TBC1D30

Summary

TBC1D30 (TBC1 domain family member 30, HGNC:29164) is a protein-coding gene on chromosome 12q14.3, encoding TBC1 domain family member 30 (Q9Y2I9). May act as a GTPase-activating protein for Rab family protein(s).

Enables GTPase activator activity and small GTPase binding activity. Involved in negative regulation of cilium assembly and positive regulation of GTPase activity. Located in several cellular components, including ciliary basal body; cytosol; and nuclear body.

Source: NCBI Gene 23329 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 120 total
• MANE Select transcript: NM_015279

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29164
Approved symbol	TBC1D30
Name	TBC1 domain family member 30
Location	12q14.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0984
Ensembl gene	ENSG00000111490
Ensembl biotype	protein_coding
OMIM	615077
Entrez	23329

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000434563, ENST00000456757, ENST00000539120, ENST00000539867, ENST00000542120, ENST00000544457, ENST00000674171, ENST00000674237

RefSeq mRNA: 5 — MANE Select: NM_015279 NM_001330186, NM_001330187, NM_001330188, NM_001364838, NM_015279

CCDS: CCDS53813, CCDS81708

Canonical transcript exons

ENST00000539867 — 12 exons

Exon	Start	End
ENSE00000802691	64838683	64838851
ENSE00000802692	64836490	64836658
ENSE00000802693	64832119	64832304
ENSE00000937230	64843380	64843485
ENSE00000937231	64864668	64864780
ENSE00000937232	64866764	64866903
ENSE00000937233	64870602	64870808
ENSE00002248502	64824647	64825033
ENSE00002296319	64875001	64881033
ENSE00003488219	64830377	64830502
ENSE00003503732	64828444	64828509
ENSE00003597554	64827835	64827896

Expression profiles

Bgee: expression breadth ubiquitous, 233 present calls, max score 95.74.

FANTOM5 (CAGE): breadth broad, TPM avg 4.1434 / max 120.5771, expressed in 785 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
126478	2.1274	263
126475	1.2425	555
126473	0.4188	204
126474	0.3113	163
126479	0.0434	25

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	95.74	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.33	gold quality
cortical plate	UBERON:0005343	91.71	gold quality
middle temporal gyrus	UBERON:0002771	88.39	gold quality
primary visual cortex	UBERON:0002436	86.64	gold quality
pigmented layer of retina	UBERON:0001782	83.84	gold quality
body of pancreas	UBERON:0001150	83.53	gold quality
occipital lobe	UBERON:0002021	83.01	gold quality
pancreas	UBERON:0001264	82.84	gold quality
islet of Langerhans	UBERON:0000006	82.53	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.30	gold quality
postcentral gyrus	UBERON:0002581	80.04	gold quality
Brodmann (1909) area 46	UBERON:0006483	79.92	gold quality
superior frontal gyrus	UBERON:0002661	79.82	gold quality
pons	UBERON:0000988	79.75	gold quality
pituitary gland	UBERON:0000007	79.71	gold quality
adenohypophysis	UBERON:0002196	79.35	gold quality
parietal lobe	UBERON:0001872	79.24	gold quality
prefrontal cortex	UBERON:0000451	79.21	gold quality
entorhinal cortex	UBERON:0002728	78.67	gold quality
cerebellar vermis	UBERON:0004720	78.11	gold quality
frontal cortex	UBERON:0001870	78.00	gold quality
neocortex	UBERON:0001950	77.79	gold quality
orbitofrontal cortex	UBERON:0004167	77.50	gold quality
cerebral cortex	UBERON:0000956	77.33	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	77.24	gold quality
CA1 field of hippocampus	UBERON:0003881	77.17	gold quality
mucosa of transverse colon	UBERON:0004991	77.14	gold quality
cerebellum	UBERON:0002037	77.00	gold quality
epithelial cell of pancreas	CL:0000083	76.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

185 targeting TBC1D30, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-9983-3P	99.94	71.48	3631

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tbc1d30	ENSDARG00000075281
mus_musculus	Tbc1d30	ENSMUSG00000052302
rattus_norvegicus	Tbc1d30	ENSRNOG00000023951

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), 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 30 — Q9Y2I9 (reviewed: Q9Y2I9)

All UniProt accessions (5): Q9Y2I9, A0A6I8PRH3, F5H0E8, F5H7L7, F8VZ81

UniProt curated annotations — full annotation on UniProt →

Function. May act as a GTPase-activating protein for Rab family protein(s).

Subcellular location. Cell membrane.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9Y2I9-1	1	yes
Q9Y2I9-2	2
Q9Y2I9-3	3
Q9Y2I9-4	4

RefSeq proteins (5): NP_001317115, NP_001317116, NP_001317117, NP_001351767, NP_056094* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000195	Rab-GAP-TBC_dom	Domain
IPR032738	Tbc1d30_C	Domain
IPR035969	Rab-GAP_TBC_sf	Homologous_superfamily

Pfam: PF00566, PF15733

UniProt features (21 total): compositionally biased region 5, region of interest 5, sequence variant 4, splice variant 3, chain 1, domain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y2I9-F1	58.63	0.20

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 (1): 800

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 131 (showing top): GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOMF_GTPASE_BINDING, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_NEGATIVE_REGULATION_OF_ORGANELLE_ASSEMBLY, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, SMID_BREAST_CANCER_LUMINAL_B_UP, GOBP_CILIUM_ORGANIZATION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, GOBP_ORGANELLE_ASSEMBLY

GO Biological Process (2): positive regulation of GTPase activity (GO:0043547), negative regulation of cilium assembly (GO:1902018)

GO Molecular Function (3): GTPase activator activity (GO:0005096), small GTPase binding (GO:0031267), protein binding (GO:0005515)

GO Cellular Component (8): cytosol (GO:0005829), plasma membrane (GO:0005886), cilium (GO:0005929), nuclear body (GO:0016604), ciliary basal body (GO:0036064), sperm midpiece (GO:0097225), sperm principal piece (GO:0097228), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
GTPase activity	2
sperm flagellum	2
regulation of GTPase activity	1
positive regulation of hydrolase activity	1
cilium assembly	1
negative regulation of plasma membrane bounded cell projection assembly	1
regulation of cilium assembly	1
negative regulation of organelle assembly	1
enzyme activator activity	1
GTPase regulator activity	1
GTPase binding	1
binding	1
cytoplasm	1
membrane	1
cell periphery	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
nucleoplasm	1
intracellular membraneless organelle	1
microtubule organizing center	1
cilium	1

Protein interactions and networks

STRING

1276 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TBC1D30	TBC1D13	Q9NVG8	544
TBC1D30	TBC1D22B	Q9NU19	515
TBC1D30	SGSM2	O43147	513
TBC1D30	TBC1D19	Q8N5T2	499
TBC1D30	LEMD3	Q9Y2U8	499
TBC1D30	RNF182	Q8N6D2	491
TBC1D30	RASSF3	Q86WH2	479
TBC1D30	TBC1D21	Q8IYX1	478
TBC1D30	LHFPL2	Q6ZUX7	477
TBC1D30	OCIAD2	Q56VL3	470
TBC1D30	TBC1D7	Q9P0N9	458
TBC1D30	TBC1D23	Q9NUY8	443
TBC1D30	TBC1D5	Q92609	434
TBC1D30	TBC1D22A	Q8WUA7	433
TBC1D30	MPPED2	Q15777	429

IntAct

11 interactions, top by confidence:

A	B	Type	Score
NIPAL1	ESYT2	psi-mi:“MI:0914”(association)	0.640
SNAP23	TBC1D30	psi-mi:“MI:0915”(physical association)	0.370
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
SCOC	SSNA1	psi-mi:“MI:0914”(association)	0.350
S100A2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
SCOC	SNAPIN	psi-mi:“MI:0914”(association)	0.350
MFSD6L	ESYT2	psi-mi:“MI:0914”(association)	0.350
NIPAL3	ILVBL	psi-mi:“MI:0914”(association)	0.350
SLC9A5	NBAS	psi-mi:“MI:0914”(association)	0.350

BioGRID (35): STX3 (Affinity Capture-Western), MYO5B (Affinity Capture-Western), SYTL4 (Affinity Capture-Western), EXOC6 (Affinity Capture-Western), TBC1D30 (Reconstituted Complex), TBC1D30 (Affinity Capture-MS), TBC1D30 (Affinity Capture-RNA), TBC1D30 (Affinity Capture-MS), TBC1D30 (Affinity Capture-MS), TBC1D30 (Affinity Capture-RNA), TBC1D30 (Two-hybrid), TBC1D30 (Two-hybrid), TBC1D30 (Two-hybrid), TBC1D30 (Two-hybrid), CEP70 (Two-hybrid)

ESM2 similar proteins: A0A088MLT8, A2AQ25, B3KU38, B5DF41, E9PSK7, O15079, O35274, P0DPB3, P0DPB4, P12755, P49140, P85299, Q0D2I5, Q14DQ1, Q1LY51, Q3B7M3, Q3SYW5, Q4KMA0, Q4R3X1, Q50H33, Q5F3L9, Q5FVG6, Q5RD40, Q5XKK7, Q60698, Q6ZNC4, Q6ZUS6, Q6ZWB6, Q80U23, Q80U62, Q80XA6, Q812A5, Q86YI8, Q8BXL9, Q8K2W6, Q8ND83, Q8NFH8, Q8QFX1, Q8TEK3, Q924W7

