Gene Gene information from NCBI Gene database.
Entrez ID 51567
Gene name Tyrosyl-DNA phosphodiesterase 2
Gene symbol TDP2
Synonyms (NCBI Gene)
AD022EAP2EAPIITTRAPdJ30M3.3hTDP2
Chromosome 6
Chromosome location 6p22.3
Summary 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
SNPs SNP information provided by dbSNP.
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
miRNA miRNA information provided by mirtarbase database.
118
miRTarBase ID miRNA Experiments Reference
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
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
605764 17768 ENSG00000111802
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
Sequence length 362
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Nonhomologous End-Joining (NHEJ)
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
11
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)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Cerebellar ataxia Pathogenic rs1240335250 RCV001250405
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Sarcoma Pathogenic rs372245668 RCV005893910
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spinocerebellar ataxia, autosomal recessive 23 Pathogenic; Likely pathogenic rs142438588, rs1778000792, rs2127617300, rs372245668, rs879255601 RCV003149159
RCV001785058
RCV001783860
RCV000211705
RCV000211707
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ATAXIA, SPINOCEREBELLAR Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE CEREBELLAR ATAXIA, EPILEPSY, INTELLECTUAL DISABILITY SYNDROME DUE TO TUD DEFICIENCY Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE CEREBELLAR ATAXIA-EPILEPSY-INTELLECTUAL DISABILITY SYNDROME DUE TO TUD DEFICIENCY Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adenocarcinoma of large intestine Colorectal Cancer GWASCAT_DG 26621817
★☆☆☆☆
Found in Text Mining only
Ataxia, Spinocerebellar Spinocerebellar Ataxia BEFREE 31410782
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Ataxia, Spinocerebellar Spinocerebellar Ataxia CTD_human_DG
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Atrioventricular Block Atrioventricular block BEFREE 23995044, 25426817
★☆☆☆☆
Found in Text Mining only
Autosomal recessive cerebellar ataxia-epilepsy-intellectual disability syndrome due to TUD deficiency Cerebellar Ataxia, Epilepsy, Mental Retardation Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Brachycephaly Brachycephaly HPO_DG
★☆☆☆☆
Found in Text Mining only
Breast Neoplasms Breast neoplasm Pubtator 28794467 Associate
★☆☆☆☆
Found in Text Mining only
Carcinogenesis Carcinogenesis Pubtator 23433115 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma of lung Lung carcinoma BEFREE 21478903, 22508727, 26701725
★☆☆☆☆
Found in Text Mining only
Carcinoma Renal Cell Renal cell carcinoma Pubtator 26255626 Associate
★☆☆☆☆
Found in Text Mining only