TBC1D13

Summary

TBC1D13 (TBC1 domain family member 13, HGNC:25571) is a protein-coding gene on chromosome 9q34.11, encoding TBC1 domain family member 13 (Q9NVG8). Acts as a GTPase-activating protein for RAB35.

Predicted to enable GTPase activator activity. Predicted to be involved in intracellular protein transport. Predicted to be located in cytosol and membrane. Predicted to be active in cytoplasm.

Source: NCBI Gene 54662 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 61 total
• MANE Select transcript: NM_018201

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25571
Approved symbol	TBC1D13
Name	TBC1 domain family member 13
Location	9q34.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10743
Ensembl gene	ENSG00000107021
Ensembl biotype	protein_coding
OMIM	616218
Entrez	54662

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000223865, ENST00000372648, ENST00000466056, ENST00000475097, ENST00000858130, ENST00000858131, ENST00000946366, ENST00000946367

RefSeq mRNA: 2 — MANE Select: NM_018201 NM_001286772, NM_018201

CCDS: CCDS6911, CCDS69677

Canonical transcript exons

ENST00000372648 — 12 exons

Exon	Start	End
ENSE00000927257	128805859	128806019
ENSE00000927258	128806254	128806311
ENSE00001110194	128787253	128787376
ENSE00001110196	128807814	128810430
ENSE00001143555	128803956	128804119
ENSE00001143562	128803250	128803460
ENSE00003459488	128788334	128788407
ENSE00003559371	128791380	128791441
ENSE00003588316	128791594	128791693
ENSE00003595202	128790735	128790775
ENSE00003609533	128792492	128792574
ENSE00003656713	128797055	128797214

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 90.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.1853 / max 85.6499, expressed in 1792 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98836	11.2159	1783
98837	0.7065	437
98835	0.2560	94
98838	0.0070	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
anterior cingulate cortex	UBERON:0009835	90.13	gold quality
cingulate cortex	UBERON:0003027	90.07	gold quality
right frontal lobe	UBERON:0002810	89.61	gold quality
amygdala	UBERON:0001876	89.59	gold quality
apex of heart	UBERON:0002098	89.10	gold quality
adult mammalian kidney	UBERON:0000082	89.07	gold quality
islet of Langerhans	UBERON:0000006	88.63	gold quality
prefrontal cortex	UBERON:0000451	88.18	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.67	gold quality
nucleus accumbens	UBERON:0001882	87.41	gold quality
putamen	UBERON:0001874	87.35	gold quality
right adrenal gland	UBERON:0001233	86.96	gold quality
left adrenal gland cortex	UBERON:0035825	86.96	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	86.93	gold quality
right adrenal gland cortex	UBERON:0035827	86.89	gold quality
left adrenal gland	UBERON:0001234	86.88	gold quality
hypothalamus	UBERON:0001898	86.85	gold quality
neocortex	UBERON:0001950	86.79	gold quality
metanephros cortex	UBERON:0010533	86.72	gold quality
caudate nucleus	UBERON:0001873	86.65	gold quality
frontal cortex	UBERON:0001870	86.58	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.52	gold quality
gastrocnemius	UBERON:0001388	86.39	gold quality
adrenal cortex	UBERON:0001235	86.35	gold quality
kidney	UBERON:0002113	86.34	gold quality
stromal cell of endometrium	CL:0002255	86.24	gold quality
muscle of leg	UBERON:0001383	86.07	gold quality
right lobe of thyroid gland	UBERON:0001119	86.01	gold quality
granulocyte	CL:0000094	85.99	gold quality
cortex of kidney	UBERON:0001225	85.88	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

110 targeting TBC1D13, 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-8485	100.00	77.57	4731
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-23A-5P	99.94	65.39	468
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-2116-3P	99.74	64.32	889
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-3202	99.66	67.70	2737

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tbc1d13	ENSMUSG00000039678
rattus_norvegicus	Tbc1d13	ENSRNOG00000015970

Paralogs (45): RABGAP1 (ENSG00000011454), TBC1D22A (ENSG00000054611), TBC1D22B (ENSG00000065491), TBC1D1 (ENSG00000065882), EVI5 (ENSG00000067208), TBC1D25 (ENSG00000068354), TBC1D2 (ENSG00000095383), TBC1D10A (ENSG00000099992), SGSM3 (ENSG00000100359), TBC1D17 (ENSG00000104946), 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 13 — Q9NVG8 (reviewed: Q9NVG8)

All UniProt accessions (2): Q9NVG8, A0A024R8C8

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a GTPase-activating protein for RAB35. Together with RAB35 may be involved in regulation of insulin-induced glucose transporter SLC2A4/GLUT4 translocation to the plasma membrane in adipocytes.

Subunit / interactions. Interacts with RAB1A and RAB10; in a GTP-dependent manner.

