TBC1D1 (TBC1 domain family member 1)

Gene

• Entrez ID: 23216
• Gene name: TBC1 domain family member 1
• Gene symbol: TBC1D1
• Synonyms (NCBI Gene): TBC, TBC1
• Chromosome: 4
• Chromosome location: 4p14
• Summary: TBC1D1 is the founding member of a family of proteins sharing a 180- to 200-amino acid TBC domain presumed to have a role in regulating cell growth and differentiation. These proteins share significant homology with TRE2 (USP6; MIM 604334), yeast Bub2, an

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT006523	hsa-miR-125b-5p	Luciferase reporter assay	19635812
MIRT006523	hsa-miR-125b-5p	Luciferase reporter assay	19635812
MIRT006523	hsa-miR-125b-5p	Luciferase reporter assay	19635812
MIRT006523	hsa-miR-125b-5p	Luciferase reporter assay	19635812
MIRT016481	hsa-miR-193b-3p	Microarray	20304954
MIRT045726	hsa-miR-125a-5p	CLASH	23622248
MIRT038677	hsa-miR-7-1-3p	CLASH	23622248
MIRT531963	hsa-miR-3714	PAR-CLIP	22012620
MIRT531962	hsa-miR-2682-5p	PAR-CLIP	22012620
MIRT531961	hsa-miR-34b-5p	PAR-CLIP	22012620
MIRT531960	hsa-miR-449c-5p	PAR-CLIP	22012620
MIRT531959	hsa-miR-548au-3p	PAR-CLIP	22012620
MIRT531958	hsa-miR-299-5p	PAR-CLIP	22012620
MIRT531963	hsa-miR-3714	PAR-CLIP	22012620
MIRT531962	hsa-miR-2682-5p	PAR-CLIP	22012620
MIRT531961	hsa-miR-34b-5p	PAR-CLIP	22012620
MIRT531960	hsa-miR-449c-5p	PAR-CLIP	22012620
MIRT531959	hsa-miR-548au-3p	PAR-CLIP	22012620
MIRT531958	hsa-miR-299-5p	PAR-CLIP	22012620
MIRT1412037	hsa-miR-1915	CLIP-seq
MIRT1412038	hsa-miR-4256	CLIP-seq
MIRT1412039	hsa-miR-4330	CLIP-seq
MIRT1412040	hsa-miR-4459	CLIP-seq
MIRT2345782	hsa-miR-128	CLIP-seq
MIRT2345783	hsa-miR-3117-5p	CLIP-seq
MIRT2345784	hsa-miR-4324	CLIP-seq
MIRT2345785	hsa-miR-520d-5p	CLIP-seq
MIRT2345786	hsa-miR-524-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005096	Function	GTPase activator activity	IBA
GO:0005096	Function	GTPase activator activity	IEA
GO:0005515	Function	Protein binding	IPI	22354992, 24879834, 32296183
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005794	Component	Golgi apparatus	IBA
GO:1902017	Process	Regulation of cilium assembly	IMP	17646400

Other IDs

• MIM: 609850
• HGNC: 11578
• e!Ensembl: ENSG00000065882

Protein

• UniProt ID: Q86TI0
• Protein name: TBC1 domain family member 1
• Protein function: May act as a GTPase-activating protein for Rab family protein(s). May play a role in the cell cycle and differentiation of various tissues. Involved in the trafficking and translocation of GLUT4-containing vesicles and insulin-stimulated glucose
• PDB: 3QYE
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00640	PID	277 → 381	Phosphotyrosine interaction domain (PTB/PID)	Domain
  PF11830	DUF3350	690 → 745	Domain of unknown function (DUF3350)	Family
  PF00566	RabGAP-TBC	803 → 1014	Rab-GTPase-TBC domain	Family

• Sequence:

  MEPITFTARKHLLSNEVSVDFGLQLVGSLPVHSLTTMPMLPWVVAEVRRLSRQSTRKEPV
  TKQVRLCVSPSGLRCEPEPGRSQQWDPLIYSSIFECKPQRVHKLIHNSHDPSYFACLIKE
  DAVHRQSICYVFKADDQTKVPEIISSIRQAGKIARQEELHCPSEFDDTFSKKFEVLFCGR
  VTVAHKKAPPALIDECIEKFNHVSGSRGSESPRPNPPHAAPTGSQEPVRRPMRKSFSQPG
  LRSLAFRKELQDGGLRSSGFFSSFEESDIENHLISGHNIVQPTDIEENRTMLFTIGQSEV
  YLISPDTKKIALEKNFKEISFCSQGIRHVDHFGFICRESSGGGGFHFVCYVFQCTNEALV
  DEIMMTLKQAFTVAAVQQTAKAPAQLCEGCPLQSLHKLCERIEGMNSSKTKLELQKHLTT
  LTNQEQATIFEEVQKLRPRNEQRENELIISFLRCLYEEKQKEHIHIGEMKQTSQMAAENI
  GSELPPSATRFRLDMLKNKAKRSLTESLESILSRGNKARGLQEHSISVDLDSSLSSTLSN
  TSKEPSVCEKEALPISESSFKLLGSSEDLSSDSESHLPEEPAPLSPQQAFRRRANTLSHF
  PIECQEPPQPARGSPGVSQRKLMRYHSVSTETPHERKDFESKANHLGDSGGTPVKTRRHS
  WRQQIFLRVATPQKACDSSSRYEDYSELGELPPRSPLEPVCEDGPFGPPPEEKKRTSREL
  RELWQKAILQQILLLRMEKENQKLQASENDLLNKRLKLDYEEITPCLKEVTTVWEKMLST
  PGRSKIKFDMEKMHSAVGQGVPRHHRGEIWKFLAEQFHLKHQFPSKQQPKDVPYKELLKQ
  LTSQQHAILIDLGRTFPTHPYFSAQLGAGQLSLYNILKAYSLLDQEVGYCQGLSFVAGIL
  LLHMSEEEAFKMLKFLMFDMGLRKQYRPDMIILQIQMYQLSRLLHDYHRDLYNHLEEHEI
  GPSLYAAPWFLTMFASQFPLGFVARVFDMIFLQGTEVIFKVALSLLGSHKPLILQHENLE
  TIVDFIKSTLPNLGLVQMEKTINQVFEMDIAKQLQAYEVEYHVLQEELIDSSPLSDNQRM
  DKLEKTNSSLRKQNLDLLEQLQVANGRIQSLEATIEKLLSSESKLKQAMLTLELERSALL
  QTVEELRRRSAEPSDREPECTQPEPTGD

• Sequence length: 1168

Pathways

KEGG:

AMPK signaling pathway

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AMYOTROPHIC LATERAL SCLEROSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CAKUT	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CLONAL HEMATOPOIESIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL ANOMALY OF KIDNEY AND URINARY TRACT	—	GenCC	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEAD AND NECK MALIGNANT NEOPLASIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Non-syndromic renal or urinary tract malformation	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PELVIC ORGAN PROLAPSE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERIODONTITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SMALL VESSEL STROKE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TBC1D1-related disorder	Uncertain significance; Likely benign; Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UPPER AERODIGESTIVE TRACT NEOPLASM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Amyotrophic lateral sclerosis 1	Amyotrophic lateral sclerosis	Pubtator	29216901	Associate	★☆☆☆☆ Found in Text Mining only
Ataxia	Ataxia	Pubtator	34130600	Associate	★☆☆☆☆ Found in Text Mining only
Brain Diseases	Brain disease	Pubtator	34130600	Associate	★☆☆☆☆ Found in Text Mining only
Cakut	Congenital anomalies of kidney and urinary tract	BEFREE	26572137		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cakut	Congenital anomalies of kidney and urinary tract	GENOMICS_ENGLAND_DG	26572137		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carcinogenesis	Carcinogenesis	Pubtator	38189823	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	BEFREE	31845331		★☆☆☆☆ Found in Text Mining only
Congenital anomaly of the kidney	Multicystic renal dysplasia	BEFREE	26572137		★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	GWASDB_DG	22763110		★☆☆☆☆ Found in Text Mining only
Depressive Disorder	Major depressive disorder	Pubtator	38111702	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	29749858		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	29749858		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	29784647, 31627187		★☆☆☆☆ Found in Text Mining only
Diabetic Cardiomyopathies	Diabetic cardiomyopathy	BEFREE	31845331		★☆☆☆☆ Found in Text Mining only
Erectile Dysfunction	Erectile dysfunction	Pubtator	38111702	Associate	★☆☆☆☆ Found in Text Mining only
Frontotemporal Dementia	Frontotemporal dementia	Pubtator	34130600	Associate	★☆☆☆☆ Found in Text Mining only
Gaucher Disease	Gaucher disease	Pubtator	34130600	Associate	★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	38189823	Inhibit	★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease	Glycogen storage disease	Pubtator	34130600	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	33986365	Associate	★☆☆☆☆ Found in Text Mining only
Huntington Disease	Huntington disease	Pubtator	34130600	Associate	★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	BEFREE	31782092		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	20418905		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	34130600	Associate	★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	16893906, 18325908, 23374713, 23667688, 25946404, 26828654, 27307439, 29784647, 31627187		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	CTD_human_DG	16893906, 18325908, 18931681		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity	Obesity	Pubtator	23667688, 23874820, 26828654, 36627697	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Obesity, Morbid	Obesity	BEFREE	16893906, 18325908		★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	Pubtator	34130600	Associate	★☆☆☆☆ Found in Text Mining only
Renal dysplasia	Renal dysplasia	BEFREE	26572137		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	23364847		★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	38374468	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	17229543	Associate	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	39231952	Associate	★☆☆☆☆ Found in Text Mining only