Incidental Mutation 'R3917:Tdp1'
ID 307374
Institutional Source Beutler Lab
Gene Symbol Tdp1
Ensembl Gene ENSMUSG00000021177
Gene Name tyrosyl-DNA phosphodiesterase 1
Synonyms 4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556
MMRRC Submission 040914-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.220) question?
Stock # R3917 (G1)
Quality Score 225
Status Validated
Chromosome 12
Chromosomal Location 99850776-99921478 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 99860976 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 205 (Y205C)
Ref Sequence ENSEMBL: ENSMUSP00000118656 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021594] [ENSMUST00000137653] [ENSMUST00000153627]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000021594
AA Change: Y205C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: Y205C

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 probably damaging
Transcript: ENSMUST00000153627
AA Change: Y205C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: Y205C

DomainStartEndE-ValueType
low complexity region 13 32 N/A INTRINSIC
Pfam:Tyr-DNA_phospho 166 583 2.4e-142 PFAM
Meta Mutation Damage Score 0.9248 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.0%
Validation Efficiency 97% (74/76)
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: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acad12 A G 5: 121,737,277 (GRCm39) V498A probably damaging Het
Adam19 A G 11: 45,951,762 (GRCm39) E37G probably benign Het
Apol11b A G 15: 77,519,504 (GRCm39) I192T probably benign Het
Appl1 A T 14: 26,650,561 (GRCm39) F537Y probably damaging Het
Atad5 A C 11: 79,994,120 (GRCm39) K785N probably null Het
Atp1b2 A G 11: 69,493,901 (GRCm39) V93A probably damaging Het
Bcam T C 7: 19,499,375 (GRCm39) Y216C probably damaging Het
Brca2 A G 5: 150,464,292 (GRCm39) E1352G probably damaging Het
C030005K15Rik A C 10: 97,561,453 (GRCm39) S93A unknown Het
Cadps C T 14: 12,457,702 (GRCm38) A1060T probably benign Het
Ccdc88c A G 12: 100,907,366 (GRCm39) probably null Het
Ccdc89 A G 7: 90,076,033 (GRCm39) D81G probably damaging Het
Ccnt1 A G 15: 98,441,940 (GRCm39) S443P probably benign Het
Cd109 CATTTATTTATTTATTTATTTATTTATTTATTTAT CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT 9: 78,619,782 (GRCm39) probably benign Het
Cdc42bpa T C 1: 179,933,719 (GRCm39) probably null Het
Cdk11b T C 4: 155,711,258 (GRCm39) S47P probably damaging Het
Cfap43 T C 19: 47,886,189 (GRCm39) D142G probably benign Het
Cntnap4 C G 8: 113,602,165 (GRCm39) P1190A probably benign Het
Colgalt2 T A 1: 152,384,362 (GRCm39) Y567* probably null Het
Dner CGCTGCTGCTGCTGCTGCTGCTGCTGC CGCTGCTGCTGCTGCTGCTGCTGC 1: 84,563,270 (GRCm39) probably benign Het
Dock7 T C 4: 98,904,922 (GRCm39) Y651C probably damaging Het
Fzd3 A T 14: 65,473,379 (GRCm39) F130I probably damaging Het
Gabarapl2 T A 8: 112,679,028 (GRCm39) F115L probably benign Het
Gm1043 G A 5: 37,350,285 (GRCm39) probably benign Het
Gm12185 A G 11: 48,806,760 (GRCm39) F144L probably benign Het
Gm21961 A T 15: 64,886,733 (GRCm39) D7E unknown Het
Gtf3a A G 5: 146,892,244 (GRCm39) K332E probably benign Het
Haao A G 17: 84,146,228 (GRCm39) probably null Het
