Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	51567
Gene name Gene Name - the full gene name approved by the HGNC.	Tyrosyl-DNA phosphodiesterase 2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	TDP2
Synonyms (NCBI Gene) Gene synonyms aliases	AD022, EAP2, EAPII, TTRAP, dJ30M3.3, hTDP2
Chromosome Chromosome number	6
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	6p22.3
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a member of a superfamily of divalent cation-dependent phosphodiesterases. The encoded protein associates with CD40, tumor necrosis factor (TNF) receptor-75 and TNF receptor associated factors (TRAFs), and inhibits nuclear factor-kappa-B

Show/Hide all(3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs372245668	C>T	Pathogenic	Splice donor variant
rs879255601	GG>TT	Pathogenic	Stop gained, coding sequence variant
rs1562148727	G>C	Pathogenic	Coding sequence variant, stop gained

Show/Hide all(118)

miRTarBase ID	miRNA	Experiments
MIRT1417080	hsa-miR-1207-3p	CLIP-seq
MIRT1417081	hsa-miR-1250	CLIP-seq
MIRT1417082	hsa-miR-1263	CLIP-seq
MIRT1417083	hsa-miR-3140-5p	CLIP-seq
MIRT1417084	hsa-miR-3148	CLIP-seq
MIRT1417085	hsa-miR-3180-5p	CLIP-seq
MIRT1417086	hsa-miR-3673	CLIP-seq
MIRT1417087	hsa-miR-3688-3p	CLIP-seq
MIRT1417088	hsa-miR-3919	CLIP-seq
MIRT1417089	hsa-miR-4267	CLIP-seq
MIRT1417090	hsa-miR-450b-5p	CLIP-seq
MIRT1417091	hsa-miR-4536	CLIP-seq
MIRT1417092	hsa-miR-4756-3p	CLIP-seq
MIRT1417093	hsa-miR-4790-3p	CLIP-seq
MIRT1417094	hsa-miR-520a-5p	CLIP-seq
MIRT1417095	hsa-miR-525-5p	CLIP-seq
MIRT1417096	hsa-miR-550a	CLIP-seq
MIRT2125082	hsa-miR-1238	CLIP-seq
MIRT2125083	hsa-miR-3120-3p	CLIP-seq
MIRT1417083	hsa-miR-3140-5p	CLIP-seq
MIRT1417085	hsa-miR-3180-5p	CLIP-seq
MIRT2125084	hsa-miR-323-3p	CLIP-seq
MIRT2125085	hsa-miR-325	CLIP-seq
MIRT1417090	hsa-miR-450b-5p	CLIP-seq
MIRT2125086	hsa-miR-4691-5p	CLIP-seq
MIRT2125087	hsa-miR-4793-5p	CLIP-seq
MIRT1417094	hsa-miR-520a-5p	CLIP-seq
MIRT1417095	hsa-miR-525-5p	CLIP-seq
MIRT2125088	hsa-miR-545	CLIP-seq
MIRT2125089	hsa-miR-628-3p	CLIP-seq
MIRT2347511	hsa-miR-4424	CLIP-seq
MIRT2347512	hsa-miR-4477b	CLIP-seq
MIRT2347513	hsa-miR-4503	CLIP-seq
MIRT2347514	hsa-miR-4653-3p	CLIP-seq
MIRT2347515	hsa-miR-587	CLIP-seq
MIRT2347516	hsa-miR-590-3p	CLIP-seq
MIRT2640463	hsa-miR-1	CLIP-seq
MIRT2125082	hsa-miR-1238	CLIP-seq
MIRT2640464	hsa-miR-1283	CLIP-seq
MIRT2640465	hsa-miR-1286	CLIP-seq
MIRT2640466	hsa-miR-206	CLIP-seq
MIRT2640467	hsa-miR-21	CLIP-seq
MIRT2640468	hsa-miR-2113	CLIP-seq
MIRT2125083	hsa-miR-3120-3p	CLIP-seq
MIRT2640469	hsa-miR-3127-5p	CLIP-seq
