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.	55775
Gene name Gene Name - the full gene name approved by the HGNC.	Tyrosyl-DNA phosphodiesterase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	TDP1
Synonyms (NCBI Gene) Gene synonyms aliases	-
Chromosome Chromosome number	14
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	14q32.11
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is involved in repairing stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3-prime phosphate of DNA. This protein may also

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SNP ID	Visualize variation	Clinical significance	Consequence
rs119467003	A>G	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs769278668	AA>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs1376503364	T>G	Likely-pathogenic	Non coding transcript variant, missense variant, initiator codon variant, 5 prime UTR variant
rs1566929134	TCCAGAACTGTATGGAAGTAAAGGTGAGACACAGATAAAGGAAAACCACGGGTGGATATGCATAAGAAAAACAAACAGAGCCCAGGAGAAGCCTTTGGTCTCAGTGGGATCCTGGCTCATGGAACCCTCTGGAAGCTCAAGTTTGCAGAGGGCCCTTTGCCAGCCTGTCTGGGGCCTTGTAGCCACTGGTTAGTCTTGGAATCCCTTTGCACTCCTATAATTACTATACAGATCCTTCCTGACTTACACTGGGGC	Likely-pathogenic	Non coding transcript variant, splice donor variant, intron variant, coding sequence variant

Show/Hide all(169)