Habp2 T A 19: 56,299,611 (GRCm39) C170S probably damaging Het
Heatr3 T G 8: 88,876,999 (GRCm39) probably null Het
Herc1 T G 9: 66,341,748 (GRCm39) C1846G possibly damaging Het
Hivep3 T C 4: 119,956,624 (GRCm39) S1647P probably benign Het
Hnrnpul1 C T 7: 25,426,300 (GRCm39) R517Q probably damaging Het
Hspg2 A G 4: 137,286,625 (GRCm39) E3648G probably damaging Het
Jaml T C 9: 45,012,449 (GRCm39) probably benign Het
Jund C T 8: 71,151,673 (GRCm39) probably benign Het
Klra14-ps T C 6: 130,134,595 (GRCm39) noncoding transcript Het
Krt88 G A 15: 101,350,809 (GRCm39) probably null Het
Lrp5 G A 19: 3,662,330 (GRCm39) R173C probably damaging Het
Lyzl4 T A 9: 121,412,101 (GRCm39) D105V probably damaging Het
Mst1 A G 9: 107,961,494 (GRCm39) I575V probably benign Het
Myd88 T C 9: 119,170,464 (GRCm39) probably benign Het
Myo1d A T 11: 80,557,404 (GRCm39) V512E probably damaging Het
Ndufv1 A G 19: 4,060,002 (GRCm39) Y33H probably damaging Het
Nwd1 T A 8: 73,394,439 (GRCm39) C608* probably null Het
Or10al2 T A 17: 37,983,684 (GRCm39) F257I probably damaging Het
Or8b37 A T 9: 37,958,841 (GRCm39) I108F probably damaging Het
Patj A T 4: 98,480,245 (GRCm39) K1317* probably null Het
Pld5 A G 1: 175,791,504 (GRCm39) S501P probably benign Het
Pnpo A G 11: 96,830,583 (GRCm39) V146A probably damaging Het
Ppdpf A G 2: 180,829,521 (GRCm39) Y16C probably benign Het
Ppp1r27 A G 11: 120,441,785 (GRCm39) V32A possibly damaging Het
Rbm28 T C 6: 29,154,788 (GRCm39) D294G probably benign Het
Sdk1 T A 5: 142,036,999 (GRCm39) D817E probably damaging Het
Shank3 A G 15: 89,387,587 (GRCm39) D252G possibly damaging Het
Slc29a1 A T 17: 45,899,899 (GRCm39) probably null Het
Slc35a5 G C 16: 44,978,521 (GRCm39) probably benign Het
Slc6a5 T C 7: 49,561,617 (GRCm39) S50P probably damaging Het
Slfn8 A T 11: 82,907,819 (GRCm39) Y241* probably null Het
Slu7 G T 11: 43,331,511 (GRCm39) probably null Het
Smad2 T A 18: 76,421,008 (GRCm39) D82E probably benign Het
Spx A C 6: 142,359,757 (GRCm39) E33A probably damaging Het
Tekt1 A G 11: 72,236,574 (GRCm39) I296T possibly damaging Het
Tgm1 G A 14: 55,950,214 (GRCm39) probably benign Het
Tnks A G 8: 35,320,515 (GRCm39) S719P probably damaging Het
Trip6 A G 5: 137,311,941 (GRCm39) C47R probably benign Het
Trpv3 A G 11: 73,174,560 (GRCm39) D309G possibly damaging Het
Tti2 A G 8: 31,643,547 (GRCm39) K221E possibly damaging Het
Ugcg C T 4: 59,207,798 (GRCm39) P46S probably benign Het
Vmn1r57 A T 7: 5,223,630 (GRCm39) N52Y probably damaging Het
Vmn2r94 A G 17: 18,464,620 (GRCm39) F557L probably benign Het
Zbed5 T C 5: 129,931,118 (GRCm39) Y356H possibly damaging Het
Zfp1005 T A 2: 150,108,039 (GRCm39) probably benign Het
Zic4 C A 9: 91,266,394 (GRCm39) probably benign Het
Other mutations in Tdp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00780:Tdp1 APN 12 99,859,907 (GRCm39) missense possibly damaging 0.79
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
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
Predicted Primers PCR Primer
(F):5'- CCTTTAACCAGGTGTTCTTCAAG -3'
(R):5'- AAAACGTGTTGTTCTCAGCAG -3'

Sequencing Primer
(F):5'- CTTCAAGATGAAGTTTGGGTTGTC -3'
(R):5'- ACTTGTAATCCCAAGGCTGG -3'
Posted On 2015-04-17