Diamond homologs: A2AWA9, A3KGB4, A6H8I2, A6QP29, B0R0W9, B1AVH7, B5DFA1, C8VDQ4, D2H0G5, O43048, O95759, P48566, P53258, P58802, P87234, Q09445, Q09830, Q0IIM8, Q12317, Q28C33, Q28CB1, Q2KI13, Q3U0J8, Q3UYK3, Q4KMP7, Q4QQU7, Q5R372, Q5RAN1, Q5RCW6, Q5SVR0, Q5TC63, Q66K14, Q69ZT9, Q6GL87, Q6P6R7, Q6ZT07, Q7T2D0, Q86UD7, Q8BHL3, Q8C9V1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	105
Likely benign	6
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1925 predictions. Top by Δscore:

Variant	Effect	Δscore
12:64827834:GGA:G	acceptor_gain	1.0000
12:64832301:GAAA:G	donor_gain	1.0000
12:64832305:G:GG	donor_gain	1.0000
12:64836487:TA:T	acceptor_loss	1.0000
12:64836488:A:AG	acceptor_gain	1.0000
12:64836489:G:GG	acceptor_gain	1.0000
12:64836489:GATT:G	acceptor_gain	1.0000
12:64836489:GATTA:G	acceptor_gain	1.0000
12:64836655:GGAG:G	donor_gain	1.0000
12:64836656:GAGG:G	donor_gain	1.0000
12:64836657:AGGT:A	donor_loss	1.0000
12:64836659:G:GG	donor_gain	1.0000
12:64838847:GGAGA:G	donor_gain	1.0000
12:64838848:GAGA:G	donor_gain	1.0000
12:64838848:GAGAG:G	donor_gain	1.0000
12:64838850:GA:G	donor_gain	1.0000
12:64838852:G:GG	donor_gain	1.0000
12:64843378:A:AG	acceptor_gain	1.0000
12:64843379:G:GG	acceptor_gain	1.0000
12:64843379:GGC:G	acceptor_gain	1.0000
12:64843379:GGCA:G	acceptor_gain	1.0000
12:64843482:GCAG:G	donor_gain	1.0000
12:64843483:CAGGT:C	donor_loss	1.0000
12:64843486:G:GA	donor_loss	1.0000
12:64843487:T:A	donor_loss	1.0000
12:64866752:A:AG	acceptor_gain	1.0000
12:64866752:AT:A	acceptor_gain	1.0000
12:64866753:T:G	acceptor_gain	1.0000
12:64866753:T:TA	acceptor_gain	1.0000
12:64866761:A:AG	acceptor_gain	1.0000

AlphaMissense

5025 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000028621 (12:64808635 A>G), RS1000035108 (12:64853419 G>C), RS1000042562 (12:64832013 T>G), RS1000043396 (12:64784818 A>G), RS1000059910 (12:64808978 G>GCC), RS1000071888 (12:64766076 G>A), RS1000104490 (12:64830259 T>C), RS1000135300 (12:64858782 C>G), RS1000150428 (12:64817358 G>A), RS1000152148 (12:64825868 G>A,T), RS1000235577 (12:64865598 G>A,T), RS1000240961 (12:64770987 T>C), RS1000270488 (12:64866627 A>T), RS1000273677 (12:64822454 T>A), RS1000286636 (12:64865176 G>T)

Disease associations

OMIM: gene MIM:615077 | 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):

Study	Trait	p-value
GCST000579_29	Cognitive performance	2.000000e-06
GCST008113_1	Proinsulin levels (late-phase conversion)	1.000000e-16
GCST009309_6	Face memory	4.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0003926	neuropsychological test
EFO:0004467	insulin measurement
EFO:0004874	memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	7
methylmercuric chloride	decreases expression	3
trichostatin A	affects cotreatment, decreases expression, increases expression	3
entinostat	decreases expression, affects cotreatment	2
Vorinostat	affects cotreatment, decreases expression	2
Panobinostat	affects cotreatment, decreases expression	2
Diethylhexyl Phthalate	decreases expression, increases abundance, increases methylation	2
Estradiol	increases expression, affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	increases expression	1
triphenyl phosphate	affects expression	1
mono-(2-ethylhexyl)phthalate	increases abundance, increases methylation	1
sulforaphane	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
NSC 689534	affects binding, decreases expression	1
Sunitinib	increases expression	1
Caffeine	affects phosphorylation	1
Carbamazepine	affects expression	1
Copper	decreases expression, affects binding	1
Selenium	decreases expression	1
Dihydrotestosterone	increases expression	1
Urethane	decreases expression	1

Clinical trials (associated diseases)

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