TOP3B (DNA topoisomerase III beta)

Gene

• Entrez ID: 8940
• Gene name: DNA topoisomerase III beta
• Gene symbol: TOP3B
• Synonyms (NCBI Gene): TOP3B1
• Chromosome: 22
• Chromosome location: 22q11.22
• Summary: This gene encodes a DNA topoisomerase, an enzyme that controls and alters the topologic states of DNA during transcription. This enzyme catalyzes the transient breaking and rejoining of a single strand of DNA which allows the strands to pass through one a

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1447331	hsa-miR-1184	CLIP-seq
MIRT1447332	hsa-miR-183	CLIP-seq
MIRT1447333	hsa-miR-346	CLIP-seq
MIRT1447334	hsa-miR-4288	CLIP-seq
MIRT1447335	hsa-miR-4418	CLIP-seq
MIRT1447336	hsa-miR-4659a-5p	CLIP-seq
MIRT1447337	hsa-miR-4659b-5p	CLIP-seq
MIRT1447338	hsa-miR-509-3-5p	CLIP-seq
MIRT1447339	hsa-miR-509-5p	CLIP-seq
MIRT1447340	hsa-miR-632	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000793	Component	Condensed chromosome	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003916	Function	DNA topoisomerase activity	IEA
GO:0003916	Function	DNA topoisomerase activity	TAS
GO:0003917	Function	DNA topoisomerase type I (single strand cut, ATP-independent) activity	IBA
GO:0003917	Function	DNA topoisomerase type I (single strand cut, ATP-independent) activity	IEA
GO:0005515	Function	Protein binding	IPI	25416956, 28176834, 29892012, 31515488, 32296183, 33961781
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	23912945
GO:0005634	Component	Nucleus	TAS
GO:0006265	Process	DNA topological change	IBA
GO:0006265	Process	DNA topological change	IEA
GO:0006265	Process	DNA topological change	NAS	23912945
GO:0006281	Process	DNA repair	IBA
GO:0006310	Process	DNA recombination	IBA
GO:0007059	Process	Chromosome segregation	IEA
GO:0016853	Function	Isomerase activity	IEA
GO:0140225	Component	DNA topoisomerase III-beta-TDRD3 complex	IPI	28176834
GO:0140226	Function	RNA topoisomerase activity	IDA	23912945

Other IDs

• MIM: 603582
• HGNC: 11993
• e!Ensembl: ENSG00000100038

Protein

• UniProt ID: O95985
• Protein name: DNA topoisomerase 3-beta-1 (EC 5.6.2.1) (DNA topoisomerase III beta-1)
• Protein function: Releases the supercoiling and torsional tension of DNA introduced during the DNA replication and transcription by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a targ
• PDB: 5GVC, 5GVE, 9C9W, 9C9Y, 9CA0, 9CA1, 9CA4, 9CAG, 9CAH, 9CAJ, 9CAK, 9CAL
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01751	Toprim	4 → 155	Toprim domain	Family
  PF01131	Topoisom_bac	169 → 583	DNA topoisomerase	Family

• Tissue specificity: TISSUE SPECIFICITY: Isoform 1 is found in testis, heart and skeletal muscle. A 4 kb transcript which probably represents isoform 2 is found in thymus, kidney and pancreas. {ECO:0000269|PubMed:9927731}.
• Sequence:

  MKTVLMVAEKPSLAQSIAKILSRGSLSSHKGLNGACSVHEYTGTFAGQPVRFKMTSVCGH
  VMTLDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDK
  EGENICFEVLDAVLPVMNKAHGGEKTVFRARFSSITDTDICNAMACLGEPDHNEALSVDA
  RQELDLRIGCAFTRFQTKYFQGKYGDLDSSLISFGPCQTPTLGFCVERHDKIQSFKPETY
  WVLQAKVNTDKDRSLLLDWDRVRVFDREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLA
  LNTVEMLRVASSSLGMGPQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANH
  PYWADTVKRLLAEGINRPRKGHDAGDHPPITPMKSATEAELGGDAWRLYEYITRHFIATV
  SHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGE
  VKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVESGRRLKPTNL
  GIVLVHGYYKIDAELVLPTIRSAVEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSI
  AGMDELMEVSFSPLAATGKPLSRCGKCHRFMKYIQAKPSRLHCSHCDETYTLPQNGTIKL
  YKELRCPLDDFELVLWSSGSRGKSYPLCPYCYNHPPFRDMKKGMGCNECTHPSCQHSLSM
  LGIGQCVECESGVLVLDPTSGPKWKVACNKCNVVAHCFENAHRVRVSADTCSVCEAALLD
  VDFNKAKSPLPGDETQHMGCVFCDPVFQELVELKHAASCHPMHRGGPGRRQGRGRGRARR
  PPGKPNPRRPKDKMSALAAYFV

• Sequence length: 862

Pathways

KEGG:

Homologous recombination
Fanconi anemia 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
SCHIZOPHRENIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOP3B-related disorder	Uncertain significance; Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOP3B-related neurodevelopmental condition	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Autistic Disorder	Autism	BEFREE	27880953, 29490292		★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	Pubtator	27880953	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Ovarian Epithelial	Epithelial ovarian carcinoma	Pubtator	27315793	Associate	★☆☆☆☆ Found in Text Mining only
Cleft Palate	Cleft palate	Pubtator	31204702	Associate	★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	23912948, 27880953, 31204702	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Abnormalities	Congenital abnormalities	Pubtator	27880953	Associate	★☆☆☆☆ Found in Text Mining only
Congenital anomaly of face	Facial dysmorphism	BEFREE	27880953		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	23912948	Associate	★☆☆☆☆ Found in Text Mining only
DiGeorge Syndrome	Digeorge syndrome	Pubtator	31204702	Associate	★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	29490292		★☆☆☆☆ Found in Text Mining only
Facial Dysmorphism with Multiple Malformations	Facial dysmorphism syndrome	Pubtator	27880953	Associate	★☆☆☆☆ Found in Text Mining only
Fragile X Syndrome	Fragile X Syndrome	BEFREE	27880953		★☆☆☆☆ Found in Text Mining only
Heart Defects Congenital	Congenital heart defect	Pubtator	25376777	Associate	★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	23912948, 27880953		★☆☆☆☆ Found in Text Mining only
Juvenile Myoclonic Epilepsy	Myoclonic Epilepsy	BEFREE	29490292		★☆☆☆☆ Found in Text Mining only
Kidney Neoplasms	Kidney neoplasm	Pubtator	31795919	Associate	★☆☆☆☆ Found in Text Mining only
Learning Disabilities	Learning disorders	Pubtator	27880953	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of kidney	Kidney Cancer	BEFREE	31795919		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	12941840		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	31795919		★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	29490292		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	28355294		★☆☆☆☆ Found in Text Mining only
Renal carcinoma	Renal Carcinoma	BEFREE	31795919		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	23912948, 29490292		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	PSYGENET_DG	23912948		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	Pubtator	23912948	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations