TBC1D31

gene
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Also known as MGC21654Gm85

Summary

TBC1D31 (TBC1 domain family member 31, HGNC:30888) is a protein-coding gene on chromosome 8q24.13, encoding TBC1 domain family member 31 (Q96DN5). Molecular adapter which is involved in cilium biogenesis.

Enables molecular adaptor activity. Involved in cilium assembly. Located in Golgi apparatus; centriolar satellite; and ciliary basal body.

Source: NCBI Gene 93594 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): congenital anomaly of kidney and urinary tract (Limited, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 206 total — 1 likely-pathogenic
  • MANE Select transcript: NM_145647

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30888
Approved symbolTBC1D31
NameTBC1 domain family member 31
Location8q24.13
Locus typegene with protein product
StatusApproved
AliasesMGC21654, Gm85
Ensembl geneENSG00000156787
Ensembl biotypeprotein_coding
Entrez93594

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 15 protein_coding, 3 retained_intron, 2 nonsense_mediated_decay

ENST00000287380, ENST00000327098, ENST00000518099, ENST00000518577, ENST00000518684, ENST00000518805, ENST00000518866, ENST00000519418, ENST00000520368, ENST00000521676, ENST00000521914, ENST00000521980, ENST00000522276, ENST00000522420, ENST00000524307, ENST00000865421, ENST00000865422, ENST00000865423, ENST00000865424, ENST00000948273

RefSeq mRNA: 12 — MANE Select: NM_145647 NM_001145088, NM_001330606, NM_001363148, NM_001363149, NM_001363150, NM_001363151, NM_001363152, NM_001363153, NM_001363154, NM_001363155, NM_001363156, NM_145647

CCDS: CCDS47916, CCDS6338, CCDS83320

Canonical transcript exons

ENST00000287380 — 22 exons

ExonStartEnd
ENSE00002108796123151806123152153
ENSE00002732245123072707123072846
ENSE00003459989123140761123140901
ENSE00003488166123077111123077257
ENSE00003494667123100807123101007
ENSE00003495373123142262123142456
ENSE00003503304123130198123130333
ENSE00003508854123126056123126189
ENSE00003514756123105288123105464
ENSE00003525781123097282123097441
ENSE00003542676123120055123120188
ENSE00003551006123084162123084340
ENSE00003583685123109317123109396
ENSE00003594513123129066123129218
ENSE00003604237123126508123126687
ENSE00003611368123144717123144855
ENSE00003622887123093591123093742
ENSE00003665187123150036123150128
ENSE00003680144123082702123082817
ENSE00003685499123128281123128513
ENSE00003693931123134114123134206
ENSE00003786120123109474123109620

Expression profiles

Bgee: expression breadth ubiquitous, 224 present calls, max score 96.41.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.1041 / max 117.0453, expressed in 1646 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
904707.48051632
904690.5906332
904680.033016

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065596.41gold quality
oocyteCL:000002391.56gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099188.17gold quality
ventricular zoneUBERON:000305386.74gold quality
granulocyteCL:000009484.10gold quality
cortical plateUBERON:000534382.92gold quality
ganglionic eminenceUBERON:000402382.48gold quality
monocyteCL:000057681.65gold quality
leukocyteCL:000073881.43gold quality
mononuclear cellCL:000084281.36gold quality
cerebellar hemisphereUBERON:000224581.01gold quality
buccal mucosa cellCL:000233680.87gold quality
cerebellar cortexUBERON:000212980.71gold quality
stromal cell of endometriumCL:000225580.60gold quality
right hemisphere of cerebellumUBERON:001489080.60gold quality
amniotic fluidUBERON:000017380.59gold quality
adrenal tissueUBERON:001830379.00gold quality
cerebellumUBERON:000203778.70gold quality
calcaneal tendonUBERON:000370178.52gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.51gold quality
colonic epitheliumUBERON:000039778.41gold quality
right uterine tubeUBERON:000130278.34gold quality
bloodUBERON:000017877.50gold quality
nucleus accumbensUBERON:000188277.35gold quality
caudate nucleusUBERON:000187377.25gold quality
bone marrow cellCL:000209276.35gold quality
embryoUBERON:000092276.30gold quality
hindlimb stylopod muscleUBERON:000425275.79gold quality
right frontal lobeUBERON:000281075.64gold quality
lymph nodeUBERON:000002975.58gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-9543yes20.99
E-CURD-112yes7.24
E-ANND-3yes5.57

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

19 targeting TBC1D31, 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-5692A100.0074.406850
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-548AW99.9972.573559
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-1213699.9872.815713
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-590-3P99.9674.346478
HSA-MIR-153-5P99.8973.866317
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646
HSA-MIR-2115-3P99.3169.682026
HSA-MIR-548L99.0670.902560
HSA-MIR-570198.9769.541502
HSA-MIR-361-5P98.9570.161340
HSA-MIR-340-3P98.1168.25679
HSA-MIR-6827-3P98.0872.27651
HSA-MIR-4446-3P97.9164.29991