miRTarBase ID	miRNA	Experiments	Reference
MIRT002780	hsa-miR-1-3p	Microarray	15685193
MIRT002780	hsa-miR-1-3p	Microarray;Other	15685193
MIRT024260	hsa-miR-215-5p	Microarray	19074876
MIRT026291	hsa-miR-192-5p	Microarray	19074876
MIRT044817	hsa-miR-320a	CLASH	23622248
MIRT041491	hsa-miR-193b-3p	CLASH	23622248
MIRT1416979	hsa-miR-1184	CLIP-seq
MIRT1416980	hsa-miR-1193	CLIP-seq
MIRT1416981	hsa-miR-1205	CLIP-seq
MIRT1416982	hsa-miR-1224-5p	CLIP-seq
MIRT1416983	hsa-miR-1267	CLIP-seq
MIRT1416984	hsa-miR-127-5p	CLIP-seq
MIRT1416985	hsa-miR-128	CLIP-seq
MIRT1416986	hsa-miR-1291	CLIP-seq
MIRT1416987	hsa-miR-1294	CLIP-seq
MIRT1416988	hsa-miR-1299	CLIP-seq
MIRT1416989	hsa-miR-146b-3p	CLIP-seq
MIRT1416990	hsa-miR-1827	CLIP-seq
MIRT1416991	hsa-miR-185	CLIP-seq
MIRT1416992	hsa-miR-18a	CLIP-seq
MIRT1416993	hsa-miR-18b	CLIP-seq
MIRT1416994	hsa-miR-1909	CLIP-seq
MIRT1416995	hsa-miR-1976	CLIP-seq
MIRT1416996	hsa-miR-214	CLIP-seq
MIRT1416997	hsa-miR-22	CLIP-seq
MIRT1416998	hsa-miR-24	CLIP-seq
MIRT1416999	hsa-miR-27a	CLIP-seq
MIRT1417000	hsa-miR-27b	CLIP-seq
MIRT1417001	hsa-miR-3120-5p	CLIP-seq
MIRT1417002	hsa-miR-3150b-3p	CLIP-seq
MIRT1417003	hsa-miR-3173-5p	CLIP-seq
MIRT1417004	hsa-miR-3179	CLIP-seq
MIRT1417005	hsa-miR-3190	CLIP-seq
MIRT1417006	hsa-miR-3202	CLIP-seq
MIRT1417007	hsa-miR-320b	CLIP-seq
MIRT1417008	hsa-miR-320c	CLIP-seq
MIRT1417009	hsa-miR-320d	CLIP-seq
MIRT1417010	hsa-miR-339-5p	CLIP-seq
MIRT1417011	hsa-miR-3545-3p	CLIP-seq
MIRT1417012	hsa-miR-3616-3p	CLIP-seq
MIRT1417013	hsa-miR-3619-5p	CLIP-seq
MIRT1417014	hsa-miR-3647-3p	CLIP-seq
MIRT1417015	hsa-miR-3689a-3p	CLIP-seq
MIRT1417016	hsa-miR-3689c	CLIP-seq
MIRT1417017	hsa-miR-370	CLIP-seq
MIRT1417018	hsa-miR-3919	CLIP-seq
MIRT1417019	hsa-miR-3978	CLIP-seq
MIRT1417020	hsa-miR-4270	CLIP-seq
MIRT1417021	hsa-miR-4284	CLIP-seq
MIRT1417022	hsa-miR-4287	CLIP-seq
MIRT1417023	hsa-miR-4306	CLIP-seq
MIRT1417024	hsa-miR-4316	CLIP-seq
MIRT1417025	hsa-miR-4330	CLIP-seq
MIRT1417026	hsa-miR-4421	CLIP-seq
MIRT1417027	hsa-miR-4429	CLIP-seq
MIRT1417028	hsa-miR-4434	CLIP-seq
MIRT1417029	hsa-miR-4441	CLIP-seq
MIRT1417030	hsa-miR-4469	CLIP-seq
MIRT1417031	hsa-miR-4474-3p	CLIP-seq
MIRT1417032	hsa-miR-4516	CLIP-seq
MIRT1417033	hsa-miR-4530	CLIP-seq
MIRT1417034	hsa-miR-4533	CLIP-seq
MIRT1417035	hsa-miR-4534	CLIP-seq
MIRT1417036	hsa-miR-4539	CLIP-seq
MIRT1417037	hsa-miR-4644	CLIP-seq
MIRT1417038	hsa-miR-4656	CLIP-seq
MIRT1417039	hsa-miR-4661-3p	CLIP-seq
MIRT1417040	hsa-miR-4670-5p	CLIP-seq
MIRT1417041	hsa-miR-4677-3p	CLIP-seq
MIRT1417042	hsa-miR-4685-3p	CLIP-seq
MIRT1417043	hsa-miR-4716-5p	CLIP-seq
MIRT1417044	hsa-miR-4728-5p	CLIP-seq
MIRT1417045	hsa-miR-4735-3p	CLIP-seq
MIRT1417046	hsa-miR-4738-5p	CLIP-seq
MIRT1417047	hsa-miR-4751	CLIP-seq
MIRT1417048	hsa-miR-4755-3p	CLIP-seq
MIRT1417049	hsa-miR-4756-3p	CLIP-seq
MIRT1417050	hsa-miR-4761-3p	CLIP-seq
MIRT1417051	hsa-miR-4766-5p	CLIP-seq
MIRT1417052	hsa-miR-4782-5p	CLIP-seq
MIRT1417053	hsa-miR-4784	CLIP-seq
MIRT1417054	hsa-miR-4802-5p	CLIP-seq
MIRT1417055	hsa-miR-4803	CLIP-seq
MIRT1417056	hsa-miR-494	CLIP-seq
MIRT1417057	hsa-miR-510	CLIP-seq
MIRT1417058	hsa-miR-512-5p	CLIP-seq
MIRT1417059	hsa-miR-513a-3p	CLIP-seq
MIRT1417060	hsa-miR-513a-5p	CLIP-seq
MIRT1417061	hsa-miR-515-3p	CLIP-seq
MIRT1417062	hsa-miR-516b	CLIP-seq
MIRT1417063	hsa-miR-519e	CLIP-seq
MIRT1417064	hsa-miR-520d-5p	CLIP-seq
MIRT1417065	hsa-miR-524-5p	CLIP-seq
MIRT1417066	hsa-miR-548l	CLIP-seq
MIRT1417067	hsa-miR-548n	CLIP-seq
MIRT1417068	hsa-miR-548t	CLIP-seq
MIRT1417069	hsa-miR-600	CLIP-seq
MIRT1417070	hsa-miR-671-5p	CLIP-seq
MIRT1417071	hsa-miR-761	CLIP-seq
MIRT1417072	hsa-miR-766	CLIP-seq
MIRT1417073	hsa-miR-885-5p	CLIP-seq
MIRT1417074	hsa-miR-1323	CLIP-seq
MIRT1417007	hsa-miR-320b	CLIP-seq
MIRT1417008	hsa-miR-320c	CLIP-seq
MIRT1417009	hsa-miR-320d	CLIP-seq
MIRT1417012	hsa-miR-3616-3p	CLIP-seq
MIRT1417075	hsa-miR-3915	CLIP-seq
MIRT1417076	hsa-miR-3928	CLIP-seq
MIRT1417027	hsa-miR-4429	CLIP-seq
MIRT1417050	hsa-miR-4761-3p	CLIP-seq
MIRT1417077	hsa-miR-488	CLIP-seq
MIRT1417057	hsa-miR-510	CLIP-seq
MIRT1417058	hsa-miR-512-5p	CLIP-seq
MIRT1417078	hsa-miR-548o	CLIP-seq
MIRT1417079	hsa-miR-548u	CLIP-seq
MIRT2125074	hsa-miR-4795-5p	CLIP-seq
MIRT2125075	hsa-miR-1324	CLIP-seq
MIRT2125076	hsa-miR-3138	CLIP-seq
MIRT2125077	hsa-miR-3942-3p	CLIP-seq
MIRT2125078	hsa-miR-4475	CLIP-seq
MIRT2125079	hsa-miR-4477b	CLIP-seq
MIRT2125080	hsa-miR-4712-5p	CLIP-seq
MIRT1417043	hsa-miR-4716-5p	CLIP-seq
MIRT2125074	hsa-miR-4795-5p	CLIP-seq
MIRT1417064	hsa-miR-520d-5p	CLIP-seq
MIRT1417065	hsa-miR-524-5p	CLIP-seq
MIRT2125081	hsa-miR-770-5p	CLIP-seq
MIRT1416982	hsa-miR-1224-5p	CLIP-seq
MIRT1416984	hsa-miR-127-5p	CLIP-seq
MIRT1416987	hsa-miR-1294	CLIP-seq
MIRT2347496	hsa-miR-1322	CLIP-seq
MIRT1416991	hsa-miR-185	CLIP-seq
MIRT2347497	hsa-miR-19a	CLIP-seq
MIRT2347498	hsa-miR-19b	CLIP-seq
MIRT1417002	hsa-miR-3150b-3p	CLIP-seq
MIRT1417007	hsa-miR-320b	CLIP-seq
MIRT1417008	hsa-miR-320c	CLIP-seq
MIRT1417009	hsa-miR-320d	CLIP-seq
MIRT2347499	hsa-miR-330-3p	CLIP-seq
MIRT1417012	hsa-miR-3616-3p	CLIP-seq
MIRT1417023	hsa-miR-4306	CLIP-seq
MIRT1417024	hsa-miR-4316	CLIP-seq
MIRT1417027	hsa-miR-4429	CLIP-seq
MIRT2347500	hsa-miR-4432	CLIP-seq
MIRT1417028	hsa-miR-4434	CLIP-seq
MIRT1417032	hsa-miR-4516	CLIP-seq
MIRT1417037	hsa-miR-4644	CLIP-seq
MIRT2347501	hsa-miR-4658	CLIP-seq
MIRT2347502	hsa-miR-4666-3p	CLIP-seq
MIRT1417040	hsa-miR-4670-5p	CLIP-seq
MIRT2347503	hsa-miR-4731-3p	CLIP-seq
MIRT1417047	hsa-miR-4751	CLIP-seq
MIRT2347504	hsa-miR-4758-5p	CLIP-seq
MIRT1417050	hsa-miR-4761-3p	CLIP-seq
MIRT1417051	hsa-miR-4766-5p	CLIP-seq
MIRT2347505	hsa-miR-4775	CLIP-seq
MIRT1417053	hsa-miR-4784	CLIP-seq
MIRT2347506	hsa-miR-4801	CLIP-seq
MIRT2347507	hsa-miR-499-5p	CLIP-seq
MIRT1417057	hsa-miR-510	CLIP-seq
MIRT2347508	hsa-miR-512-3p	CLIP-seq
MIRT1417058	hsa-miR-512-5p	CLIP-seq
MIRT2347509	hsa-miR-590-3p	CLIP-seq
MIRT2347510	hsa-miR-628-5p	CLIP-seq
MIRT2461285	hsa-miR-3663-5p	CLIP-seq
MIRT2461286	hsa-miR-4281	CLIP-seq
MIRT1417056	hsa-miR-494	CLIP-seq
MIRT2640462	hsa-miR-3646	CLIP-seq
MIRT1417056	hsa-miR-494	CLIP-seq