Subcellular location. Membrane. Cytoplasm.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NVG8-1	1	yes
Q9NVG8-2	2
Q9NVG8-3	3

RefSeq proteins (2): NP_001273701, NP_060671* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF00566

UniProt features (8 total): sequence conflict 3, splice variant 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NVG8-F1	88.57	0.69

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-8854214	TBC/RABGAPs
R-HSA-199991	Membrane Trafficking
R-HSA-5653656	Vesicle-mediated transport
R-HSA-9007101	Rab regulation of trafficking

MSigDB gene sets: 178 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOMF_GTPASE_BINDING, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, PATIL_LIVER_CANCER, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, GOBP_CILIUM_ORGANIZATION, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, GOBP_ORGANELLE_ASSEMBLY, LIAO_METASTASIS, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, DOUGLAS_BMI1_TARGETS_DN, GOBP_REGULATION_OF_CILIUM_ASSEMBLY

GO Biological Process (1): intracellular protein transport (GO:0006886)

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

GO Cellular Component (3): cytoplasm (GO:0005737), cytosol (GO:0005829), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Rab regulation of trafficking	1
Vesicle-mediated transport	1
Membrane Trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
intracellular protein localization	1
protein transport	1
intracellular transport	1
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	1
GTPase binding	1
binding	1
intracellular anatomical structure	1
cytoplasm	1

Protein interactions and networks

STRING

856 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TBC1D13	SPOUT1	Q5T280	931
TBC1D13	KYAT1	Q16773	901
TBC1D13	ENDOG	Q14249	838
TBC1D13	TBC1D19	Q8N5T2	641
TBC1D13	TBC1D10A	Q9BXI6	629
TBC1D13	TBC1D21	Q8IYX1	626
TBC1D13	TBC1D10C	Q8IV04	618
TBC1D13	TBC1D10B	Q4KMP7	584
TBC1D13	TBC1D24	Q9ULP9	551
TBC1D13	TBC1D30	Q9Y2I9	544
TBC1D13	SGSM3	Q96HU1	541
TBC1D13	TBC1D2B	Q9UPU7	514
TBC1D13	TBC1D1	Q86TI0	506
TBC1D13	TBC1D8	O95759	506
TBC1D13	TBC1D14	Q9P2M4	506

IntAct

21 interactions, top by confidence:

A	B	Type	Score
ZNF618	TBC1D13	psi-mi:“MI:0915”(physical association)	0.560
ARHGEF5	TBC1D13	psi-mi:“MI:0915”(physical association)	0.560
PLIN3	TBC1D13	psi-mi:“MI:0915”(physical association)	0.560
TEPSIN	TBC1D13	psi-mi:“MI:0915”(physical association)	0.560
SPDYE4	TBC1D13	psi-mi:“MI:0915”(physical association)	0.560
VPS35	ILVBL	psi-mi:“MI:0914”(association)	0.350
HRAS	IGHV1-45	psi-mi:“MI:0914”(association)	0.350
TBC1D13	ZNF618	psi-mi:“MI:0915”(physical association)	0.000
ARHGEF5	TBC1D13	psi-mi:“MI:0915”(physical association)	0.000
TBC1D13	ARHGEF5	psi-mi:“MI:0915”(physical association)	0.000
TBC1D13	PLIN3	psi-mi:“MI:0915”(physical association)	0.000
TBC1D13	TEPSIN	psi-mi:“MI:0915”(physical association)	0.000
TBC1D13	SPDYE4	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (19): TBC1D13 (Two-hybrid), TBC1D13 (Two-hybrid), ZNF618 (Two-hybrid), ENTHD2 (Two-hybrid), SPDYE4 (Two-hybrid), TBC1D13 (Proximity Label-MS), TBC1D13 (Co-fractionation), TBC1D13 (Co-fractionation), ARMC1 (Co-fractionation), TBC1D13 (Affinity Capture-MS), TBC1D13 (Positive Genetic), TBC1D13 (Proximity Label-MS), TBC1D13 (Proximity Label-MS), TBC1D13 (Proximity Label-MS), TBC1D13 (Proximity Label-MS)

ESM2 similar proteins: A0A0G2QC33, A6H7I8, F1N9S8, O60447, O70566, O73787, O88597, O95453, P58854, P69341, P97366, Q01061, Q01064, Q01065, Q01066, Q0J035, Q14457, Q2T9Q1, Q3U4G0, Q4A1L3, Q4A1L4, Q4A1L5, Q5CD77, Q5E9S8, Q5F361, Q5R878, Q5RC51, Q5ZKS6, Q61143, Q64395, Q69ZT9, Q6DG88, Q6GP52, Q80YV4, Q8BGE6, Q8BM85, Q8CGA2, Q8R3D1, Q8TEA7, Q8UUU2

Diamond homologs: Q54TA5, Q8R3D1, Q9NVG8, Q9URY3, A1A5B6, O43147, P09379, P48365, Q28CB1, Q2NKQ1, Q3MII6, Q6BU76, Q6FWI1, Q80U12, Q8BPQ7, Q8BYH7, Q8TBP0, Q8TC07, Q9CXF4, Q9HA65, Q9UUH7, Q95LL3, Q9NU19, O59737, Q08484, Q54VM3, Q8R5A6, Q8WUA7, Q95KI1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	47
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1856 predictions. Top by Δscore:

