCDS: CCDS58150, CCDS8162

Canonical transcript exons

ENST00000542590 — 9 exons

ExonStartEnd
ENSE000021541486740408367404354
ENSE000022272026740940767410089
ENSE000034619416740539967405506
ENSE000035005506740590367406017
ENSE000035579636740662767406692
ENSE000035705856740559567405701
ENSE000035965006740508567405184
ENSE000036425586740897967409133
ENSE000036939196740682767407016

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 99.24.

FANTOM5 (CAGE): breadth broad, TPM avg 4.2513 / max 159.2340, expressed in 325 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1154492.6904255
1154480.7466185
1154520.345783
1154530.200490
1154500.149074
1154510.119266

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009499.24gold quality
bloodUBERON:000017896.71gold quality
spleenUBERON:000210695.98gold quality
lymph nodeUBERON:000002995.54gold quality
bone marrow cellCL:000209294.77gold quality
vermiform appendixUBERON:000115494.19gold quality
thymusUBERON:000237092.73gold quality
leukocyteCL:000073891.98gold quality
monocyteCL:000057691.49gold quality
bone marrowUBERON:000237190.35gold quality
caecumUBERON:000115387.75gold quality
small intestine Peyer’s patchUBERON:000345486.48gold quality
tonsilUBERON:000237285.31gold quality
small intestineUBERON:000210883.92gold quality
mucosa of transverse colonUBERON:000499182.74gold quality
right lobe of thyroid glandUBERON:000111982.62gold quality
upper lobe of left lungUBERON:000895281.80gold quality
left lobe of thyroid glandUBERON:000112081.73gold quality
right lungUBERON:000216781.33gold quality
thyroid glandUBERON:000204681.10gold quality
upper lobe of lungUBERON:000894880.81gold quality
colonic epitheliumUBERON:000039780.61gold quality
gall bladderUBERON:000211080.44gold quality
trabecular bone tissueUBERON:000248379.54gold quality
epithelium of nasopharynxUBERON:000195178.80gold quality
right uterine tubeUBERON:000130277.44gold quality
lungUBERON:000204875.98gold quality
body of stomachUBERON:000116175.43gold quality
superficial temporal arteryUBERON:000161475.13silver quality
duodenumUBERON:000211475.01gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-MTAB-6701yes32.50
E-MTAB-10287yes30.65
E-MTAB-8410yes13.84
E-ANND-3yes8.88
E-CURD-120no7.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting TBC1D10C, 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-5193100.0067.261744
HSA-MIR-5580-5P99.3866.961139
HSA-MIR-4758-3P99.1263.96869
HSA-MIR-4699-5P98.9967.501210
HSA-MIR-4742-5P98.8968.411542
HSA-MIR-5006-5P98.7966.921246
HSA-MIR-26B-3P98.7167.491102
HSA-MIR-615-5P98.1063.76591
HSA-MIR-63797.9164.051517
HSA-MIR-1271-3P97.5664.85865
HSA-MIR-550A-3-5P97.5665.35823
HSA-MIR-550A-5P97.5665.35823
HSA-MIR-428697.2064.371587
HSA-MIR-5588-3P94.9665.59500

Literature-anchored findings (GeneRIF, showing 5)

  • Carabin inhibits calcineurin and Ras and was identified by a yeast-two-hybrid screen with calcineurin (PMID:17230191)
  • Carabin is a negative feedback inhibitor of the calcineurin signalling pathway that also mediates crosstalk between calcineurin and Ras (PMID:17230191)
  • Carabin as a new negative regulator of B-cell function, whose deficiency in B cells speeds up early B-cell responses (PMID:23109291)
  • identify prolyl 4-hydroxylase 2 (P4HA2) as a specific proline hydroxylase of Carabin. Carabin hydroxylation leads to its proteasomal degradation, thereby activating the Ras/extracellular signal-regulated kinase pathway and increasing B-cell lymphoma proliferation. (PMID:29437589)
  • Weighted Gene Coexpression Network Analysis Identifies TBC1D10C as a New Prognostic Biomarker for Breast Cancer. (PMID:35425695)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotbc1d10cENSDARG00000037408
mus_musculusTbc1d10cENSMUSG00000040247
rattus_norvegicusTbc1d10cENSRNOG00000021510

