Incidental Mutation 'IGL01295:Tdp1'
| ID |
73072 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| 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 # |
IGL01295
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
12 |
| Chromosomal Location |
99850776-99921478 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 99857929 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Asparagine to Aspartic acid
at position 163
(N163D)
|
| 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
AA Change: N163D
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: N163D
| 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
AA Change: N163D
PolyPhen 2
Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
|
| SMART Domains |
Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: N163D
| 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
|
| Coding Region Coverage |
|
| 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 3425401B19Rik |
G |
T |
14: 32,383,893 (GRCm39) |
L691I |
possibly damaging |
Het |
| Ano7 |
A |
G |
1: 93,308,200 (GRCm39) |
D77G |
probably benign |
Het |
| Apol10b |
A |
T |
15: 77,469,796 (GRCm39) |
V127E |
probably damaging |
Het |
| Apol11b |
G |
A |
15: 77,522,219 (GRCm39) |
T26M |
probably damaging |
Het |
| Atn1 |
T |
C |
6: 124,726,239 (GRCm39) |
E80G |
probably damaging |
Het |
| Carmil2 |
T |
C |
8: 106,422,148 (GRCm39) |
M1139T |
probably benign |
Het |
| Cd4 |
G |
A |
6: 124,856,341 (GRCm39) |
T50I |
probably benign |
Het |
| Celf5 |
G |
T |
10: 81,302,914 (GRCm39) |
|
probably benign |
Het |
| Chd6 |
G |
A |
2: 160,830,290 (GRCm39) |
|
probably benign |
Het |
| Col12a1 |
A |
T |
9: 79,551,208 (GRCm39) |
V2136E |
probably damaging |
Het |
| Col4a1 |
G |
T |
8: 11,286,075 (GRCm39) |
|
probably benign |
Het |
| Dph1 |
A |
G |
11: 75,071,775 (GRCm39) |
|
probably benign |
Het |
| Dvl2 |
G |
T |
11: 69,900,410 (GRCm39) |
V735F |
possibly damaging |
Het |
| Eif3b |
A |
G |
5: 140,427,495 (GRCm39) |
I709V |
possibly damaging |
Het |
| Elp5 |
C |
T |
11: 69,859,296 (GRCm39) |
|
probably benign |
Het |
| Exd1 |
A |
T |
2: 119,360,560 (GRCm39) |
|
probably benign |
Het |
| Fbxl4 |
C |
A |
4: 22,427,348 (GRCm39) |
R530S |
probably benign |
Het |
| Fmo4 |
A |
T |
1: 162,626,693 (GRCm39) |
D284E |
probably damaging |
Het |
| Fn3krp |
A |
G |
11: 121,312,380 (GRCm39) |
Y31C |
probably damaging |
Het |
| Galnt14 |
G |
T |
17: 73,811,914 (GRCm39) |
Q436K |
probably benign |
Het |
| Gm5114 |
A |
T |
7: 39,057,241 (GRCm39) |
W793R |
probably damaging |
Het |
| Gm9376 |
T |
G |
14: 118,505,059 (GRCm39) |
S164A |
possibly damaging |
Het |
| Gtf2ird2 |
G |
A |
5: 134,221,603 (GRCm39) |
D69N |
probably damaging |
Het |
| Hfm1 |
A |
C |
5: 107,065,472 (GRCm39) |
M69R |
possibly damaging |
Het |
| Ighv9-1 |
A |
C |
12: 114,057,619 (GRCm39) |
S94A |
probably damaging |
Het |
| Ikzf2 |
C |
T |
1: 69,617,146 (GRCm39) |
R67H |
probably benign |
Het |
| Ipcef1 |
A |
T |
10: 6,850,642 (GRCm39) |
F316L |
probably damaging |
Het |
| Kdsr |
A |
G |
1: 106,683,187 (GRCm39) |
V62A |
possibly damaging |
Het |
| Kif23 |
A |
T |
9: 61,839,411 (GRCm39) |
C279S |
possibly damaging |