MIRT1417083	hsa-miR-3140-5p	CLIP-seq
MIRT1417085	hsa-miR-3180-5p	CLIP-seq
MIRT2125084	hsa-miR-323-3p	CLIP-seq
MIRT2125085	hsa-miR-325	CLIP-seq
MIRT2640470	hsa-miR-3613-3p	CLIP-seq
MIRT2640471	hsa-miR-3918	CLIP-seq
MIRT2640472	hsa-miR-409-3p	CLIP-seq
MIRT2640473	hsa-miR-4275	CLIP-seq
MIRT2347511	hsa-miR-4424	CLIP-seq
MIRT2640474	hsa-miR-4438	CLIP-seq
MIRT2640475	hsa-miR-4452	CLIP-seq
MIRT2640476	hsa-miR-4477a	CLIP-seq
MIRT2347512	hsa-miR-4477b	CLIP-seq
MIRT2347513	hsa-miR-4503	CLIP-seq
MIRT1417090	hsa-miR-450b-5p	CLIP-seq
MIRT2347514	hsa-miR-4653-3p	CLIP-seq
MIRT2125086	hsa-miR-4691-5p	CLIP-seq
MIRT2640477	hsa-miR-4694-3p	CLIP-seq
MIRT2640478	hsa-miR-4722-5p	CLIP-seq
MIRT2640479	hsa-miR-4757-5p	CLIP-seq
MIRT2640480	hsa-miR-4766-5p	CLIP-seq
MIRT2125087	hsa-miR-4793-5p	CLIP-seq
MIRT1417094	hsa-miR-520a-5p	CLIP-seq
MIRT2640481	hsa-miR-522	CLIP-seq
MIRT1417095	hsa-miR-525-5p	CLIP-seq
MIRT2125088	hsa-miR-545	CLIP-seq
MIRT2640482	hsa-miR-549	CLIP-seq
MIRT2640483	hsa-miR-570	CLIP-seq
MIRT2347516	hsa-miR-590-3p	CLIP-seq
MIRT2640484	hsa-miR-590-5p	CLIP-seq
MIRT2640485	hsa-miR-613	CLIP-seq
MIRT2125089	hsa-miR-628-3p	CLIP-seq
MIRT2640486	hsa-miR-653	CLIP-seq
MIRT2640487	hsa-miR-938	CLIP-seq
MIRT2640463	hsa-miR-1	CLIP-seq
MIRT2125082	hsa-miR-1238	CLIP-seq
MIRT2640464	hsa-miR-1283	CLIP-seq
MIRT2640465	hsa-miR-1286	CLIP-seq
MIRT2640466	hsa-miR-206	CLIP-seq
MIRT2640467	hsa-miR-21	CLIP-seq
MIRT2640468	hsa-miR-2113	CLIP-seq
MIRT2125083	hsa-miR-3120-3p	CLIP-seq
MIRT1417083	hsa-miR-3140-5p	CLIP-seq
MIRT1417085	hsa-miR-3180-5p	CLIP-seq
MIRT2125084	hsa-miR-323-3p	CLIP-seq
MIRT2125085	hsa-miR-325	CLIP-seq
MIRT2640470	hsa-miR-3613-3p	CLIP-seq
MIRT2640472	hsa-miR-409-3p	CLIP-seq
MIRT2640473	hsa-miR-4275	CLIP-seq
MIRT2347511	hsa-miR-4424	CLIP-seq
MIRT2640474	hsa-miR-4438	CLIP-seq
MIRT2640475	hsa-miR-4452	CLIP-seq
MIRT2640476	hsa-miR-4477a	CLIP-seq
MIRT2347512	hsa-miR-4477b	CLIP-seq
MIRT2347513	hsa-miR-4503	CLIP-seq
MIRT1417090	hsa-miR-450b-5p	CLIP-seq
MIRT2347514	hsa-miR-4653-3p	CLIP-seq
MIRT2125086	hsa-miR-4691-5p	CLIP-seq
MIRT2640477	hsa-miR-4694-3p	CLIP-seq
MIRT2640478	hsa-miR-4722-5p	CLIP-seq
MIRT2640479	hsa-miR-4757-5p	CLIP-seq
MIRT2125087	hsa-miR-4793-5p	CLIP-seq
MIRT1417094	hsa-miR-520a-5p	CLIP-seq
MIRT2640481	hsa-miR-522	CLIP-seq
MIRT1417095	hsa-miR-525-5p	CLIP-seq
MIRT2125088	hsa-miR-545	CLIP-seq
MIRT2640482	hsa-miR-549	CLIP-seq
MIRT2347516	hsa-miR-590-3p	CLIP-seq
MIRT2640484	hsa-miR-590-5p	CLIP-seq
MIRT2640485	hsa-miR-613	CLIP-seq
MIRT2125089	hsa-miR-628-3p	CLIP-seq
MIRT2640486	hsa-miR-653	CLIP-seq
MIRT2640487	hsa-miR-938	CLIP-seq

