Incidental Mutation 'R5348:Tdp1'
ID 422746
Institutional Source Beutler Lab
Gene Symbol Tdp1
Ensembl Gene ENSMUSG00000021177
Gene Name tyrosyl-DNA phosphodiesterase 1
Synonyms 4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556
MMRRC Submission 042927-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.220) question?
Stock # R5348 (G1)
Quality Score 225
Status Not validated
Chromosome 12
Chromosomal Location 99850776-99921478 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 99881765 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 498 (Y498C)
Ref Sequence ENSEMBL: ENSMUSP00000118656 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021594] [ENSMUST00000153627]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000021594
AA Change: Y498C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: Y498C

DomainStartEndE-ValueType
low complexity region 13 32 N/A INTRINSIC
Pfam:Tyr-DNA_phospho 164 583 2.7e-142 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126424
Predicted Effect noncoding transcript
Transcript: ENSMUST00000128739
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151019
Predicted Effect probably damaging
Transcript: ENSMUST00000153627
AA Change: Y498C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: Y498C

DomainStartEndE-ValueType
low complexity region 13 32 N/A INTRINSIC
Pfam:Tyr-DNA_phospho 166 583 2.4e-142 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000220685
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.8%
  • 10x: 97.6%
  • 20x: 96.0%
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: 36 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcg5 A T 17: 84,978,634 (GRCm39) C275S possibly damaging Het
Bltp1 A G 3: 37,102,295 (GRCm39) E1331G probably damaging Het
Cdk12 T A 11: 98,095,118 (GRCm39) S309T probably benign Het
Cep295nl T C 11: 118,224,425 (GRCm39) R140G probably damaging Het
Chd8 A G 14: 52,470,155 (GRCm39) V485A probably damaging Het
Chn2 A G 6: 54,277,203 (GRCm39) I279V probably damaging Het
Cux2 A G 5: 122,004,041 (GRCm39) S1032P probably damaging Het
Ddx55 T A 5: 124,692,628 (GRCm39) M44K probably damaging Het
Dpyd T A 3: 118,575,592 (GRCm39) H143Q probably benign Het
Fbxo10 A G 4: 45,058,934 (GRCm39) W268R probably damaging Het
Gmfg A G 7: 28,145,819 (GRCm39) D86G probably benign Het
Gpd1 T C 15: 99,620,021 (GRCm39) V273A possibly damaging Het
Grhpr T C 4: 44,985,393 (GRCm39) I158T probably damaging Het
Itpr2 A G 6: 146,378,191 (GRCm39) F53L possibly damaging Het
Kctd21 A G 7: 96,997,177 (GRCm39) I217V probably benign Het
Lrfn2 A G 17: 49,403,718 (GRCm39) T614A probably benign Het
Lrrc7 T A 3: 157,880,963 (GRCm39) D491V probably benign Het
Myo7b T C 18: 32,116,972 (GRCm39) E916G probably damaging Het
Nf1 C T 11: 79,455,725 (GRCm39) T550I probably damaging Het
Nsd1 A G 13: 55,460,147 (GRCm39) T2125A probably benign Het
Olfml2b A G 1: 170,489,995 (GRCm39) E205G probably benign Het
Or8k37 A T 2: 86,469,150 (GRCm39) L301I probably benign Het
Papolb T C 5: 142,514,972 (GRCm39) T224A possibly damaging Het
Pcnx2 T C 8: 126,545,495 (GRCm39) E1172G probably damaging Het
Ppip5k2 A G 1: 97,675,317 (GRCm39) L362S possibly damaging Het
Ppp1r9b T A 11: 94,887,438 (GRCm39) Y59* probably null Het
Pramel12 T C 4: 143,143,351 (GRCm39) L39P probably damaging Het
Rapgef5 T A 12: 117,652,346 (GRCm39) S76R probably benign Het
Rnh1 A T 7: 140,743,321 (GRCm39) V218D probably damaging Het
Robo4 CGG CG 9: 37,322,786 (GRCm39) probably null Het
Slc4a7 G T 14: 14,786,310 (GRCm38) V999L probably benign Het
Slco4c1 A T 1: 96,770,254 (GRCm39) I270N probably damaging Het
Tfip11 A G 5: 112,483,534 (GRCm39) S650G probably benign Het
Ttn T C 2: 76,608,638 (GRCm39) T17793A possibly damaging Het
Ulk2 T C 11: 61,674,439 (GRCm39) T856A probably benign Het
Vps13d C T 4: 144,792,459 (GRCm39) G3726E probably damaging 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
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
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'- CTGAACAGAGTCCCATCAGC -3'
(R):5'- TAGTCACAGGCCTCCTTTCAGG -3'

Sequencing Primer
(F):5'- AGTCCCAGACTGCTCCTG -3'
(R):5'- CTTTCAGGCTCAGTGACGGAAG -3'
Posted On 2016-08-04