Show/Hide all(25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000012	Process	Single strand break repair	IDA	15811850
GO:0000012	Process	Single strand break repair	IEA
GO:0000012	Process	Single strand break repair	IMP	17600775
GO:0003690	Function	Double-stranded DNA binding	IBA
GO:0003690	Function	Double-stranded DNA binding	IDA	15811850
GO:0003697	Function	Single-stranded DNA binding	IBA
GO:0003697	Function	Single-stranded DNA binding	IDA	15811850
GO:0004518	Function	Nuclease activity	IEA
GO:0004527	Function	Exonuclease activity	IEA
GO:0005515	Function	Protein binding	IPI	15744309, 19851285, 24981860, 32814053, 33961781, 35271311
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IDA	17948061
GO:0005737	Component	Cytoplasm	IEA
GO:0005886	Component	Plasma membrane	IDA
GO:0006281	Process	DNA repair	IBA
GO:0006281	Process	DNA repair	IDA	17948061
GO:0006281	Process	DNA repair	IEA
GO:0006302	Process	Double-strand break repair	IDA	12023295
GO:0006974	Process	DNA damage response	IEA
GO:0008081	Function	Phosphoric diester hydrolase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0017005	Function	3'-tyrosyl-DNA phosphodiesterase activity	IBA
GO:0017005	Function	3'-tyrosyl-DNA phosphodiesterase activity	IDA	17118488, 17576665, 17948061, 22822062

