Incidental Mutation 'R3790:Tdp1'
| ID |
272504 |
| Institutional Source |
Beutler Lab
|
| 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 # |
R3790 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
12 |
| Chromosomal Location |
99850776-99921478 bp(+) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
A to G
at 99858011 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| 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 benign
Transcript: ENSMUST00000021594
|
| SMART Domains |
Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
| 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: ENSMUST00000125639
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000137653
|
| SMART Domains |
Protein: ENSMUSP00000123269
Gene: ENSMUSG00000021177
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
13 |
32 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151019
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000153627
|
| SMART Domains |
Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
| 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: ENSMUST00000221396
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.0%
|
| Validation Efficiency |
98% (47/48) |
| 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: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acat3 |
G |
A |
17: 13,147,460 (GRCm39) |
Q186* |
probably null |
Het |
| Alk |
A |
G |
17: 72,910,427 (GRCm39) |
L93P |
possibly damaging |
Het |
| Ankrd24 |
C |
T |
10: 81,478,513 (GRCm39) |
|
probably benign |
Het |
| Anks6 |
A |
T |
4: 47,049,212 (GRCm39) |
V231E |
probably damaging |
Het |
| Ap5z1 |
C |
T |
5: 142,456,168 (GRCm39) |
S329L |
probably benign |
Het |
| Asic4 |
C |
A |
1: 75,446,485 (GRCm39) |
|
probably benign |
Het |
| Cemip2 |
T |
G |
19: 21,784,816 (GRCm39) |
I433S |
probably damaging |
Het |
| Cers4 |
C |
A |
8: 4,568,285 (GRCm39) |
Q113K |
possibly damaging |
Het |
| Ces3b |
A |
T |
8: 105,813,520 (GRCm39) |
I264F |
possibly damaging |
Het |
| Cops3 |
T |
C |
11: 59,718,797 (GRCm39) |
M166V |
probably benign |
Het |
| Corin |
T |
C |
5: 72,592,641 (GRCm39) |
Q184R |
probably benign |
Het |
| Dnah8 |
G |
A |
17: 31,073,872 (GRCm39) |
R4514H |
probably damaging |
Het |
| Drosha |
T |
A |
15: 12,912,623 (GRCm39) |
Y1080* |
probably null |
Het |
| Gm53 |
T |
C |
11: 96,142,477 (GRCm39) |
|
noncoding transcript |
Het |
| Hmcn1 |
A |
G |
1: 150,498,745 (GRCm39) |
S4045P |
probably benign |
Het |
| Kif22 |
A |
G |
7: 126,628,668 (GRCm39) |
L480P |
probably damaging |
Het |
| Lepr |
A |
T |
4: 101,648,111 (GRCm39) |
|
probably benign |
Het |
| Lnpk |
A |
T |
2: 74,352,607 (GRCm39) |
S358R |
probably benign |
Het |
| Lnx1 |
A |
G |
5: 74,789,027 (GRCm39) |
|
probably benign |
Het |
| Lrsam1 |
T |
C |
2: 32,848,171 (GRCm39) |
E43G |
probably null |
Het |
| Mug1 |
G |
A |
6: 121,861,587 (GRCm39) |
V1350I |
probably benign |
Het |
| Nbea |
T |
A |
3: 55,912,450 (GRCm39) |
E1112D |
probably benign |
Het |
| Nepn |
T |
A |
10: 52,276,626 (GRCm39) |
L60I |
probably damaging |
Het |
| Oas1e |
T |
C |
5: 120,933,475 (GRCm39) |
E30G |
probably damaging |
Het |
| Or4c122 |
A |
G |
2: 89,079,337 (GRCm39) |
F234L |
probably benign |
Het |
| Or4k5 |
A |
C |
14: 50,386,026 (GRCm39) |
F102V |
possibly damaging |
Het |
| Pou2f1 |
G |
C |
1: 165,722,538 (GRCm39) |
P349R |
probably damaging |
Het |
| Prmt8 |
A |
T |
6: 127,688,110 (GRCm39) |
I236N |
probably damaging |
Het |
| Psg23 |
C |
A |
7: 18,346,126 (GRCm39) |
V190L |
probably benign |
Het |
| Psg29 |
A |
G |
7: 16,938,950 (GRCm39) |
K75E |
possibly damaging |
Het |
| Ranbp17 |
GCCTGGATACTGACC |
GCC |
11: 33,169,203 (GRCm39) |
|
probably benign |
Het |
| Rgs4 |
A |
G |
1: 169,571,991 (GRCm39) |
S103P |
probably damaging |
Het |
| Sis |
T |
C |
3: 72,828,747 (GRCm39) |
Y1144C |
probably damaging |
Het |
| Slc16a14 |
T |
C |
1: 84,907,001 (GRCm39) |
|
probably benign |
Het |
| Snrnp35 |
T |
A |
5: 124,628,248 (GRCm39) |
D20E |
probably damaging |
Het |
| Syce1l |
C |
A |
8: 114,369,897 (GRCm39) |
A10E |
possibly damaging |
Het |
| Tmem212 |
T |
C |
3: 27,940,594 (GRCm39) |
|
probably null |
Het |
| Tomm20l |
C |
T |
12: 71,158,516 (GRCm39) |
A58V |
possibly damaging |
Het |
| Ttn |
C |
A |
2: 76,568,471 (GRCm39) |
C27474F |
probably damaging |
Het |
| Ttn |
A |
G |
2: 76,804,552 (GRCm39) |
V240A |
probably benign |
Het |
| Vars1 |
A |
G |
17: 35,218,310 (GRCm39) |
V48A |
probably benign |
Het |
| Vmn2r1 |
T |
C |
3: 63,994,185 (GRCm39) |
|
probably null |
Het |
| Washc2 |
A |
G |
6: 116,224,933 (GRCm39) |
|
probably benign |
Het |
| Zfp943 |
A |
G |
17: 22,211,403 (GRCm39) |
D163G |
possibly damaging |
Het |
| Zmym5 |
T |
C |
14: 57,031,230 (GRCm39) |
Y626C |
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 |
|
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- AGTTGTGGATAGAAGCCCTCC -3'
(R):5'- CAGTGCCAAGAACTACCAGG -3'
Sequencing Primer
(F):5'- GATAGAAGCCCTCCTGCCAG -3'
(R):5'- CTATAGGGCTTTGAGGAAGACTC -3'
|
| Posted On |
2015-03-25 |
Incidental Mutation