Incidental Mutation 'R1692:Tdp1'
| ID |
191886 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tdp1
|
| Ensembl Gene |
ENSMUSG00000021177 |
| Gene Name |
tyrosyl-DNA phosphodiesterase 1 |
| Synonyms |
4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556 |
| MMRRC Submission |
039725-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.220)
|
| Stock # |
R1692 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
12 |
| Chromosomal Location |
99850776-99921478 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 99921260 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Proline to Serine
at position 599
(P599S)
|
| 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: P599S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: P599S
| 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: ENSMUST00000128739
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000153627
AA Change: P599S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: P599S
| 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: 96.6%
- 20x: 93.5%
|
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam12 |
A |
T |
7: 133,489,673 (GRCm39) |
*582R |
probably null |
Het |
| Agfg2 |
A |
G |
5: 137,662,633 (GRCm39) |
Y145H |
probably damaging |
Het |
| Aldh1a1 |
C |
T |
19: 20,608,182 (GRCm39) |
P335S |
probably damaging |
Het |
| Amotl1 |
T |
C |
9: 14,463,018 (GRCm39) |
R732G |
possibly damaging |
Het |
| Ankef1 |
A |
T |
2: 136,392,346 (GRCm39) |
I512F |
probably benign |
Het |
| Atg9a |
A |
T |
1: 75,166,999 (GRCm39) |
D17E |
probably benign |
Het |
| Atpsckmt |
T |
C |
15: 31,602,297 (GRCm39) |
|
probably null |
Het |
| Brd8 |
A |
T |
18: 34,742,886 (GRCm39) |
S253R |
probably damaging |
Het |
| Ccnq |
T |
C |
11: 78,642,157 (GRCm39) |
E111G |
probably benign |
Het |
| Cd79a |
T |
A |
7: 24,600,881 (GRCm39) |
M192K |
probably damaging |
Het |
| Clcn1 |
T |
G |
6: 42,290,032 (GRCm39) |
F822L |
possibly damaging |
Het |
| Dnajb12 |
A |
G |
10: 59,732,199 (GRCm39) |
Y346C |
probably damaging |
Het |
| Erbb3 |
A |
G |
10: 128,407,594 (GRCm39) |
I918T |
probably benign |
Het |
| Fbxw20 |
G |
T |
9: 109,050,777 (GRCm39) |
T377K |
possibly damaging |
Het |
| Fry |
A |
G |
5: 150,293,692 (GRCm39) |
I462V |
probably damaging |
Het |
| Gmip |
A |
G |
8: 70,266,553 (GRCm39) |
N251S |
probably benign |
Het |
| Gpx1 |
A |
G |
9: 108,216,674 (GRCm39) |
T55A |
possibly damaging |
Het |
| Hmcn2 |
T |
C |
2: 31,340,856 (GRCm39) |
V4443A |
possibly damaging |
Het |
| Kdm4d |
A |
T |
9: 14,375,807 (GRCm39) |
I17K |
probably benign |
Het |
| Lamc3 |
A |
G |
2: 31,811,793 (GRCm39) |
S927G |
probably null |
Het |
| Map7d1 |
G |
A |
4: 126,136,101 (GRCm39) |
P36S |
probably damaging |
Het |
| Mfsd13a |
C |
A |
19: 46,360,515 (GRCm39) |
H356N |
probably benign |
Het |
| Mtap |
C |
T |
4: 89,095,151 (GRCm39) |
R268C |
probably benign |
Het |
| Myo1a |
C |
T |
10: 127,555,203 (GRCm39) |
|
probably null |
Het |
| Myom3 |
T |
C |
4: 135,502,862 (GRCm39) |
L313P |
probably benign |
Het |
| Nrxn2 |
T |
A |
19: 6,569,298 (GRCm39) |
V1391E |
probably damaging |
Het |
| Otoa |
A |
C |
7: 120,690,774 (GRCm39) |
Q3P |
probably damaging |
Het |
| Phldb1 |
T |
C |
9: 44,626,717 (GRCm39) |
E576G |
probably damaging |
Het |
| Pigw |
A |
C |
11: 84,767,892 (GRCm39) |
L479R |
probably damaging |
Het |
| Pip5k1a |
A |
G |
3: 94,971,041 (GRCm39) |
I507T |
probably benign |
Het |
| Ppp4r3b |
T |
A |
11: 29,138,123 (GRCm39) |
I157N |
probably benign |
Het |
| Rrm2b |
G |
A |
15: 37,927,566 (GRCm39) |
R115* |
probably null |
Het |
| Sall1 |
C |
T |
8: 89,755,028 (GRCm39) |
S1317N |
probably benign |
Het |
| Serpinb6b |
T |
G |
13: 33,158,978 (GRCm39) |
F179V |
probably damaging |
Het |
| Slc4a8 |
T |
A |
15: 100,698,454 (GRCm39) |
F648I |
probably damaging |
Het |
| Slc5a7 |
T |
C |
17: 54,588,754 (GRCm39) |
T298A |
probably damaging |
Het |
| Slit3 |
T |
C |
11: 35,550,171 (GRCm39) |
L830P |
probably damaging |
Het |
| Smarcc1 |
T |
A |
9: 110,003,072 (GRCm39) |
N387K |
possibly damaging |
Het |
| Tanc2 |
C |
T |
11: 105,748,326 (GRCm39) |
T486I |
probably benign |
Het |
| Tmem33 |
A |
G |
5: 67,425,897 (GRCm39) |
D38G |
probably null |
Het |
| Uvrag |
C |
T |
7: 98,653,870 (GRCm39) |
R247Q |
probably benign |
Het |
| Vars1 |
T |
C |
17: 35,232,701 (GRCm39) |
V875A |
probably damaging |
Het |
| Vcl |
A |
G |
14: 21,074,250 (GRCm39) |
E879G |
probably damaging |
Het |
| Vmn1r231 |
C |
T |
17: 21,110,871 (GRCm39) |
V15I |
probably benign |
Het |
| Zfp609 |
T |
C |
9: 65,702,593 (GRCm39) |
T20A |
probably damaging |
Het |
| Zfp747l1 |
G |
T |
7: 126,983,652 (GRCm39) |
H483Q |
possibly damaging |
Het |
| Zfp959 |
T |
A |
17: 56,205,299 (GRCm39) |
H445Q |
probably damaging |
Het |
| Zmiz2 |
T |
A |
11: 6,350,795 (GRCm39) |
V515E |
probably damaging |
Het |
| Zmym5 |
G |
A |
14: 57,041,650 (GRCm39) |
T151M |
probably damaging |
Het |
| Zxdc |
C |
T |
6: 90,355,933 (GRCm39) |
Q481* |
probably null |
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 |
|
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 |
|
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'- CTTCACAACTTGGAGAGCTGAGCAC -3'
(R):5'- TTTCTGCTGCCAGCAACTGTAGCC -3'
Sequencing Primer
(F):5'- TGAGCACCAAATGCTTTGAC -3'
(R):5'- ACTTTTGCGAGGAGTCCTGT -3'
|
| Posted On |
2014-05-14 |
Incidental Mutation