Literature-anchored findings (GeneRIF, showing 2)

  • A novel homozygous missense variant in TBC1D31 in a consanguineous family with congenital anomalies of the kidney and urinary tract (CAKUT). (PMID:37468454)
  • Genomic Amplification of TBC1D31 Promotes Hepatocellular Carcinoma Through Reducing the Rab22A-Mediated Endolysosomal Trafficking and Degradation of EGFR. (PMID:39206796)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotbc1d31ENSDARG00000074623
mus_musculusTbc1d31ENSMUSG00000022364
rattus_norvegicusTbc1d31ENSRNOG00000006103
drosophila_melanogasterCG16896FBGN0035073
caenorhabditis_elegansWBGENE00017435

Paralogs (1): WDR3 (ENSG00000065183)

Protein

Protein identifiers

TBC1 domain family member 31Q96DN5 (reviewed: Q96DN5)

Alternative names: WD repeat-containing protein 67

All UniProt accessions (11): Q96DN5, E5RFG6, E5RG45, E5RHC6, E5RI27, E5RI94, E7ERK7, E7EWW7, F5GYF1, H0YCP2, H0YCY3

UniProt curated annotations — full annotation on UniProt →

Function. Molecular adapter which is involved in cilium biogenesis. Part of a functional complex including OFD1 a centriolar protein involved in cilium assembly. Could regulate the cAMP-dependent phosphorylation of OFD1, and its subsequent ubiquitination by PJA2 which ultimately leads to its proteasomal degradation.

Subunit / interactions. Interacts with PJA2; the interaction is direct and recruits PJA2 to centrosomes. Interacts with OFD1; regulates its activity in cilium assembly. Interacts with PRKACA.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriolar satellite. Cilium basal body.

Isoforms (3)

UniProt IDNamesCanonical?
Q96DN5-11yes
Q96DN5-22
Q96DN5-33

RefSeq proteins (12): NP_001138560, NP_001317535, NP_001350077, NP_001350078, NP_001350079, NP_001350080, NP_001350081, NP_001350082, NP_001350083, NP_001350084, NP_001350085, NP_663622* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000195Rab-GAP-TBC_domDomain
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR035969Rab-GAP_TBC_sfHomologous_superfamily
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR051570TBC1_cilium_biogenesisFamily

Pfam: PF00400, PF00566

UniProt features (23 total): repeat 7, sequence variant 3, region of interest 2, coiled-coil region 2, compositionally biased region 2, splice variant 2, sequence conflict 2, chain 1, mutagenesis site 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96DN5-F176.360.23

Functional residue map

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

Mutagenesis-validated functional residues (1):

PositionPhenotype
1053–1056loss of interaction with pja2.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 157 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, BROWNE_HCMV_INFECTION_6HR_DN, GOCC_MICROTUBULE_ORGANIZING_CENTER, PUJANA_CHEK2_PCC_NETWORK, MORF_ZNF10, GOBP_CILIUM_ORGANIZATION, GOCC_CENTROSOME, GOBP_ORGANELLE_ASSEMBLY, MORF_EPHA7, MORF_RAB3A, MORF_BMPR2, FISCHER_DREAM_TARGETS, GOBP_CELL_PROJECTION_ORGANIZATION, LIU_VMYB_TARGETS_UP, WANG_PROSTATE_CANCER_ANDROGEN_INDEPENDENT

GO Biological Process (2): cilium assembly (GO:0060271), cell projection organization (GO:0030030)

GO Molecular Function (2): molecular adaptor activity (GO:0060090), protein binding (GO:0005515)

GO Cellular Component (7): Golgi apparatus (GO:0005794), centrosome (GO:0005813), centriolar satellite (GO:0034451), ciliary basal body (GO:0036064), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
binding2
microtubule organizing center2
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
cellular component organization1
molecular_function1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
centriole1
centrosome1
cilium1
intracellular anatomical structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

1262 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TBC1D31DHX35Q9H5Z1625
TBC1D31CCDC138Q96M89602
TBC1D31CCDC61Q9Y6R9553
TBC1D31RAB5IFQ9BUV8508
TBC1D31PIBF1Q8WXW3504
TBC1D31NOL10Q9BSC4492
TBC1D31DERL1Q9BUN8491
TBC1D31CEP20Q96NB1488
TBC1D31WDFY2Q96P53488
TBC1D31ATAD2Q6PL18469
TBC1D31ZHX3Q9H4I2456
TBC1D31GGT7Q9UJ14456
TBC1D31RPN2P04844450
TBC1D31ZNF704Q6ZNC4447
TBC1D31CSTPP1Q9H6J7445

