Incidental Mutation 'R4209:Tdp1'
| ID |
319086 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tdp1
|
| Ensembl Gene |
ENSMUSG00000021177 |
| Gene Name |
tyrosyl-DNA phosphodiesterase 1 |
| Synonyms |
4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556 |
| MMRRC Submission |
041038-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.220)
|
| Stock # |
R4209 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
12 |
| Chromosomal Location |
99850776-99921478 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 99864588 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Alanine to Glutamic Acid
at position 243
(A243E)
|
| 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: A243E
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: A243E
| 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: ENSMUST00000151019
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000153627
AA Change: A243E
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: A243E
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
13 |
32 |
N/A |
INTRINSIC |
|
Pfam:Tyr-DNA_phospho
|
166 |
583 |
2.4e-142 |
PFAM |
|
| Meta Mutation Damage Score |
0.6467 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.4%
|
| Validation Efficiency |
98% (45/46) |
| 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 |
|---|
| Aadacl2fm3 |
A |
T |
3: 59,784,577 (GRCm39) |
Y350F |
probably damaging |
Het |
| Ahnak |
G |
A |
19: 8,979,964 (GRCm39) |
G416D |
probably damaging |
Het |
| Ap3b2 |
C |
A |
7: 81,126,884 (GRCm39) |
A289S |
probably benign |
Het |
| Arhgap23 |
C |
A |
11: 97,345,322 (GRCm39) |
T657K |
probably damaging |
Het |
| Bcl9 |
A |
G |
3: 97,117,269 (GRCm39) |
L475P |
probably damaging |
Het |
| Bean1 |
T |
A |
8: 104,940,566 (GRCm39) |
M1K |
probably null |
Het |
| Cand1 |
T |
A |
10: 119,047,463 (GRCm39) |
I676F |
probably benign |
Het |
| Casp3 |
G |
T |
8: 47,088,423 (GRCm39) |
D107Y |
probably damaging |
Het |
| Cops4 |
T |
A |
5: 100,695,352 (GRCm39) |
|
probably benign |
Het |
| Dchs1 |
A |
T |
7: 105,415,397 (GRCm39) |
D626E |
probably damaging |
Het |
| Dpysl2 |
T |
C |
14: 67,052,926 (GRCm39) |
S308G |
probably damaging |
Het |
| Fezf1 |
T |
C |
6: 23,246,616 (GRCm39) |
K323E |
probably damaging |
Het |
| Gm10272 |
T |
C |
10: 77,542,665 (GRCm39) |
V69A |
possibly damaging |
Het |
| Gtf2f1 |
A |
G |
17: 57,318,003 (GRCm39) |
V11A |
probably benign |
Het |
| Hnf4a |
T |
C |
2: 163,410,809 (GRCm39) |
S378P |
probably benign |
Het |
| Inpp5j |
T |
G |
11: 3,451,107 (GRCm39) |
H514P |
probably damaging |
Het |
| Irf8 |
T |
A |
8: 121,480,208 (GRCm39) |
Y149N |
probably damaging |
Het |
| Kel |
C |
T |
6: 41,675,359 (GRCm39) |
W297* |
probably null |
Het |
| Man1c1 |
G |
C |
4: 134,430,749 (GRCm39) |
P11R |
probably damaging |
Het |
| Mcpt8 |
G |
A |
14: 56,321,375 (GRCm39) |
H30Y |
probably damaging |
Het |
| Mycl |
G |
T |
4: 122,893,715 (GRCm39) |
V172L |
possibly damaging |
Het |
| Pcgf5 |
C |
A |
19: 36,414,740 (GRCm39) |
N26K |
possibly damaging |
Het |
| Ppp2r2a |
A |
G |
14: 67,266,328 (GRCm39) |
L111S |
probably damaging |
Het |
| Prdm2 |
T |
C |
4: 142,861,007 (GRCm39) |
D761G |
probably damaging |
Het |
| Sec11a |
A |
T |
7: 80,584,790 (GRCm39) |
I49N |
probably damaging |
Het |
| Sesn3 |
T |
C |
9: 14,217,505 (GRCm39) |
I30T |
probably benign |
Het |
| Slc22a21 |
A |
G |
11: 53,846,881 (GRCm39) |
S331P |
probably benign |
Het |
| Slc38a3 |
T |
G |
9: 107,532,547 (GRCm39) |
S358R |
possibly damaging |
Het |
| Slc9a5 |
A |
G |
8: 106,085,103 (GRCm39) |
N535D |
possibly damaging |
Het |
| Spns2 |
T |
C |
11: 72,345,012 (GRCm39) |
D492G |
probably benign |
Het |
| Tcn2 |
T |
C |
11: 3,872,114 (GRCm39) |
K338E |
possibly damaging |
Het |
| Tex16 |
T |
A |
X: 111,030,640 (GRCm39) |
D1046E |
probably benign |
Het |
| Tmem120a |
T |
C |
5: 135,764,559 (GRCm39) |
N340S |
probably benign |
Het |
| Tnik |
A |
T |
3: 28,413,214 (GRCm39) |
|
probably benign |
Het |
| Trim36 |
A |
G |
18: 46,329,191 (GRCm39) |
L71P |
probably benign |
Het |
| Tube1 |
A |
G |
10: 39,020,930 (GRCm39) |
|
probably null |
Het |
| Urgcp |
C |
A |
11: 5,665,878 (GRCm39) |
G820V |
probably damaging |
Het |
| Veph1 |
A |
T |
3: 66,151,967 (GRCm39) |
L154Q |
probably damaging |
Het |
| Vmn1r113 |
T |
C |
7: 20,521,535 (GRCm39) |
V109A |
probably benign |
Het |
| Vmn1r152 |
A |
T |
7: 22,223,004 (GRCm39) |
T205S |
possibly damaging |
Het |
| Wdsub1 |
G |
A |
2: 59,707,149 (GRCm39) |
P28S |
probably damaging |
Het |
| Ybx2 |
G |
T |
11: 69,826,767 (GRCm39) |
|
probably benign |
Het |
| Zfyve1 |
A |
T |
12: 83,621,909 (GRCm39) |
V162E |
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 |
|
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'- GGAAGTAATGAGTGAGCCCC -3'
(R):5'- GGTGGCATGAGTTACTTGAGCC -3'
Sequencing Primer
(F):5'- AGTCACTGCATGATGTCAGC -3'
(R):5'- GCATGAGTTACTTGAGCCACAATAAG -3'
|
| Posted On |
2015-06-10 |
Incidental Mutation