Incidental Mutation 'R5457:Tdp1'
| ID |
432839 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tdp1
|
| Ensembl Gene |
ENSMUSG00000021177 |
| Gene Name |
tyrosyl-DNA phosphodiesterase 1 |
| Synonyms |
4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556 |
| MMRRC Submission |
043020-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.220)
|
| Stock # |
R5457 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
12 |
| Chromosomal Location |
99850776-99921478 bp(+) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
C to T
at 99861005 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamine to Stop codon
at position 215
(Q215*)
|
| 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 null
Transcript: ENSMUST00000021594
AA Change: Q215*
|
| SMART Domains |
Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: Q215*
| 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
AA Change: Q215*
|
| SMART Domains |
Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: Q215*
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
13 |
32 |
N/A |
INTRINSIC |
|
Pfam:Tyr-DNA_phospho
|
166 |
583 |
2.4e-142 |
PFAM |
|
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 96.9%
- 20x: 94.3%
|
| 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: 64 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcc12 |
C |
A |
8: 87,236,473 (GRCm39) |
V1114L |
probably benign |
Het |
| Actr5 |
G |
A |
2: 158,477,918 (GRCm39) |
|
probably null |
Het |
| Adcy7 |
T |
C |
8: 89,037,649 (GRCm39) |
L239P |
probably damaging |
Het |
| Afg3l1 |
T |
A |
8: 124,216,707 (GRCm39) |
F315L |
possibly damaging |
Het |
| Agps |
A |
G |
2: 75,684,596 (GRCm39) |
Y188C |
probably benign |
Het |
| Akt1 |
T |
C |
12: 112,623,525 (GRCm39) |
T312A |
probably damaging |
Het |
| Ang2 |
T |
C |
14: 51,433,292 (GRCm39) |
Y30C |
probably damaging |
Het |
| Angpt1 |
G |
A |
15: 42,386,916 (GRCm39) |
T146I |
probably damaging |
Het |
| Atg16l1 |
T |
C |
1: 87,702,813 (GRCm39) |
S288P |
probably damaging |
Het |
| Atp1b2 |
C |
T |
11: 69,493,558 (GRCm39) |
G4R |
probably damaging |
Het |
| Best3 |
T |
C |
10: 116,840,416 (GRCm39) |
F282S |
probably damaging |
Het |
| Cdkn2b |
A |
G |
4: 89,225,391 (GRCm39) |
L98P |
probably damaging |
Het |
| Cenps |
A |
G |
4: 149,216,094 (GRCm39) |
|
probably null |
Het |
| Clec16a |
G |
T |
16: 10,363,396 (GRCm39) |
|
probably null |
Het |
| Cxcl13 |
A |
T |
5: 96,104,830 (GRCm39) |
M1L |
unknown |
Het |
| Dcun1d4 |
A |
T |
5: 73,688,908 (GRCm39) |
E149D |
probably damaging |
Het |
| Dlst |
G |
A |
12: 85,168,914 (GRCm39) |
|
probably null |
Het |
| Dock10 |
C |
A |
1: 80,501,781 (GRCm39) |
C1803F |
probably damaging |
Het |
| Dpp10 |
T |
A |
1: 123,339,539 (GRCm39) |
K329N |
possibly damaging |
Het |
| Drosha |
T |
G |
15: 12,926,115 (GRCm39) |
Y1235D |
probably benign |
Het |
| Eif2s3y |
G |
A |
Y: 1,016,057 (GRCm39) |
G213D |
probably damaging |
Homo |
| Eps8 |
A |
T |
6: 137,489,175 (GRCm39) |
S408T |
probably damaging |
Het |
| Fam171a2 |
T |
C |
11: 102,328,362 (GRCm39) |
D799G |
possibly damaging |
Het |
| Fcho2 |
T |
C |
13: 98,926,275 (GRCm39) |
K103E |
probably damaging |
Het |
| Fcrlb |
T |
C |
1: 170,739,726 (GRCm39) |
T59A |
probably damaging |
Het |
| Fgd4 |
T |
C |
16: 16,279,873 (GRCm39) |
R395G |