IntAct

34 interactions, top by confidence:

ABTypeScore
MED4MED19psi-mi:“MI:2364”(proximity)0.900
CEP290CCP110psi-mi:“MI:2364”(proximity)0.890
LTBRZNF724psi-mi:“MI:0914”(association)0.530
DYNC2I2TCP1psi-mi:“MI:0914”(association)0.530
KIAA0753OFD1psi-mi:“MI:2364”(proximity)0.480
Cep135psi-mi:“MI:0914”(association)0.350
Cep131WBP2psi-mi:“MI:0914”(association)0.350
OFD1CCDC14psi-mi:“MI:0914”(association)0.350
Lrrcc1CCDC14psi-mi:“MI:0914”(association)0.350
CEP162IPO5psi-mi:“MI:0914”(association)0.350
TANKCNOT1psi-mi:“MI:0914”(association)0.350
RYBPFAM186Apsi-mi:“MI:0914”(association)0.350
CEP63CIBAR1psi-mi:“MI:0914”(association)0.350
FTLSH3PXD2Bpsi-mi:“MI:0914”(association)0.350
RNF7SOCS2psi-mi:“MI:0914”(association)0.350
PCM1CCDC66psi-mi:“MI:2364”(proximity)0.270
KIAA0753DVL1psi-mi:“MI:2364”(proximity)0.270
CEP128CCDC66psi-mi:“MI:2364”(proximity)0.270
ODF2CCDC66psi-mi:“MI:2364”(proximity)0.270
CEP162CCDC66psi-mi:“MI:2364”(proximity)0.270
CEP135CCDC66psi-mi:“MI:2364”(proximity)0.270
CNTRLCCDC85Cpsi-mi:“MI:2364”(proximity)0.270
LCA5CCDC66psi-mi:“MI:2364”(proximity)0.270
SPICE1CCDC66psi-mi:“MI:2364”(proximity)0.270
CEP120CCDC66psi-mi:“MI:2364”(proximity)0.270
CEP63CCDC66psi-mi:“MI:2364”(proximity)0.270
CEP89CCDC66psi-mi:“MI:2364”(proximity)0.270
SSX2IPCNOT1psi-mi:“MI:2364”(proximity)0.270

BioGRID (78): TBC1D31 (Affinity Capture-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Affinity Capture-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS), TBC1D31 (Proximity Label-MS)

ESM2 similar proteins: A0JM23, A4IGD2, A5PKL6, A6NHR9, A6QQZ0, D3ZAT9, F1QWA8, O35099, O88741, O94952, P0CI65, P58005, Q29RL0, Q2TBQ7, Q3U213, Q3UMF9, Q4R6P7, Q4R6Y8, Q5E9N5, Q5F204, Q5HYI7, Q5I0G3, Q5IH14, Q5R5S1, Q5R9R1, Q5RL51, Q5TGI0, Q60649, Q6AZT7, Q6DDI6, Q6DDT5, Q6DEY8, Q6NXY1, Q6YXW6, Q7TNH6, Q7Z494, Q8NBP0, Q8NEC7, Q8TB36, Q94E75

Diamond homologs: H2LP95, Q29RL0, Q5RD21, Q6DDI6, Q6DEY8, Q6NXY1, Q96DN5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 44 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
Loss of Nlp from mitotic centrosomes845.3×2e-10
Loss of proteins required for interphase microtubule organization from the centrosome845.3×2e-10
AURKA Activation by TPX2843.5×2e-10
Anchoring of the basal body to the plasma membrane1040.4×3e-12
Recruitment of mitotic centrosome proteins and complexes838.8×4e-10
Regulation of PLK1 Activity at G2/M Transition836.2×6e-10
Recruitment of NuMA to mitotic centrosomes833.3×1e-09
Cilium Assembly519.4×8e-05

GO biological processes:

GO termPartnersFoldFDR
cilium assembly1120.2×1e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance153
Likely benign18
Benign1

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2671821NM_145647.4(TBC1D31):c.187C>G (p.Gln63Glu)Likely pathogenic

SpliceAI

4834 predictions. Top by Δscore:

