Incidental Mutation 'R3788:Tdp1'
| ID |
272399 |
| 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 # |
R3788 (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: 95.1%
|
| Validation Efficiency |
100% (61/61) |
| 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: 61 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca4 |
T |
A |
3: 121,846,561 (GRCm39) |
V26E |
possibly damaging |
Het |
| Abhd16a |
A |
G |
17: 35,320,563 (GRCm39) |
N411S |
probably damaging |
Het |
| Akap13 |
G |
A |
7: 75,351,901 (GRCm39) |
|
probably null |
Het |
| Aph1b |
T |
C |
9: 66,701,348 (GRCm39) |
|
probably benign |
Het |
| Aspm |
C |
T |
1: 139,390,941 (GRCm39) |
T742I |
probably damaging |
Het |
| Bclaf3 |
A |
G |
X: 158,349,492 (GRCm39) |
H619R |
probably benign |
Het |
| Bltp2 |
T |
A |
11: 78,179,123 (GRCm39) |
|
probably null |
Het |
| Cemip |
A |
T |
7: 83,593,106 (GRCm39) |
L1199H |
probably damaging |
Het |
| Chd2 |
G |
A |
7: 73,096,878 (GRCm39) |
|
probably benign |
Het |
| Clnk |
A |
G |
5: 38,872,341 (GRCm39) |
Y310H |
probably damaging |
Het |
| Crmp1 |
A |
G |
5: 37,441,484 (GRCm39) |
D522G |
probably damaging |
Het |
| Cyth3 |
A |
G |
5: 143,622,298 (GRCm39) |
|
probably benign |
Het |
| Dcbld1 |
T |
A |
10: 52,195,754 (GRCm39) |
Y392N |
probably damaging |
Het |
| Flnc |
T |
C |
6: 29,454,056 (GRCm39) |
F1820L |
probably damaging |
Het |
| Galnt18 |
G |
A |
7: 111,119,322 (GRCm39) |
R385* |
probably null |
Het |
| Gpatch3 |
C |
A |
4: 133,302,479 (GRCm39) |
R137S |
possibly damaging |
Het |
| Gpc6 |
C |
T |
14: 117,861,878 (GRCm39) |
P265S |
probably damaging |
Het |
| Harbi1 |
T |
A |
2: 91,550,952 (GRCm39) |
D308E |
probably benign |
Het |
| Hdhd2 |
G |
A |
18: 77,042,883 (GRCm39) |
|
probably null |
Het |
| Hk1 |
T |
C |
10: 62,111,467 (GRCm39) |
K737E |
possibly damaging |
Het |
| Hnrnpr |
G |
A |
4: 136,063,624 (GRCm39) |
V345M |
probably damaging |
Het |
| Ift56 |
T |
A |
6: 38,380,459 (GRCm39) |
|
probably null |
Het |
| Kalrn |
T |
C |
16: 34,040,610 (GRCm39) |
H944R |
probably damaging |
Het |
| Kdm2a |
A |
T |
19: 4,401,833 (GRCm39) |
C207S |
probably damaging |
Het |
| Kirrel1 |
C |
T |
3: 86,996,458 (GRCm39) |
M380I |
probably null |
Het |
| Krt75 |
C |
T |
15: 101,481,956 (GRCm39) |
G104D |
possibly damaging |
Het |
| Lnpk |
A |
T |
2: 74,352,607 (GRCm39) |
S358R |
probably benign |
Het |
| Map2 |
A |
G |
1: 66,456,022 (GRCm39) |
T1512A |
probably damaging |
Het |
| Marchf10 |
T |
A |
11: 105,287,905 (GRCm39) |
L132F |
probably damaging |
Het |
| Mfrp |
G |
A |
9: 44,016,754 (GRCm39) |
W65* |
probably null |
Het |
| Mgat5 |
A |
G |
1: 127,294,180 (GRCm39) |
D174G |