MIM	HGNC	e!Ensembl
607198	18884	ENSG00000042088

Protein

UniProt ID

Q9NUW8

Protein name

Tyrosyl-DNA phosphodiesterase 1 (Tyr-DNA phosphodiesterase 1) (EC 3.1.4.-)

Protein function

DNA repair enzyme that can remove a variety of covalent adducts from DNA through hydrolysis of a 3'-phosphodiester bond, giving rise to DNA with a free 3' phosphate. Catalyzes the hydrolysis of dead-end complexes between DNA and the topoisomeras

PDB

1JY1 , 1MU7 , 1MU9 , 1NOP , 1QZQ , 1RFF , 1RFI , 1RG1 , 1RG2 , 1RGT , 1RGU , 1RH0 , 5NW9 , 5NWA , 6DHU , 6DIE , 6DIH , 6DIM , 6DJD , 6DJE , 6DJF , 6DJG , 6DJH , 6DJI , 6DJJ , 6MJ5 , 6MYZ , 6MZ0 , 6N0D , 6N0N , 6N0O , 6N0R , 6N17 , 6N19 , 6W4R , 6W7J , 6W7K , 6W7L , 7UFY , 7UFZ , 8CVQ , 8CW2 , 8UV1 , 8UZV , 8UZZ , 8V0B , 8V0C , 9B3B

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF06087	Tyr-DNA_phospho	165 → 582	Tyrosyl-DNA phosphodiesterase	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitously expressed. Similar expression throughout the central nervous system (whole brain, amygdala, caudate nucleus, cerebellum, cerebral cortex, frontal lobe, hippocampus, medulla oblongata, occipital lobe, putamen, substantia ni

Sequence

MSQEGDYGRWTISSSDESEEEKPKPDKPSTSSLLCARQGAANEPRYTCSEAQKAAHKRKI
SPVKFSNTDSVLPPKRQKSGSQEDLGWCLSSSDDELQPEMPQKQAEKVVIKKEKDISAPN
DGTAQRTENHGAPACHRLKEEEDEYETSGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNS
GALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHA
QAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSP
LYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPG
RFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESM
LTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKW
SAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELG
VLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDT
HGNMWVPS

Sequence length

608

Interactions

View interactions

	KEGG		Reactome
	Base excision repair		Nonhomologous End-Joining (NHEJ)

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Spinocerebellar Ataxia, WITH AXONAL NEUROPATHY	Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 1	rs119467003	N/A

Show/Hide Unknown Diseases (2)

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.
Cerebellar Ataxia	Autosomal recessive cerebellar ataxia	N/A	N/A	ClinVar
Uveal Melanoma	Uveal melanoma	N/A	N/A	GWAS

Show/Hide Text Mining Associations (33)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma Bronchiolo Alveolar	Associate	31383554
Alcoholic Neuropathy	Associate	16141202
Breast Neoplasms	Associate	30947698
Carcinoma Non Small Cell Lung	Associate	17118488, 28802254
Cardiovascular Diseases	Associate	22503546
Carotid Stenosis	Associate	22503546
Cerebral Hemorrhage	Associate	30836997
Charcot Marie Tooth Disease	Associate	25841101
Chromosomal Instability	Stimulate	27551064
Colorectal Neoplasms	Associate	25522766
Drug Hypersensitivity	Associate	16751265, 19505854, 28802254
Drug Related Side Effects and Adverse Reactions	Associate	23913164, 25609251, 34008967
Emphysema	Associate	31383554
Glioblastoma	Associate	24335147
Heredodegenerative Disorders Nervous System	Associate	25609251
Leukemia Lymphoma Adult T Cell	Inhibit	28993637
Lung Neoplasms	Associate	24355542
Mitochondrial Diseases	Associate	31383554
Neoplasms	Associate	15333697, 24335147, 24355542, 25841101, 27551064, 28802254, 34008967, 39596476
Neoplasms	Stimulate	23913164
Neurodegenerative Diseases	Associate	16141202, 26578593
Neuroinflammatory Diseases	Associate	30836997
Neurologic Manifestations	Associate	31533039
Neutropenia	Associate	19604089
Reinjuries	Associate	21628532
Rhabdomyosarcoma	Associate	23913164, 29898404
Rhabdomyosarcoma	Stimulate	27551064
Small Cell Lung Carcinoma	Associate	28974547
Spinocerebellar ataxia autosomal recessive 1	Associate	15647511, 15920477, 19505854, 22155078
Spinocerebellar ataxia autosomal recessive with axonal neuropathy	Associate	25609251, 25841101, 26578593
Spinocerebellar Ataxias	Associate	15333697, 16141202
Syndrome	Associate	26578593
Tourette Syndrome	Associate	23852793

TDP1 (tyrosyl-DNA phosphodiesterase 1)