probably benign |
Het |
| Gm14496 |
A |
T |
2: 181,639,401 (GRCm39) |
D497V |
probably damaging |
Het |
| Gpt2 |
A |
C |
8: 86,238,967 (GRCm39) |
N267H |
possibly damaging |
Het |
| Grb14 |
A |
T |
2: 64,747,442 (GRCm39) |
C43S |
probably damaging |
Het |
| Hjurp |
T |
TN |
1: 88,194,247 (GRCm39) |
|
probably null |
Het |
| Igkv8-16 |
A |
G |
6: 70,363,689 (GRCm39) |
V111A |
possibly damaging |
Het |
| Klra2 |
T |
A |
6: 131,198,852 (GRCm39) |
S230C |
possibly damaging |
Het |
| Lamb3 |
G |
A |
1: 193,008,302 (GRCm39) |
R245H |
probably damaging |
Het |
| Lamc3 |
A |
G |
2: 31,821,997 (GRCm39) |
E1315G |
probably benign |
Het |
| Lpin2 |
A |
G |
17: 71,550,367 (GRCm39) |
T672A |
probably damaging |
Het |
| Mcoln3 |
T |
A |
3: 145,833,877 (GRCm39) |
I139N |
probably benign |
Het |
| Mcpt8 |
C |
T |
14: 56,319,793 (GRCm39) |
C219Y |
probably benign |
Het |
| Mtcl3 |
A |
C |
10: 29,072,720 (GRCm39) |
I671L |
probably benign |
Het |
| Mug2 |
G |
T |
6: 122,026,688 (GRCm39) |
G541* |
probably null |
Het |
| Myo7b |
G |
T |
18: 32,104,503 (GRCm39) |
|
probably null |
Het |
| Or10j2 |
C |
T |
1: 173,098,141 (GRCm39) |
S133L |
probably benign |
Het |
| Or10j7 |
A |
G |
1: 173,011,180 (GRCm39) |
S274P |
probably damaging |
Het |
| Or5ac22 |
T |
C |
16: 59,135,213 (GRCm39) |
I186V |
probably benign |
Het |
| Or5k8 |
A |
T |
16: 58,644,796 (GRCm39) |
I92N |
probably damaging |
Het |
| Or7e176 |
A |
T |
9: 20,171,574 (GRCm39) |
Y146F |
probably damaging |
Het |
| Pclo |
C |
T |
5: 14,726,157 (GRCm39) |
|
probably benign |
Het |
| Pdk2 |
C |
T |
11: 94,919,408 (GRCm39) |
S289N |
probably damaging |
Het |
| Pex19 |
G |
T |
1: 171,958,245 (GRCm39) |
G75W |
probably damaging |
Het |
| Psma3 |
T |
G |
12: 71,031,339 (GRCm39) |
S26A |
probably benign |
Het |
| Pth1r |
A |
T |
9: 110,555,522 (GRCm39) |
I326N |
possibly damaging |
Het |
| Sbf2 |
T |
C |
7: 109,912,037 (GRCm39) |
T1670A |
probably benign |
Het |
| Scn10a |
A |
G |
9: 119,523,193 (GRCm39) |
Y67H |
probably damaging |
Het |
| Sec16a |
A |
T |
2: 26,330,280 (GRCm39) |
D578E |
probably benign |
Het |
| Spta1 |
C |
T |
1: 174,044,759 (GRCm39) |
A1465V |
probably damaging |
Het |
| Taar9 |
A |
G |
10: 23,985,003 (GRCm39) |
F144L |
probably damaging |
Het |
| Tal1 |
T |
C |
4: 114,925,777 (GRCm39) |
V282A |
probably benign |
Het |
| Tbrg4 |
C |
T |
11: 6,570,947 (GRCm39) |
R175Q |
probably damaging |
Het |
| Thsd4 |
A |
T |
9: 59,887,060 (GRCm39) |
W921R |
probably damaging |
Het |
| Trrap |
A |
G |
5: 144,786,787 (GRCm39) |
E3462G |
probably damaging |
Het |
| Try4 |
T |
C |
6: 41,280,355 (GRCm39) |
S60P |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,541,265 (GRCm39) |
E25580G |
probably damaging |
Het |
| Ttn |
A |
T |
2: 76,776,299 (GRCm39) |
I1581N |
possibly damaging |
Het |
| Vmn2r50 |
T |
C |
7: 9,781,873 (GRCm39) |
T291A |
probably damaging |
Het |
| Zkscan14 |
T |
C |
5: 145,138,169 (GRCm39) |
D106G |
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 |
|
|
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 |
|
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'- CCTTTAACCAGGTGTTCTTCAAG -3'
(R):5'- AGGTAAAACGTGTTGTTCTCAGC -3'
Sequencing Primer
(F):5'- CTTCAAGATGAAGTTTGGGTTGTC -3'
(R):5'- ACTTGTAATCCCAAGGCTGG -3'
|
| Posted On |
2016-10-06 |
Incidental Mutation