Het |
| Klf5 |
C |
T |
14: 99,539,157 (GRCm39) |
T110I |
probably benign |
Het |
| Klhl25 |
T |
A |
7: 75,515,620 (GRCm39) |
H175Q |
probably benign |
Het |
| Malrd1 |
G |
A |
2: 16,106,768 (GRCm39) |
|
probably null |
Het |
| Nfatc4 |
T |
C |
14: 56,069,962 (GRCm39) |
V710A |
probably benign |
Het |
| Optn |
G |
A |
2: 5,037,967 (GRCm39) |
T409I |
possibly damaging |
Het |
| Or10j3b |
A |
T |
1: 173,043,440 (GRCm39) |
Y74F |
probably damaging |
Het |
| Or52a5 |
C |
T |
7: 103,427,448 (GRCm39) |
V35I |
probably benign |
Het |
| Pabpc2 |
T |
A |
18: 39,907,082 (GRCm39) |
Y116N |
probably damaging |
Het |
| Pafah1b1 |
G |
T |
11: 74,574,473 (GRCm39) |
R238S |
probably damaging |
Het |
| Pdzd9 |
C |
T |
7: 120,267,618 (GRCm39) |
G66R |
probably damaging |
Het |
| Pih1d1 |
T |
C |
7: 44,809,388 (GRCm39) |
L285P |
probably damaging |
Het |
| Pirb |
G |
A |
7: 3,720,405 (GRCm39) |
P323S |
probably damaging |
Het |
| Pkd1l1 |
A |
G |
11: 8,883,685 (GRCm39) |
F396L |
possibly damaging |
Het |
| Pla2g4d |
G |
A |
2: 120,112,207 (GRCm39) |
T108M |
probably damaging |
Het |
| Plin3 |
T |
C |
17: 56,586,814 (GRCm39) |
Y411C |
probably damaging |
Het |
| Ppfibp2 |
T |
C |
7: 107,346,746 (GRCm39) |
|
probably benign |
Het |
| Prrc2c |
T |
C |
1: 162,510,061 (GRCm39) |
S995G |
probably damaging |
Het |
| Ptf1a |
T |
C |
2: 19,451,429 (GRCm39) |
I253T |
probably damaging |
Het |
| Ptprb |
A |
G |
10: 116,198,553 (GRCm39) |
I1684V |
probably benign |
Het |
| Ptprk |
G |
A |
10: 28,351,174 (GRCm39) |
V556I |
probably benign |
Het |
| Rffl |
A |
T |
11: 82,709,283 (GRCm39) |
C47S |
probably damaging |
Het |
| Rnf17 |
C |
T |
14: 56,700,521 (GRCm39) |
Q569* |
probably null |
Het |
| Shprh |
A |
G |
10: 11,059,612 (GRCm39) |
E1121G |
probably damaging |
Het |
| Slc1a5 |
A |
G |
7: 16,529,787 (GRCm39) |
D402G |
probably damaging |
Het |
| Slc24a3 |
G |
A |
2: 145,458,634 (GRCm39) |
|
probably null |
Het |
| Slc2a13 |
T |
A |
15: 91,234,335 (GRCm39) |
|
probably null |
Het |
| Slc30a8 |
A |
T |
15: 52,169,955 (GRCm39) |
N61Y |
possibly damaging |
Het |
| Slitrk6 |
A |
T |
14: 110,988,868 (GRCm39) |
S280T |
possibly damaging |
Het |
| Smad2 |
G |
A |
18: 76,435,501 (GRCm39) |
A365T |
probably benign |
Het |
| Tcp10b |
C |
T |
17: 13,299,047 (GRCm39) |
P367S |
probably damaging |
Het |
| Thbs1 |
A |
G |
2: 117,948,808 (GRCm39) |
D488G |
possibly damaging |
Het |
| Trappc12 |
C |
T |
12: 28,796,761 (GRCm39) |
S257N |
probably damaging |
Het |
| Treml1 |
T |
C |
17: 48,672,627 (GRCm39) |
|
probably benign |
Het |
| Ugt2b36 |
A |
G |
5: 87,228,744 (GRCm39) |
V234A |
probably damaging |
Het |
| Vmn2r86 |
T |
G |
10: 130,288,895 (GRCm39) |
H202P |
probably damaging |
Het |
| Vmn2r87 |
C |
A |
10: 130,307,878 (GRCm39) |
V787F |
probably damaging |
Het |
| Wbp2nl |
T |
A |
15: 82,190,619 (GRCm39) |
M129K |
probably damaging |
Het |
| Zdhhc15 |
T |
C |
X: 103,588,519 (GRCm39) |
|
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 |
|
|
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 |
|
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 |
|
|
| Posted On |
2013-10-07 |
Incidental Mutation