Incidental Mutation 'IGL00780:Tdp1'
ID 14415
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Tdp1
Ensembl Gene ENSMUSG00000021177
Gene Name tyrosyl-DNA phosphodiesterase 1
Synonyms 4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556
Accession Numbers
Essential gene? Probably non essential (E-score: 0.220) question?
Stock # IGL00780
Quality Score
Status
Chromosome 12
Chromosomal Location 99850776-99921478 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 99859907 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 198 (V198A)
Ref Sequence ENSEMBL: ENSMUSP00000118656 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021594] [ENSMUST00000137653] [ENSMUST00000153627]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000021594
AA Change: V198A

PolyPhen 2 Score 0.788 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: V198A

DomainStartEndE-ValueType
low complexity region 13 32 N/A INTRINSIC
Pfam:Tyr-DNA_phospho 164 583 2.7e-142 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000137653
SMART Domains Protein: ENSMUSP00000123269
Gene: ENSMUSG00000021177

DomainStartEndE-ValueType
low complexity region 13 32 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151019
Predicted Effect possibly damaging
Transcript: ENSMUST00000153627
AA Change: V198A

PolyPhen 2 Score 0.788 (Sensitivity: 0.85; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: V198A

DomainStartEndE-ValueType
low complexity region 13 32 N/A INTRINSIC
Pfam:Tyr-DNA_phospho 166 583 2.4e-142 PFAM
Coding Region Coverage
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] 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 remove glycolate from single-stranded DNA containing 3-prime phosphoglycolate, suggesting a role in repair of free-radical mediated DNA double-strand breaks. This gene is a member of the phospholipase D family and contains two PLD phosphodiesterase domains. Mutations in this gene are associated with the disease spinocerebellar ataxia with axonal neuropathy (SCAN1). [provided by RefSeq, Aug 2016]
PHENOTYPE: Mice homozygous for a null allele exhibit defective single strand DNA repair in neurons, decreased cerebellum size and increased sensitivity to topotecan. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 40 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abi3bp A G 16: 56,423,168 (GRCm39) D440G probably null Het
Acvrl1 T A 15: 101,035,248 (GRCm39) F258Y probably damaging Het
Ano1 A G 7: 144,209,367 (GRCm39) S278P probably damaging Het
Aoc1l3 A G 6: 48,964,673 (GRCm39) D227G probably damaging Het
AW146154 T C 7: 41,129,883 (GRCm39) Y411C probably damaging Het
Blnk T A 19: 40,922,890 (GRCm39) K412M probably benign Het
Clpb C T 7: 101,427,815 (GRCm39) R387* probably null Het
Dach1 A T 14: 98,138,858 (GRCm39) N528K possibly damaging Het
Dag1 A T 9: 108,086,818 (GRCm39) W108R probably damaging Het
Elapor2 A G 5: 9,472,367 (GRCm39) T355A probably damaging Het
Fbn2 T C 18: 58,229,060 (GRCm39) T717A probably damaging Het
Fnbp1l T C 3: 122,342,898 (GRCm39) D394G possibly damaging Het
Gaa T A 11: 119,165,117 (GRCm39) probably null Het
Gpr158 A T 2: 21,831,629 (GRCm39) K910* probably null Het
Grb14 G A 2: 64,745,062 (GRCm39) P99S probably damaging Het
Gtf2h2 T C 13: 100,615,729 (GRCm39) D264G probably benign Het
Heatr3 A G 8: 88,897,568 (GRCm39) I667V probably benign Het
Hsp90ab1 T C 17: 45,880,490 (GRCm39) N407S probably damaging Het
Htr2a A T 14: 74,943,645 (GRCm39) L408F possibly damaging Het
Itgb5 G A 16: 33,705,345 (GRCm39) V212I probably damaging Het
Kmt2c G A 5: 25,516,049 (GRCm39) T2598I probably benign Het
Lcorl T C 5: 45,904,637 (GRCm39) N137S probably damaging Het
Lef1 T C 3: 130,986,779 (GRCm39) F212L possibly damaging Het
Map2k5 T C 9: 63,188,359 (GRCm39) probably benign Het
Med15 G A 16: 17,471,351 (GRCm39) T642I probably damaging Het
Nasp C A 4: 116,461,196 (GRCm39) E274* probably null Het
Nup210l A T 3: 90,098,156 (GRCm39) probably benign Het
Pgghg T C 7: 140,525,264 (GRCm39) probably null Het
Plpp1 A G 13: 112,988,040 (GRCm39) I54M probably damaging Het
Poldip3 C T 15: 83,022,680 (GRCm39) G35R probably damaging Het
Ppig A T 2: 69,563,268 (GRCm39) E81D possibly damaging Het
Ptpn21 G T 12: 98,646,630 (GRCm39) T999K probably damaging Het
Rad9b T C 5: 122,482,310 (GRCm39) I142V probably benign Het
Ralgps1 A T 2: 33,163,639 (GRCm39) H139Q probably damaging Het
Rdh16f2 T C 10: 127,710,961 (GRCm39) probably null Het
Sema3d G A 5: 12,574,293 (GRCm39) R265Q probably damaging Het
Trim43c A T 9: 88,723,909 (GRCm39) D145V probably benign Het
Trpc4 C T 3: 54,209,596 (GRCm39) P654S probably damaging Het
Yy1 T G 12: 108,781,463 (GRCm39) I376S probably damaging Het
Zfp773 T A 7: 7,136,113 (GRCm39) Q161L probably benign Het
Other mutations in Tdp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01099:Tdp1 APN 12 99,881,704 (GRCm39) splice site probably benign
IGL01295:Tdp1 APN 12 99,857,929 (GRCm39) missense probably benign 0.00
IGL01409:Tdp1 APN 12 99,875,940 (GRCm39) missense possibly damaging 0.83
IGL01482:Tdp1 APN 12 99,857,639 (GRCm39) missense probably benign
IGL03116:Tdp1 APN 12 99,921,290 (GRCm39) missense probably benign 0.27
BB004:Tdp1 UTSW 12 99,878,555 (GRCm39) missense probably damaging 1.00
BB014:Tdp1 UTSW 12 99,878,555 (GRCm39) missense probably damaging 1.00
R0008:Tdp1 UTSW 12 99,921,217 (GRCm39) splice site probably benign
R0033:Tdp1 UTSW 12 99,901,311 (GRCm39) missense probably benign 0.30
R0092:Tdp1 UTSW 12 99,921,248 (GRCm39) missense probably damaging 1.00
R0485:Tdp1 UTSW 12 99,876,101 (GRCm39) missense probably benign 0.30
R0611:Tdp1 UTSW 12 99,875,970 (GRCm39) missense probably benign
R0853:Tdp1 UTSW 12 99,901,326 (GRCm39) missense probably damaging 0.96
R1539:Tdp1 UTSW 12 99,878,571 (GRCm39) missense probably damaging 1.00
R1692:Tdp1 UTSW 12 99,921,260 (GRCm39) missense probably damaging 1.00
R1751:Tdp1 UTSW 12 99,857,602 (GRCm39) splice site probably null
R1767:Tdp1 UTSW 12 99,857,602 (GRCm39) splice site probably null
R3788:Tdp1 UTSW 12 99,858,011 (GRCm39) splice site probably benign
R3790:Tdp1 UTSW 12 99,858,011 (GRCm39) splice site probably benign
R3837:Tdp1 UTSW 12 99,860,967 (GRCm39) critical splice acceptor site probably null
R3917:Tdp1 UTSW 12 99,860,976 (GRCm39) missense probably damaging 1.00
R4209:Tdp1 UTSW 12 99,864,588 (GRCm39) missense probably damaging 1.00
R4211:Tdp1 UTSW 12 99,864,588 (GRCm39) missense probably damaging 1.00
R4509:Tdp1 UTSW 12 99,921,324 (GRCm39) utr 3 prime probably benign
R4774:Tdp1 UTSW 12 99,868,623 (GRCm39) missense possibly damaging 0.56
R4859:Tdp1 UTSW 12 99,876,070 (GRCm39) missense probably benign 0.20
R5229:Tdp1 UTSW 12 99,859,919 (GRCm39) missense probably damaging 1.00
R5348:Tdp1 UTSW 12 99,881,765 (GRCm39) missense probably damaging 1.00
R5441:Tdp1 UTSW 12 99,876,544 (GRCm39) missense probably damaging 1.00
R5457:Tdp1 UTSW 12 99,861,005 (GRCm39) nonsense probably null
R5685:Tdp1 UTSW 12 99,868,611 (GRCm39) missense possibly damaging 0.51
R6329:Tdp1 UTSW 12 99,880,331 (GRCm39) missense probably benign 0.02
R6329:Tdp1 UTSW 12 99,880,330 (GRCm39) missense probably damaging 0.99
R7060:Tdp1 UTSW 12 99,877,947 (GRCm39) missense probably benign 0.02
R7066:Tdp1 UTSW 12 99,860,991 (GRCm39) missense probably benign
R7479:Tdp1 UTSW 12 99,857,654 (GRCm39) missense probably benign 0.00
R7927:Tdp1 UTSW 12 99,878,555 (GRCm39) missense probably damaging 1.00
R8556:Tdp1 UTSW 12 99,857,527 (GRCm39) missense probably benign 0.07
R8774:Tdp1 UTSW 12 99,877,917 (GRCm39) missense probably damaging 1.00
R8774-TAIL:Tdp1 UTSW 12 99,877,917 (GRCm39) missense probably damaging 1.00
R9521:Tdp1 UTSW 12 99,877,906 (GRCm39) missense probably damaging 0.98
Z1177:Tdp1 UTSW 12 99,877,892 (GRCm39) missense probably benign
Posted On 2012-12-06