Variant	Effect	Δscore
9:128787373:GCCG:G	donor_gain	1.0000
9:128787375:CGGT:C	donor_loss	1.0000
9:128787376:GGTA:G	donor_loss	1.0000
9:128787377:G:GG	donor_gain	1.0000
9:128788332:A:AG	acceptor_gain	1.0000
9:128788333:G:GA	acceptor_gain	1.0000
9:128788333:GA:G	acceptor_gain	1.0000
9:128788333:GAA:G	acceptor_gain	1.0000
9:128788405:GTG:G	donor_gain	1.0000
9:128788406:TG:T	donor_gain	1.0000
9:128788406:TGG:T	donor_loss	1.0000
9:128788407:GG:G	donor_gain	1.0000
9:128788408:G:GC	donor_loss	1.0000
9:128788408:G:GG	donor_gain	1.0000
9:128788409:T:A	donor_loss	1.0000
9:128791589:TGCA:T	acceptor_loss	1.0000
9:128791591:CAGGG:C	acceptor_gain	1.0000
9:128791592:A:AG	acceptor_gain	1.0000
9:128791592:AG:A	acceptor_gain	1.0000
9:128791592:AGG:A	acceptor_gain	1.0000
9:128791592:AGGGA:A	acceptor_gain	1.0000
9:128791593:G:A	acceptor_loss	1.0000
9:128791593:G:GG	acceptor_gain	1.0000
9:128791593:GG:G	acceptor_gain	1.0000
9:128791593:GGG:G	acceptor_gain	1.0000
9:128791593:GGGA:G	acceptor_gain	1.0000
9:128791593:GGGAG:G	acceptor_gain	1.0000
9:128791673:G:GT	donor_gain	1.0000
9:128791693:TG:T	donor_loss	1.0000
9:128791694:G:GA	donor_loss	1.0000

AlphaMissense

2656 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:128790770:T:A	W45R	1.000
9:128790770:T:C	W45R	1.000
9:128792496:T:C	L102P	1.000
9:128792519:T:A	W110R	1.000
9:128792519:T:C	W110R	1.000
9:128792521:G:C	W110C	1.000
9:128792521:G:T	W110C	1.000
9:128792550:T:C	L120P	1.000
9:128792567:G:C	D126H	1.000
9:128792568:A:C	D126A	1.000
9:128792568:A:G	D126G	1.000
9:128792568:A:T	D126V	1.000
9:128792569:T:A	D126E	1.000
9:128792569:T:G	D126E	1.000
9:128797057:G:C	R129T	1.000
9:128797057:G:T	R129M	1.000
9:128797058:G:C	R129S	1.000
9:128797058:G:T	R129S	1.000
9:128797154:A:C	R161S	1.000
9:128797154:A:T	R161S	1.000
9:128803344:G:C	R213P	1.000
9:128803350:T:C	L215P	1.000
9:128803368:T:C	L221P	1.000
9:128803385:T:C	Y227H	1.000
9:128803393:A:C	Q229H	1.000
9:128803393:A:T	Q229H	1.000
9:128803394:G:A	G230S	1.000
9:128803394:G:C	G230R	1.000
9:128803394:G:T	G230C	1.000
9:128803395:G:A	G230D	1.000

dbSNP variants (sampled 300 via entrez): RS1000065038 (9:128792221 C>T), RS1000283732 (9:128787648 A>C), RS1000321743 (9:128796863 G>A), RS1000358573 (9:128785459 T>C), RS1000381521 (9:128803191 G>C), RS1000454353 (9:128790379 G>A), RS1000713701 (9:128801456 G>A), RS1000765167 (9:128801259 C>A), RS1000882016 (9:128802951 T>A), RS1001124577 (9:128790312 G>A), RS1001176636 (9:128790036 C>G), RS1001432002 (9:128809981 T>C,G), RS1001498387 (9:128796518 T>C), RS1001511189 (9:128786936 G>A,C), RS1001538733 (9:128802212 C>T)

Disease associations

OMIM: gene MIM:616218 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST006879_1	Blood metabolite levels	1.000000e-09
GCST006879_18	Blood metabolite levels	3.000000e-43
GCST006879_19	Blood metabolite levels	4.000000e-83
GCST006879_2	Blood metabolite levels	2.000000e-12
GCST006879_20	Blood metabolite levels	5.000000e-12
GCST006879_21	Blood metabolite levels	2.000000e-22
GCST006879_22	Blood metabolite levels	2.000000e-20
GCST010242_388	HDL cholesterol levels	4.000000e-10
GCST012020_405	Serum metabolite levels	1.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
bisphenol A	decreases expression	1
sodium arsenite	decreases expression	1
manganese chloride	decreases expression, increases abundance	1
nickel sulfate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
Leflunomide	decreases expression	1
Cisplatin	decreases expression	1
Dexamethasone	increases expression, affects cotreatment	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	increases O-linked glycosylation, decreases activity	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Manganese	decreases expression, increases abundance	1
Smoke	decreases expression	1
Tretinoin	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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