Incidental Mutation 'R9521:Tdp1'
| ID |
718903 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tdp1
|
| Ensembl Gene |
ENSMUSG00000021177 |
| Gene Name |
tyrosyl-DNA phosphodiesterase 1 |
| Synonyms |
4921509N21Rik, SCAN1, 2810481F14Rik, E430034L06Rik, Gm40556 |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.215)
|
| Stock # |
R9521 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
12 |
| Chromosomal Location |
99850776-99921478 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 99877906 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 396
(V396A)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000021594
(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: V396A
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000021594
Gene: ENSMUSG00000021177
AA Change: V396A
| 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 damaging
Transcript: ENSMUST00000153627
AA Change: V396A
PolyPhen 2
Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
|
| SMART Domains |
Protein: ENSMUSP00000118656
Gene: ENSMUSG00000021177
AA Change: V396A
| 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: 100.0%
- 3x: 99.9%
- 10x: 99.7%
- 20x: 99.1%
|
| 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: 56 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4833420G17Rik |
T |
C |
13: 119,608,778 (GRCm39) |
|
probably null |
Het |
| A030005K14Rik |
C |
A |
1: 83,036,980 (GRCm39) |
G17V |
unknown |
Het |
| Afap1l1 |
C |
T |
18: 61,879,863 (GRCm39) |
A336T |
probably benign |
Het |
| Akap8 |
C |
T |
17: 32,530,036 (GRCm39) |
R395H |
possibly damaging |
Het |
| Ankrd26 |
G |
A |
6: 118,517,420 (GRCm39) |
A467V |
possibly damaging |
Het |
| Ano9 |
A |
T |
7: 140,682,227 (GRCm39) |
S683T |
probably benign |
Het |
| Aox3 |
C |
A |
1: 58,164,222 (GRCm39) |
A164E |
probably benign |
Het |
| Apc |
T |
C |
18: 34,445,738 (GRCm39) |
I878T |
probably benign |
Het |
| Apcdd1 |
C |
T |
18: 63,055,731 (GRCm39) |
|
probably benign |
Het |
| Atg9b |
T |
C |
5: 24,593,107 (GRCm39) |
N432S |
probably benign |
Het |
| Atp1b3 |
A |
G |
9: 96,227,911 (GRCm39) |
F49L |
probably damaging |
Het |
| Cacnb2 |
A |
T |
2: 14,609,138 (GRCm39) |
|
probably benign |
Het |
| Ccdc180 |
T |
A |
4: 45,916,283 (GRCm39) |
L828Q |
probably null |
Het |
| Chd3 |
C |
T |
11: 69,249,133 (GRCm39) |
R748Q |
probably benign |
Het |
| Chst13 |
G |
A |
6: 90,286,506 (GRCm39) |
P152L |
probably damaging |
Het |
| Cldn18 |
T |
A |
9: 99,581,028 (GRCm39) |
|
probably null |
Het |
| Cmklr1 |
C |
T |
5: 113,752,480 (GRCm39) |
V174I |
probably benign |
Het |
| Cyp2d22 |
A |
T |
15: 82,256,688 (GRCm39) |
V362D |
probably damaging |
Het |
| Dock10 |
T |
C |
1: 80,501,763 (GRCm39) |
K1810R |
probably damaging |
Het |
| Duox1 |
T |
A |
2: 122,159,216 (GRCm39) |
V661E |
possibly damaging |
Het |
| Ercc2 |
G |
A |
7: 19,125,899 (GRCm39) |
R518Q |
probably damaging |
Het |
| Fam186a |
A |
G |
15: 99,841,471 (GRCm39) |
L1591P |
probably damaging |
Het |
| Fam186b |
G |
T |
15: 99,178,419 (GRCm39) |
D302E |