probably benign |
Het |
| Miga2 |
T |
A |
2: 30,261,237 (GRCm39) |
Y177* |
probably null |
Het |
| Mroh3 |
T |
C |
1: 136,113,213 (GRCm39) |
D747G |
probably damaging |
Het |
| Muc5b |
A |
G |
7: 141,417,571 (GRCm39) |
T3506A |
possibly damaging |
Het |
| Myo7b |
G |
T |
18: 32,107,165 (GRCm39) |
P1277T |
possibly damaging |
Het |
| Naaa |
C |
T |
5: 92,420,413 (GRCm39) |
|
probably null |
Het |
| Ndufs2 |
T |
C |
1: 171,062,889 (GRCm39) |
D410G |
possibly damaging |
Het |
| Or51a25 |
A |
G |
7: 102,372,694 (GRCm39) |
|
probably null |
Het |
| Or5p78 |
T |
A |
7: 108,212,280 (GRCm39) |
Y255* |
probably null |
Het |
| Or7e177 |
A |
G |
9: 20,211,666 (GRCm39) |
I58V |
probably benign |
Het |
| Or8g35 |
A |
G |
9: 39,381,365 (GRCm39) |
I219T |
probably benign |
Het |
| Osbp |
A |
T |
19: 11,956,285 (GRCm39) |
Y409F |
probably benign |
Het |
| Plxnb1 |
T |
A |
9: 108,938,355 (GRCm39) |
V1303D |
possibly damaging |
Het |
| Prkcg |
G |
A |
7: 3,362,263 (GRCm39) |
D246N |
probably damaging |
Het |
| Ranbp17 |
GCCTGGATACTGACC |
GCC |
11: 33,169,203 (GRCm39) |
|
probably benign |
Het |
| Sbf1 |
G |
A |
15: 89,183,731 (GRCm39) |
R1261* |
probably null |
Het |
| Scn4a |
T |
C |
11: 106,235,100 (GRCm39) |
N341S |
probably damaging |
Het |
| Sec61a2 |
C |
A |
2: 5,884,436 (GRCm39) |
|
probably null |
Het |
| Sgcd |
T |
A |
11: 47,246,032 (GRCm39) |
K57* |
probably null |
Het |
| Sinhcaf |
A |
G |
6: 148,827,617 (GRCm39) |
S134P |
possibly damaging |
Het |
| Slc12a5 |
T |
C |
2: 164,835,695 (GRCm39) |
L861P |
probably damaging |
Het |
| Slc6a16 |
A |
G |
7: 44,909,386 (GRCm39) |
D184G |
probably benign |
Het |
| Snx7 |
A |
G |
3: 117,632,639 (GRCm39) |
|
probably benign |
Het |
| Sptbn2 |
A |
G |
19: 4,795,950 (GRCm39) |
I1710V |
probably damaging |
Het |
| Sytl2 |
A |
T |
7: 90,025,289 (GRCm39) |
I426F |
probably benign |
Het |
| Tmem232 |
C |
A |
17: 65,689,628 (GRCm39) |
D496Y |
possibly damaging |
Het |
| Tomm20l |
C |
T |
12: 71,158,516 (GRCm39) |
A58V |
possibly damaging |
Het |
| Ttn |
T |
C |
2: 76,775,618 (GRCm39) |
E1854G |
unknown |
Het |
| Ttn |
A |
G |
2: 76,804,552 (GRCm39) |
V240A |
probably benign |
Het |
| Vmn2r98 |
A |
T |
17: 19,300,887 (GRCm39) |
T630S |
probably benign |
Het |
| Xrcc1 |
G |
C |
7: 24,266,333 (GRCm39) |
A220P |
probably benign |
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 |
|
|
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 |
|
|
| Predicted Primers |
PCR Primer
(F):5'- AAACATGTCTCCTCACCCGATG -3'
(R):5'- TGAGGAAGACTCTAGGAATGCC -3'
Sequencing Primer
(F):5'- TGACTACTGCCCAGAAAGTTGTG -3'
(R):5'- TCTAGGAATGCCACCGACCTG -3'
|
| Posted On |
2015-03-25 |
Incidental Mutation