Show/Hide all(37)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000287	Function	Magnesium ion binding	IDA	22405347, 22822062
GO:0000287	Function	Magnesium ion binding	TAS	19794497
GO:0003677	Function	DNA binding	IEA
GO:0003697	Function	Single-stranded DNA binding	IBA
GO:0003697	Function	Single-stranded DNA binding	IDA	22822062
GO:0003714	Function	Transcription corepressor activity	TAS	10764746
GO:0003824	Function	Catalytic activity	IEA
GO:0004518	Function	Nuclease activity	IEA
GO:0005515	Function	Protein binding	IPI	18039968, 32296183, 32814053
GO:0005634	Component	Nucleus	IDA	22908287
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	22908287
GO:0005737	Component	Cytoplasm	IEA
GO:0006281	Process	DNA repair	IEA
GO:0006302	Process	Double-strand break repair	IBA
GO:0006302	Process	Double-strand break repair	IDA	19794497
GO:0006302	Process	Double-strand break repair	IMP	21030584
GO:0006974	Process	DNA damage response	IEA
GO:0007166	Process	Cell surface receptor signaling pathway	TAS	10764746
GO:0016235	Component	Aggresome	IDA
GO:0016604	Component	Nuclear body	IDA
GO:0016605	Component	PML body	IBA
GO:0016605	Component	PML body	IDA	19794497
GO:0016605	Component	PML body	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0030145	Function	Manganese ion binding	IDA	22822062
GO:0036317	Function	Tyrosyl-RNA phosphodiesterase activity	IDA	22908287
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048666	Process	Neuron development	IMP	24658003
GO:0070259	Function	Tyrosyl-DNA phosphodiesterase activity	IEA
GO:0070260	Function	5'-tyrosyl-DNA phosphodiesterase activity	IBA
GO:0070260	Function	5'-tyrosyl-DNA phosphodiesterase activity	IDA	19794497, 22405347, 22822062
GO:0070260	Function	5'-tyrosyl-DNA phosphodiesterase activity	IMP	21030584

MIM	HGNC	e!Ensembl
605764	17768	ENSG00000111802

Protein

UniProt ID

O95551

Protein name

Tyrosyl-DNA phosphodiesterase 2 (Tyr-DNA phosphodiesterase 2) (hTDP2) (EC 3.1.4.-) (5'-tyrosyl-DNA phosphodiesterase) (5'-Tyr-DNA phosphodiesterase) (ETS1-associated protein 2) (ETS1-associated protein II) (EAPII) (TRAF and TNF receptor-associated protein

Protein function

DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 5'-phosphodiester bond, giving rise to DNA with a free 5' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomeras

PDB

5INO , 5J3P , 5J3S , 6Q00 , 6Q01

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF14555	UBA_4	28 → 67		Domain
PF03372	Exo_endo_phos	117 → 351	Endonuclease/Exonuclease/phosphatase family	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed (PubMed:10764746). Highly expressed in various brain regions, including the frontal and occipital lobes, the hippocampus, the striatum and the cerebellum (PubMed:24658003). {ECO:0000269|PubMed:10764746, ECO:0000269|Pub

Sequence

MELGSCLEGGREAAEEEGEPEVKKRRLLCVEFASVASCDAAVAQCFLAENDWEMERALNS
YFEPPVEESALERRPETISEPKTYVDLTNEETTDSTTSKISPSEDTQQENGSMFSLITWN
IDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYEIITGHEEGYFT
AIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQ
LKMVLKKMQEAPESATVIFAGDTNLRDREVTRCGGLPNNIVDVWEFLGKPKHCQYTWDTQ
MNSNLGITAACKLRFDRIFFRAAAEEGHIIPRSLDLLGLEKLDCGRFPSDHWGLLCNLDI
IL

Sequence length

362

Interactions

View interactions

	Reactome
			Nonhomologous End-Joining (NHEJ)

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
cerebellar ataxia	Cerebellar ataxia	rs1240335250	N/A
Spinocerebellar Ataxia	spinocerebellar ataxia, autosomal recessive 23	rs372245668, rs879255601	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Schizophrenia	Schizophrenia	N/A	N/A	GWAS

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Breast Neoplasms	Associate	28794467
Carcinogenesis	Associate	23433115
Carcinoma Non Small Cell Lung	Associate	21478903
Carcinoma Renal Cell	Associate	26255626
Congenital Abnormalities	Associate	37558815
Dyslexia	Associate	15717286, 22262880, 27484312, 30593505
Dyslexia Acquired	Associate	22262880
Fanconi Anemia	Associate	37558815
Frontotemporal Dementia	Associate	27484312
Language Development Disorders	Associate	22262880
Leukemia	Associate	28794467
Lung Neoplasms	Associate	21478903, 22508727
Neoplasms	Associate	21478903, 30593505
Neurologic Manifestations	Associate	30593505
Osteosarcoma	Associate	23433115
Parkinson Disease	Associate	22532838, 30593505
Polypoidal Choroidal Vasculopathy	Associate	22549408
Spinocerebellar ataxia 23	Associate	37558815
Spinocerebellar Ataxias	Associate	37558815

TDP2 (tyrosyl-DNA phosphodiesterase 2)