probably benign |
Het |
| Fap |
T |
C |
2: 62,372,500 (GRCm39) |
D326G |
probably benign |
Het |
| Gm42669 |
T |
A |
5: 107,655,892 (GRCm39) |
D135E |
|
Het |
| Keap1 |
A |
T |
9: 21,143,136 (GRCm39) |
V463E |
probably damaging |
Het |
| Mga |
T |
C |
2: 119,794,979 (GRCm39) |
S2888P |
probably damaging |
Het |
| Mgam |
A |
G |
6: 40,722,118 (GRCm39) |
D403G |
probably damaging |
Het |
| Mios |
C |
T |
6: 8,233,171 (GRCm39) |
T773I |
probably benign |
Het |
| Nav3 |
T |
C |
10: 109,835,845 (GRCm39) |
D79G |
possibly damaging |
Het |
| Nxt2 |
C |
T |
X: 141,020,747 (GRCm39) |
A118V |
possibly damaging |
Het |
| Or52d3 |
A |
G |
7: 104,228,855 (GRCm39) |
M1V |
probably null |
Het |
| Or8k35 |
C |
A |
2: 86,424,771 (GRCm39) |
V134F |
|
Het |
| Orc6 |
T |
C |
8: 86,026,615 (GRCm39) |
V20A |
possibly damaging |
Het |
| Peli2 |
A |
G |
14: 48,490,052 (GRCm39) |
K175E |
probably benign |
Het |
| Plec |
C |
G |
15: 76,062,924 (GRCm39) |
R2382P |
possibly damaging |
Het |
| Ppp1r12b |
T |
A |
1: 134,705,063 (GRCm39) |
D875V |
probably damaging |
Het |
| Pramel6 |
T |
A |
2: 87,340,629 (GRCm39) |
C320* |
probably null |
Het |
| Qrich2 |
A |
T |
11: 116,339,208 (GRCm39) |
M26K |
probably damaging |
Het |
| Rapgef1 |
A |
G |
2: 29,624,291 (GRCm39) |
I1006V |
probably benign |
Het |
| Rasgrp3 |
T |
A |
17: 75,821,158 (GRCm39) |
L455Q |
probably null |
Het |
| Scaf8 |
C |
T |
17: 3,248,285 (GRCm39) |
R1203W |
probably damaging |
Het |
| Senp6 |
C |
T |
9: 79,974,687 (GRCm39) |
|
probably benign |
Het |
| Senp7 |
A |
G |
16: 55,992,144 (GRCm39) |
Y700C |
probably damaging |
Het |
| Siglec1 |
A |
G |
2: 130,915,246 (GRCm39) |
|
probably null |
Het |
| Slc12a7 |
G |
A |
13: 73,947,087 (GRCm39) |
V592I |
probably benign |
Het |
| Slfn3 |
T |
C |
11: 83,103,825 (GRCm39) |
V232A |
probably benign |
Het |
| Ticam1 |
T |
C |
17: 56,578,388 (GRCm39) |
T236A |
probably benign |
Het |
| Tob1 |
AGCAGCAGCAGCAGCAGCAGCCGTCATCATCCCAGCCGCCGCCTCCACTACCGCAGCAGCAGCAGCAGCAGCC |
AGCAGCAGCAGCAGCAGCAGCC |
11: 94,105,205 (GRCm39) |
|
probably benign |
Het |
| Ttc21a |
C |
A |
9: 119,787,181 (GRCm39) |
D729E |
probably damaging |
Het |
| Ubtd2 |
T |
C |
11: 32,449,432 (GRCm39) |
I93T |
possibly damaging |
Het |
| Unc45b |
A |
G |
11: 82,808,586 (GRCm39) |
D224G |
probably benign |
Het |
| Usp48 |
G |
A |
4: 137,340,996 (GRCm39) |
G332E |
probably benign |
Het |
| Vmn2r61 |
A |
G |
7: 41,916,626 (GRCm39) |
E413G |
probably damaging |
Het |
| Zfp423 |
A |
T |
8: 88,509,033 (GRCm39) |
L437Q |
probably damaging |
Het |
| Zfp810 |
A |
G |
9: 22,190,227 (GRCm39) |
V227A |
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 |
|
|
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 |
|
Z1177:Tdp1
|
UTSW |
12 |
99,877,892 (GRCm39) |
missense |
probably benign |
|
|
| Predicted Primers |
PCR Primer
(F):5'- CCGTTCAGAGTTTCCTTGTAAG -3'
(R):5'- CTGTTCGAGGTTCCTGAACG -3'
Sequencing Primer
(F):5'- CCTTGTAAGTTAGACATCCTGAAGG -3'
(R):5'- GTTCGAGGTTCCTGAACGACCTC -3'
|
| Posted On |
2022-07-18 |
Incidental Mutation