VariantEffectΔscore
8:123077106:GACA:Gacceptor_loss1.0000
8:123077107:ACAG:Aacceptor_loss1.0000
8:123077108:CAG:Cacceptor_loss1.0000
8:123077109:A:AGacceptor_gain1.0000
8:123077109:A:Cacceptor_loss1.0000
8:123077110:G:GAacceptor_gain1.0000
8:123077110:G:GTacceptor_loss1.0000
8:123077110:GA:Gacceptor_gain1.0000
8:123077110:GAATT:Gacceptor_gain1.0000
8:123077254:ACAGG:Adonor_loss1.0000
8:123077255:CAGGT:Cdonor_loss1.0000
8:123077256:AGGTA:Adonor_loss1.0000
8:123077258:GT:Gdonor_loss1.0000
8:123077259:T:Gdonor_loss1.0000
8:123084160:A:AGacceptor_gain1.0000
8:123084161:G:GGacceptor_gain1.0000
8:123097271:T:Aacceptor_gain1.0000
8:123097276:A:AGacceptor_gain1.0000
8:123097277:T:Gacceptor_gain1.0000
8:123097279:T:Gacceptor_gain1.0000
8:123097280:A:AGacceptor_gain1.0000
8:123097280:A:Cacceptor_loss1.0000
8:123097281:G:GAacceptor_gain1.0000
8:123097281:GA:Gacceptor_gain1.0000
8:123097281:GAGA:Gacceptor_gain1.0000
8:123097281:GAGAT:Gacceptor_gain1.0000
8:123097437:ATCAG:Adonor_loss1.0000
8:123097439:CAGG:Cdonor_loss1.0000
8:123097440:AGGTT:Adonor_loss1.0000
8:123097441:GG:Gdonor_loss1.0000

AlphaMissense

7098 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:123084275:T:AW152R1.000
8:123084275:T:CW152R1.000
8:123093624:A:CS185R0.999
8:123093626:C:AS185R0.999
8:123093626:C:GS185R0.999
8:123093654:T:AW195R0.999
8:123093654:T:CW195R0.999
8:123109484:T:AW434R0.999
8:123109484:T:CW434R0.999
8:123084243:C:AA141D0.998
8:123084249:C:AT143K0.998
8:123084277:G:CW152C0.998
8:123084277:G:TW152C0.998
8:123093656:G:CW195C0.998
8:123093656:G:TW195C0.998
8:123126565:T:AW588R0.998
8:123126565:T:CW588R0.998
8:123082782:C:AA102E0.997
8:123084249:C:GT143R0.997
8:123084276:G:CW152S0.997
8:123084309:T:CL163P0.996
8:123097331:T:AW241R0.996
8:123097331:T:CW241R0.996
8:123120168:A:TE517V0.996
8:123084267:C:AA149E0.995
8:123093622:T:CL184P0.995
8:123093655:G:CW195S0.995
8:123109380:T:GY425D0.995
8:123109396:G:CR430T0.995
8:123126580:G:CD593H0.995

dbSNP variants (sampled 300 via entrez): RS1000044187 (8:123102826 T>C), RS1000060093 (8:123126236 T>A,C), RS1000093734 (8:123109708 T>C), RS1000116599 (8:123103933 C>G), RS1000154921 (8:123156848 G>A), RS1000155803 (8:123110023 G>A), RS1000189035 (8:123148872 A>G), RS1000189438 (8:123155184 T>TTGA), RS1000222498 (8:123084462 CAAGCA>C), RS1000241813 (8:123161039 G>A), RS1000294610 (8:123084241 T>C,G), RS1000321967 (8:123109865 G>A), RS1000322948 (8:123080358 A>G), RS1000332792 (8:123135772 A>C,G), RS1000347381 (8:123155449 C>A,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
congenital anomaly of kidney and urinary tractLimitedAutosomal recessive

Mondo (1): congenital anomaly of kidney and urinary tract (MONDO:0019719)

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST003098_17Diabetic kidney disease6.000000e-08

MeSH disease descriptors (1)

DescriptorNameTree numbers
C566906Cakut (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression, affects expression4
Benzo(a)pyrenedecreases expression, decreases methylation, increases expression3
bisphenol Adecreases expression, increases expression2
Cisplatinaffects cotreatment, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Tetrachlorodibenzodioxindecreases expression2
bisphenol Fincreases methylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
trichostatin Aincreases expression1
methylparabendecreases expression1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangaffects cotreatment, increases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomideincreases expression1
Acetaminophenincreases expression1
Ethanoldecreases expression, increases abundance, affects cotreatment1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Doxorubicindecreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Methyl Methanesulfonateincreases expression1
Nickelincreases expression1
Perfumeincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT04115345PHASE1COMPLETEDA Study of a Renal Autologous Cell Therapy (REACT) in Patients With Chronic Kidney Disease (CKD) From Congenital Anomalies of the Kidney and Urinary Tract (CAKUT).
NCT05694169PHASE1TERMINATEDA Study of Participants With Chronic Kidney Disease Previously Treated With REACT
NCT04537364Not specifiedCOMPLETEDPrediction of Renal Parenchymal Damage of CAKUT
NCT06921733Not specifiedRECRUITINGUltrasound Localization Microscopy in Patient With Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)