Incidental Mutation 'R3837:Tdp1'
| ID |
275709 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tdp1
|
| Ensembl Gene |
ENSMUSG00000021177 |
| Gene Name |
tyrosyl-DNA phosphodiesterase 1 |
| Synonyms |
4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556 |
| MMRRC Submission |
040778-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.220)
|
| Stock # |
R3837 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
12 |
| Chromosomal Location |
99850776-99921478 bp(+) (GRCm39) |
| Type of Mutation |
critical splice acceptor site |
| DNA Base Change (assembly) |
A to G
at 99860967 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000118656
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000021594]
[ENSMUST00000021594]
[ENSMUST00000137653]
[ENSMUST00000153627]
[ENSMUST00000153627]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably null
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 |
probably null
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 |
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 null
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 |
probably null
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 |
|
| Meta Mutation Damage Score |
0.9590 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.5%
|
| Validation Efficiency |
98% (52/53) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700028I16Rik |
A |
G |
10: 82,648,219 (GRCm39) |
|
noncoding transcript |
Het |
| 4930474N05Rik |
G |
A |
14: 35,817,435 (GRCm39) |
G112S |
probably benign |
Het |
| Adam24 |
T |
C |
8: 41,133,584 (GRCm39) |
S351P |
probably benign |
Het |
| Amigo2 |
T |
C |
15: 97,143,196 (GRCm39) |
I409V |
probably damaging |
Het |
| Arhgef25 |
T |
C |
10: 127,025,605 (GRCm39) |
T12A |
probably benign |
Het |
| Atg10 |
A |
T |
13: 91,085,499 (GRCm39) |
I150K |
probably damaging |
Het |
| AW551984 |
T |
C |
9: 39,509,204 (GRCm39) |
|
probably benign |
Het |
| Cdc20b |
T |
C |
13: 113,220,542 (GRCm39) |
W432R |
probably damaging |
Het |
| Cdh9 |
G |
T |
15: 16,823,524 (GRCm39) |
E169* |
probably null |
Het |
| Col28a1 |
C |
T |
6: 8,014,601 (GRCm39) |
V935M |
possibly damaging |
Het |
| Col6a3 |
T |
C |
1: 90,707,803 (GRCm39) |
N1948D |
unknown |
Het |
| Dnajb2 |
G |
A |
1: 75,218,124 (GRCm39) |
|
probably null |
Het |
| Fam13c |
C |
T |
10: 70,378,478 (GRCm39) |
S336L |
probably damaging |
Het |
| Fn1 |
A |
T |
1: 71,692,314 (GRCm39) |
|
probably null |
Het |
| Fryl |
T |
C |
5: 73,228,608 (GRCm39) |
T1708A |
probably benign |
Het |
| Gcnt4 |
A |
T |
13: 97,083,522 (GRCm39) |
R273* |
probably null |
Het |
| Gldc |
T |
A |
19: 30,096,075 (GRCm39) |
|
probably benign |
Het |
| Glra2 |
C |
T |
X: 164,072,612 (GRCm39) |
V85I |
probably benign |
Het |
| Gm11562 |
A |
G |
11: 99,511,026 (GRCm39) |
I58T |
possibly damaging |
Het |
| Gpam |
T |
C |
19: 55,068,890 (GRCm39) |
N450S |
probably benign |
Het |
| Hivep2 |
C |
A |
10: 14,004,713 (GRCm39) |
T437K |
probably benign |
Het |
| Hmcn2 |
T |
C |
2: 31,303,419 (GRCm39) |
L3020P |
probably damaging |
Het |
| Hmgcr |
A |
G |
13: 96,795,597 (GRCm39) |
I324T |
probably benign |
Het |
| Itih1 |
T |
A |
14: 30,657,785 (GRCm39) |
N429Y |
probably damaging |
Het |
| Lamtor1 |
T |
C |
7: 101,559,315 (GRCm39) |
|
probably null |
Het |
| Lrrd1 |
A |
T |
5: 3,900,204 (GRCm39) |
I170L |
possibly damaging |
Het |
| Magi2 |
G |
A |
5: 20,420,466 (GRCm39) |
D301N |
probably benign |
Het |
| Mid1ip1 |
T |
C |
X: 10,584,620 (GRCm39) |
V51A |
possibly damaging |
Het |
| Mmrn1 |
G |
A |
6: 60,921,831 (GRCm39) |
S96N |
probably benign |
Het |
| Mrc2 |
G |
A |
11: 105,239,257 (GRCm39) |
|
probably null |
Het |
| Msh3 |
C |
A |
13: 92,491,366 (GRCm39) |
G15C |
probably damaging |
Het |
| Myl12b |
C |
A |
17: 71,281,480 (GRCm39) |
E120* |
probably null |
Het |
| Myo3a |
T |
G |
2: 22,455,121 (GRCm39) |
|
probably benign |
Het |
| Nagk |
A |
T |
6: 83,778,139 (GRCm39) |
H245L |
possibly damaging |
Het |
| Nap1l1 |
T |
A |
10: 111,331,183 (GRCm39) |
|
probably null |
Het |
| Nlrc5 |
A |
G |
8: 95,237,929 (GRCm39) |
|
probably benign |
Het |
| Ogfrl1 |
G |
A |
1: 23,409,041 (GRCm39) |
T395I |
probably benign |
Het |
| Polr1b |
T |
A |
2: 128,961,027 (GRCm39) |
F662Y |
possibly damaging |
Het |
| Rrbp1 |
T |
C |
2: 143,831,478 (GRCm39) |
K230E |
probably damaging |
Het |
| Shld2 |
A |
G |
14: 33,971,142 (GRCm39) |
V581A |
probably damaging |
Het |
| Skap2 |
C |
T |
6: 51,886,279 (GRCm39) |
|
probably null |
Het |
| Skint5 |
A |
T |
4: 113,797,938 (GRCm39) |
M215K |
probably damaging |
Het |
| Slc17a4 |
C |
T |
13: 24,085,752 (GRCm39) |
R387H |
probably benign |
Het |
| Tlr3 |
G |
A |
8: 45,849,976 (GRCm39) |
L898F |
probably damaging |
Het |
| Tmem210 |
A |
G |
2: 25,178,444 (GRCm39) |
E35G |
possibly damaging |
Het |
| Tpbg |
T |
C |
9: 85,725,167 (GRCm39) |
|
probably benign |
Het |
| Tubb2a |
G |
T |
13: 34,259,294 (GRCm39) |
N165K |
probably benign |
Het |
| Usp14 |
A |
G |
18: 10,024,532 (GRCm39) |
|
probably null |
Het |
| Vmn1r33 |
A |
T |
6: 66,588,701 (GRCm39) |
D284E |
possibly damaging |
Het |
| Wnk1 |
T |
C |
6: 119,927,004 (GRCm39) |
E1265G |
probably damaging |
Het |
| Yme1l1 |
A |
T |
2: 23,081,092 (GRCm39) |
T455S |
possibly damaging |
Het |
| Zfp111 |
T |
C |
7: 23,898,891 (GRCm39) |
N241S |
possibly 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 |
|
|
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'- TCACGTTAGGGAAACTTTGTAATCCTG -3'
(R):5'- TGCTTACAATGATGTCAAGCG -3'
Sequencing Primer
(F):5'- CCTTAGAACCTCTTTGGGAATCTGG -3'
(R):5'- TACAATGATGTCAAGCGAAATATGG -3'
|
| Posted On |
2015-04-06 |
Incidental Mutation