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), TBC1D10B (ENSG00000169221), TBC1D28 (ENSG00000189375), TBC1D9B (ENSG00000197226), TBC1D8 (ENSG00000204634), TBC1D26 (ENSG00000214946), TBC1D3G (ENSG00000260287), TBC1D3K (ENSG00000273513), TBC1D3H (ENSG00000274226), TBC1D3D (ENSG00000274419), TBC1D3L (ENSG00000274512), TBC1D3 (ENSG00000274611)

Protein

Protein identifiers

CarabinQ8IV04 (reviewed: Q8IV04)

Alternative names: TBC1 domain family member 10C

All UniProt accessions (2): E9PSB7, Q8IV04

UniProt curated annotations — full annotation on UniProt →

Function. Inhibits the Ras signaling pathway through its intrinsic Ras GTPase-activating protein (GAP) activity. Acts as a negative feedback inhibitor of the calcineurin signaling pathway that also mediates crosstalk between calcineurin and Ras.

Subunit / interactions. Interacts with both calcineurin and HRAS.

Tissue specificity. Most abundant in spleen and peripheral blood leukocytes.

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 (2)

UniProt IDNamesCanonical?
Q8IV04-11yes
Q8IV04-22

RefSeq proteins (8): NP_001243437, NP_001356421, NP_001356423, NP_001356424, NP_001356425, NP_001356426, NP_001356427, NP_940919 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000195Rab-GAP-TBC_domDomain
IPR035969Rab-GAP_TBC_sfHomologous_superfamily
IPR050302Rab_GAP_TBC_domainFamily

Pfam: PF00566

UniProt features (13 total): region of interest 3, compositionally biased region 3, splice variant 2, site 2, chain 1, domain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IV04-F182.080.69

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): 137 (arginine finger); 178 (glutamine finger)

Mutagenesis-validated functional residues (1):

PositionPhenotype
141loss of gap activity.

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-6798695Neutrophil degranulation
R-HSA-8854214TBC/RABGAPs
R-HSA-168249Innate Immune System
R-HSA-168256Immune System
R-HSA-199991Membrane Trafficking
R-HSA-5653656Vesicle-mediated transport
R-HSA-9007101Rab regulation of trafficking

MSigDB gene sets: 169 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_NEGATIVE_REGULATION_OF_ERK1_AND_ERK2_CASCADE, REACTOME_INNATE_IMMUNE_SYSTEM, ZHAN_MULTIPLE_MYELOMA_PR_DN, GOBP_REGULATION_OF_CALCIUM_MEDIATED_SIGNALING, GOBP_B_CELL_ACTIVATION, GOCC_SECRETORY_GRANULE, GOBP_NEGATIVE_REGULATION_OF_B_CELL_ACTIVATION, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, chr11q13, GOBP_NEGATIVE_REGULATION_OF_MAPK_CASCADE, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS

GO Biological Process (7): calcineurin-NFAT signaling cascade (GO:0033173), B cell activation (GO:0042113), retrograde transport, endosome to Golgi (GO:0042147), negative regulation of B cell activation (GO:0050869), ERK1 and ERK2 cascade (GO:0070371), negative regulation of ERK1 and ERK2 cascade (GO:0070373), negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)

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

GO Cellular Component (5): cytosol (GO:0005829), plasma membrane (GO:0005886), membrane (GO:0016020), filopodium membrane (GO:0031527), ficolin-1-rich granule membrane (GO:0101003)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Innate Immune System1
Rab regulation of trafficking1
Immune System1
Vesicle-mediated transport1
Membrane Trafficking1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
calcineurin-mediated signaling1
lymphocyte activation1
intercellular transport1
endosomal transport1
cytosolic transport1
B cell activation1
regulation of B cell activation1
negative regulation of lymphocyte activation1
MAPK cascade1
negative regulation of MAPK cascade1
ERK1 and ERK2 cascade1
regulation of ERK1 and ERK2 cascade1
calcineurin-NFAT signaling cascade1
regulation of calcineurin-NFAT signaling cascade1
negative regulation of calcineurin-mediated signaling1
GTPase activity1
enzyme activator activity1
GTPase regulator activity1
binding1
cytoplasm1
membrane1
cell periphery1
filopodium1
cell projection membrane1
secretory granule membrane1
tertiary granule1
ficolin-1-rich granule1

