Incidental Mutation 'IGL01409:Tdp1'
| ID |
79903 |
| 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)
|
| Stock # |
IGL01409
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
12 |
| Chromosomal Location |
99850776-99921478 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 99875940 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Threonine
at position 297
(I297T)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000118656
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021594]
[ENSMUST00000153627]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000021594
AA Change: I297T
PolyPhen 2
Score 0.827 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: I297T
| 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 |
possibly damaging
Transcript: ENSMUST00000153627
AA Change: I297T
PolyPhen 2
Score 0.827 (Sensitivity: 0.84; Specificity: 0.93)
|
| SMART Domains |
Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: I297T
| 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: ENSMUST00000221445
|
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abtb3 |
C |
T |
10: 85,494,029 (GRCm39) |
A1049V |
possibly damaging |
Het |
| Arhgap26 |
C |
T |
18: 39,243,504 (GRCm39) |
|
probably benign |
Het |
| Asxl1 |
T |
C |
2: 153,234,860 (GRCm39) |
|
probably benign |
Het |
| Atm |
A |
T |
9: 53,410,471 (GRCm39) |
V1037E |
probably benign |
Het |
| Bmp6 |
A |
G |
13: 38,669,865 (GRCm39) |
N383S |
probably damaging |
Het |
| Btf3l4 |
A |
C |
4: 108,676,394 (GRCm39) |
S103R |
probably damaging |
Het |
| Cadps2 |
T |
C |
6: 23,587,440 (GRCm39) |
D321G |
probably damaging |
Het |
| Col24a1 |
G |
A |
3: 145,244,319 (GRCm39) |
S1531N |
probably benign |
Het |
| Cpb1 |
T |
A |
3: 20,303,969 (GRCm39) |
Y365F |
possibly damaging |
Het |
| Dpp6 |
T |
C |
5: 27,762,599 (GRCm39) |
Y238H |
probably damaging |
Het |
| Epha6 |
G |
A |
16: 59,476,100 (GRCm39) |
R1089* |
probably null |
Het |
| Fga |
T |
C |
3: 82,940,059 (GRCm39) |
F571S |
probably damaging |
Het |
| Focad |
A |
G |
4: 88,260,542 (GRCm39) |
T933A |
unknown |
Het |
| Gm57858 |
T |
A |
3: 36,080,077 (GRCm39) |
M227L |
possibly damaging |
Het |
| Gria2 |
A |
G |
3: 80,615,004 (GRCm39) |
|
probably null |
Het |
| Hnrnpul1 |
T |
C |
7: 25,424,077 (GRCm39) |
N725S |
unknown |
Het |
| Ik |
A |
T |
18: 36,889,974 (GRCm39) |
K534N |
probably damaging |
Het |
| Itga8 |
T |
C |
2: 12,196,525 (GRCm39) |
T631A |
probably benign |
Het |
| Kcnip1 |
G |
T |
11: 33,580,593 (GRCm39) |
D214E |
probably benign |
Het |
| Kcnk10 |
A |
T |
12: 98,456,322 (GRCm39) |
Y170N |
probably damaging |
Het |
| Lalba |
A |
G |
15: 98,379,948 (GRCm39) |
|
probably null |
Het |
| Ly75 |
A |
T |
2: 60,152,036 (GRCm39) |
|
probably null |
Het |
| Myh10 |
T |
C |
11: 68,698,045 (GRCm39) |
L1629P |
probably damaging |
Het |
| Myo15b |
C |
A |
11: 115,760,330 (GRCm39) |
C1127* |
probably null |
Het |
| Neurl4 |
T |
G |
11: 69,797,925 (GRCm39) |
N728K |
probably damaging |
Het |
| Nrxn3 |
T |
A |
12: 89,477,128 (GRCm39) |
F801Y |
probably damaging |
Het |
| Nup214 |
G |
T |
2: 31,916,943 (GRCm39) |
|
probably null |
Het |
| Obscn |
G |
A |
11: 58,921,884 (GRCm39) |
R6624C |
probably damaging |
Het |
| Or2g1 |
T |
C |
17: 38,106,413 (GRCm39) |
F26S |
probably damaging |
Het |
| Pdk1 |
A |
G |
2: 71,726,123 (GRCm39) |
T344A |
probably benign |
Het |
| Pitx2 |
C |
A |
3: 129,008,413 (GRCm39) |
S63Y |
probably damaging |
Het |
| Ppara |
A |
C |
15: 85,661,844 (GRCm39) |
L28F |
probably damaging |
Het |
| Rad54l |
G |
A |
4: 115,963,074 (GRCm39) |
T308I |
probably damaging |
Het |
| Sbds |
T |
C |
5: 130,282,907 (GRCm39) |
E7G |
probably damaging |
Het |
| Slc22a19 |
T |
C |
19: 7,688,495 (GRCm39) |
I22V |
probably benign |
Het |
| Slfn10-ps |
T |
C |
11: 82,926,322 (GRCm39) |
|
noncoding transcript |
Het |
| Spag4 |
T |
C |
2: 155,911,252 (GRCm39) |
S396P |
possibly damaging |
Het |
| Spef2 |
C |
A |
15: 9,716,499 (GRCm39) |
L362F |
probably damaging |
Het |
| Srebf2 |
A |
G |
15: 82,055,419 (GRCm39) |
T208A |
probably damaging |
Het |
| Ssc5d |
A |
G |
7: 4,945,808 (GRCm39) |
T947A |
probably benign |
Het |
| Tent5c |
A |
T |
3: 100,380,485 (GRCm39) |
D90E |
probably damaging |
Het |
| Tsen2 |
T |
C |
6: 115,536,555 (GRCm39) |
Y104H |
possibly damaging |
Het |
| Was |
G |
A |
X: 7,954,055 (GRCm39) |
R229C |
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 |
|
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 |
2013-11-05 |
Incidental Mutation