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)
|
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
Domain | Start | End | E-Value | Type |
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
Domain | Start | End | E-Value | Type |
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
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
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 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH 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 |