Protein interactions and networks

STRING

940 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TBC1D10CRASA1P20936667
TBC1D10CTBC1D13Q9NVG8618
TBC1D10CRAB35Q15286609
TBC1D10CTBC1D22BQ9NU19593
TBC1D10CTBC1D19Q8N5T2592
TBC1D10CTBC1D21Q8IYX1589
TBC1D10CTBC1D20Q96BZ9539
TBC1D10CTBC1D5Q92609527
TBC1D10CTBC1D22AQ8WUA7482
TBC1D10CTBC1D7Q9P0N9474
TBC1D10CTBC1D15Q8TC07440
TBC1D10CTBC1D16Q8TBP0427
TBC1D10CTBC1D17Q9HA65426
TBC1D10CIL2P01585424
TBC1D10CACAP1Q15027415

IntAct

25 interactions, top by confidence:

ABTypeScore
TBC1D10CHOXA1psi-mi:“MI:0915”(physical association)0.720
KLHL12TBC1D10Cpsi-mi:“MI:0915”(physical association)0.720
HOXA1TBC1D10Cpsi-mi:“MI:0915”(physical association)0.720
TBC1D10CKLHL12psi-mi:“MI:0915”(physical association)0.720
TBC1D10CKRTAP5-9psi-mi:“MI:0915”(physical association)0.560
NOTCH2NLATBC1D10Cpsi-mi:“MI:0915”(physical association)0.560
TBC1D10Cpsi-mi:“MI:0915”(physical association)0.560
KRTAP5-9TBC1D10Cpsi-mi:“MI:0915”(physical association)0.560
TBC1D10CNOTCH2NLApsi-mi:“MI:0915”(physical association)0.560
SHANK1TBC1D10Cpsi-mi:“MI:0407”(direct interaction)0.440
METTL3TUBAL3psi-mi:“MI:0914”(association)0.350
CHD8IGLV4-60psi-mi:“MI:0914”(association)0.350
TBC1D10CKLHL12psi-mi:“MI:0915”(physical association)0.000
TBC1D10CHOXA1psi-mi:“MI:0915”(physical association)0.000

BioGRID (16): TBC1D10C (Two-hybrid), TBC1D10C (Two-hybrid), TBC1D10C (Two-hybrid), TBC1D10C (Two-hybrid), NOTCH2NL (Two-hybrid), TBC1D10C (Affinity Capture-MS), TBC1D10C (Two-hybrid), TBC1D10C (Two-hybrid), TBC1D10C (Affinity Capture-MS), TBC1D10C (Affinity Capture-RNA), TBC1D10C (Affinity Capture-MS), TBC1D10C (Affinity Capture-MS), TBC1D10C (Affinity Capture-MS), TBC1D10C (Affinity Capture-MS), TBC1D10C (Reconstituted Complex)

ESM2 similar proteins: A6H8I2, A6QP29, B1AVH7, B2DD29, B5DFA1, D2H0G5, O14976, O43147, O60343, O95398, P58802, P98171, Q08493, Q2KI13, Q3U1Y4, Q4KMP7, Q5DU57, Q5RJI5, Q5SVR0, Q60949, Q66K14, Q69Z98, Q6P6R7, Q6TLK4, Q7T2D0, Q7TSI1, Q80U12, Q86TI0, Q86VW2, Q8BHL3, Q8BYJ6, Q8C9V1, Q8IV04, Q8IWQ3, Q8K337, Q8TC07, Q8TDC3, Q8TDY4, Q8VCC8, Q8VCZ6

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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance70
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2637 predictions. Top by Δscore:

VariantEffectΔscore
11:67398643:GAT:Gacceptor_gain1.0000
11:67398646:C:CCacceptor_gain1.0000
11:67398646:CTA:Cacceptor_loss1.0000
11:67398717:CTCA:Cdonor_loss1.0000
11:67398718:TCA:Tdonor_loss1.0000
11:67398719:CACCT:Cdonor_loss1.0000
11:67398720:A:ACdonor_gain1.0000
11:67398720:ACCTG:Adonor_loss1.0000
11:67398721:C:CCdonor_gain1.0000
11:67398721:C:CTdonor_loss1.0000
11:67398721:CCT:Cdonor_gain1.0000
11:67398852:ACCAC:Aacceptor_gain1.0000
11:67398853:CCAC:Cacceptor_gain1.0000
11:67398853:CCACC:Cacceptor_gain1.0000
11:67398854:C:CTacceptor_gain1.0000
11:67398854:CAC:Cacceptor_gain1.0000
11:67398855:AC:Aacceptor_gain1.0000
11:67398856:CC:Cacceptor_gain1.0000
11:67398857:C:CCacceptor_gain1.0000
11:67398857:C:Tacceptor_gain1.0000
11:67398862:C:CTacceptor_gain1.0000
11:67398937:CACC:Cdonor_loss1.0000
11:67398938:ACC:Adonor_loss1.0000
11:67399159:CAGGC:Cacceptor_gain1.0000
11:67399160:AGGC:Aacceptor_gain1.0000
11:67399161:GGC:Gacceptor_gain1.0000
11:67399164:C:CCacceptor_gain1.0000
11:67399164:CTG:Cacceptor_loss1.0000
11:67399173:C:CTacceptor_gain1.0000
11:67399555:CCTCA:Cdonor_loss1.0000

AlphaMissense

2817 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:67405450:T:AW102R0.999
11:67405450:T:CW102R0.999
11:67405452:G:CW102C0.999
11:67405452:G:TW102C0.999
11:67405679:T:CF149L0.999
11:67405681:T:AF149L0.999
11:67405681:T:GF149L0.999
11:67404326:T:CF42L0.998
11:67404327:T:CF42S0.998
11:67404328:C:AF42L0.998
11:67404328:C:GF42L0.998
11:67405131:T:AW67R0.998
11:67405131:T:CW67R0.998
11:67405133:G:CW67C0.998
11:67405133:G:TW67C0.998
11:67405680:T:CF149S0.998
11:67405680:T:GF149C0.998
11:67406998:G:CD274H0.998
11:67405638:T:AI135N0.997
11:67405647:A:CD138A0.997
11:67405661:T:CF143L0.997
11:67405662:T:CF143S0.997
11:67405663:C:AF143L0.997
11:67405663:C:GF143L0.997
11:67405679:T:AF149I0.997
11:67405989:C:AA185D0.997
11:67406633:T:CF197L0.997
11:67406635:C:AF197L0.997
11:67406635:C:GF197L0.997
11:67406995:T:AW273R0.997

dbSNP variants (sampled 300 via entrez): RS1000494452 (11:67405426 C>G), RS1000661218 (11:67410532 C>T), RS1000966734 (11:67407765 C>T), RS1001102815 (11:67407496 G>A,C), RS1001692033 (11:67403596 G>A,C), RS1001955345 (11:67405769 TAGCCC>T), RS1001984746 (11:67402021 G>T), RS1002136281 (11:67408147 G>C), RS1002247918 (11:67402240 C>G), RS1002455779 (11:67410088 G>A), RS1002565261 (11:67408710 C>T), RS1002614623 (11:67408442 A>C), RS1002962900 (11:67404913 T>A,C), RS1003113814 (11:67404560 G>A), RS1003704599 (11:67403352 A>T)

Disease associations

OMIM: gene MIM:610831 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST007293_14Body fat distribution (arm fat ratio)9.000000e-08
GCST007294_129Body fat distribution (trunk fat ratio)8.000000e-28
GCST007294_95Body fat distribution (trunk fat ratio)1.000000e-35
GCST007295_43Body fat distribution (leg fat ratio)1.000000e-25
GCST007295_76Body fat distribution (leg fat ratio)1.000000e-21

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004341body fat distribution

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
GSK-J4decreases expression1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
perfluorooctanoic aciddecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression, affects response to substance, increases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
perfluoro-n-nonanoic aciddecreases expression1
perfluorohexanesulfonic aciddecreases expression1
(+)-JQ1 compounddecreases expression1
Air Pollutantsaffects expression, increases abundance1
Benzo(a)pyreneincreases expression1
Lipopolysaccharidesdecreases expression, affects response to substance, increases expression, affects cotreatment1
Nickelincreases expression1
Ozoneaffects expression, increases abundance1
Tretinoinincreases expression1
Aflatoxin B1increases expression1
Antirheumatic Agentsdecreases expression1

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.