Incidental Mutation 'R3955:Tdp2'
| ID |
310663 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Tdp2
|
| Ensembl Gene |
ENSMUSG00000035958 |
| Gene Name |
tyrosyl-DNA phosphodiesterase 2 |
| Synonyms |
D13Ertd656e, Ttrap |
| MMRRC Submission |
040832-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly essential
(E-score: 0.705)
|
| Stock # |
R3955 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
13 |
| Chromosomal Location |
25015662-25026136 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 25020082 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Threonine to Isoleucine
at position 123
(T123I)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000035660
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006900]
[ENSMUST00000038039]
[ENSMUST00000223804]
[ENSMUST00000225138]
|
| AlphaFold |
Q9JJX7 |
| PDB Structure |
Mus Musculus Tdp2 Bound to dAMP and Mg2+ [X-RAY DIFFRACTION]
Mus Musculus Tdp2-DNA Substrate Analog (5'-6-aminohexanol) Complex [X-RAY DIFFRACTION]
Mus Musculus Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex at 1.5 Angstroms resolution [X-RAY DIFFRACTION]
Mus Musculus Tdp2 excluded ssDNA complex [X-RAY DIFFRACTION]
Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and Mg2+ [X-RAY DIFFRACTION]
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000006900
|
| SMART Domains |
Protein: ENSMUSP00000006900
Gene: ENSMUSG00000006717
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:4HBT
|
52 |
129 |
1.1e-19 |
PFAM |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000038039
AA Change: T123I
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000035660
Gene: ENSMUSG00000035958
AA Change: T123I
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
9 |
30 |
N/A |
INTRINSIC |
|
Pfam:Exo_endo_phos
|
127 |
359 |
3.9e-20 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130788
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000223804
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224542
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224839
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000225138
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000225490
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226055
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.3%
|
| Validation Efficiency |
100% (56/56) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a superfamily of divalent cation-dependent phosphodiesterases. The encoded protein associates with CD40, tumor necrosis factor (TNF) receptor-75 and TNF receptor associated factors (TRAFs), and inhibits nuclear factor-kappa-B activation. This protein has sequence and structural similarities with APE1 endonuclease, which is involved in both DNA repair and the activation of transcription factors. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutant mice carrying a gene trap insertion into intron 5 but subsequently shown to harbor a partial duplication of the wild-type allele at the ES cell level are born with a normal Mendelian distribution. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 49 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110002E22Rik |
A |
G |
3: 137,773,834 (GRCm39) |
T1008A |
probably benign |
Het |
| Abcc5 |
G |
C |
16: 20,224,293 (GRCm39) |
H97D |
probably damaging |
Het |
| Acbd7 |
T |
C |
2: 3,337,250 (GRCm39) |
S2P |
probably benign |
Het |
| Acta2 |
G |
T |
19: 34,229,126 (GRCm39) |
|
probably benign |
Het |
| Adam2 |
G |
A |
14: 66,295,059 (GRCm39) |
S262L |
probably damaging |
Het |
| Ajm1 |
G |
T |
2: 25,467,583 (GRCm39) |
S776* |
probably null |
Het |
| Ccnq |
C |
A |
11: 78,641,849 (GRCm39) |
E214* |
probably null |
Het |
| Cd69 |
A |
T |
6: 129,245,343 (GRCm39) |
|
probably null |
Het |
| Cpsf3 |
A |
G |
12: 21,363,806 (GRCm39) |
D632G |
probably benign |
Het |
| Dennd5a |
A |
G |
7: 109,504,906 (GRCm39) |
M868T |
probably benign |
Het |
| Dscc1 |
T |
C |
15: 54,946,949 (GRCm39) |
T259A |
probably benign |
Het |
| Dsg4 |
G |
A |
18: 20,582,432 (GRCm39) |
|
probably null |
Het |
| Igfn1 |
A |
G |
1: 135,894,918 (GRCm39) |
Y1883H |
possibly damaging |
Het |
| Insyn1 |
A |
T |
9: 58,406,906 (GRCm39) |
D272V |
probably damaging |
Het |
| Krt20 |
G |
A |
11: 99,323,037 (GRCm39) |
Q262* |
probably null |
Het |
| Lmf1 |
G |
A |
17: 25,873,445 (GRCm39) |
V317M |
probably damaging |
Het |
| Lmod2 |
G |
T |
6: 24,603,870 (GRCm39) |
V282L |
probably benign |
Het |
| Lrrc49 |
A |
G |
9: 60,578,642 (GRCm39) |
I228T |
probably damaging |
Het |
| Matn1 |
G |
A |
4: 130,678,726 (GRCm39) |
|
probably null |
Het |
| Nek7 |
C |
A |
1: 138,462,127 (GRCm39) |
C79F |
probably damaging |
Het |
| Nmt2 |
A |
G |
2: 3,313,535 (GRCm39) |
D132G |
probably benign |
Het |
| Nup210l |
A |
T |
3: 90,100,361 (GRCm39) |
R1462S |
possibly damaging |
Het |
| Obscn |
G |
A |
11: 58,927,594 (GRCm39) |
S6118F |
probably damaging |
Het |
| Or14j6 |
A |
T |
17: 38,214,500 (GRCm39) |
H21L |
probably benign |
Het |
| Or1j21 |
T |
A |
2: 36,683,565 (GRCm39) |
L106M |
probably benign |
Het |
| Or4c12 |
T |
A |
2: 89,774,172 (GRCm39) |
M96L |
possibly damaging |
Het |
| Or51f1 |
A |
G |
7: 102,505,824 (GRCm39) |
C222R |
probably damaging |
Het |
| Or5al1 |
A |
G |
2: 85,990,282 (GRCm39) |
V144A |
probably benign |
Het |
| Plxnb3 |
T |
C |
X: 72,814,826 (GRCm39) |
V1789A |
probably benign |
Het |
| Ptgir |
A |
G |
7: 16,640,794 (GRCm39) |
M29V |
possibly damaging |
Het |
| Qrfprl |
A |
T |
6: 65,430,092 (GRCm39) |
I263L |
possibly damaging |
Het |
| Rab3gap1 |
A |
G |
1: 127,862,254 (GRCm39) |
Q675R |
probably damaging |
Het |
| Rasgrf2 |
A |
G |
13: 92,130,974 (GRCm39) |
S696P |
probably damaging |
Het |
| Sergef |
T |
A |
7: 46,268,176 (GRCm39) |
E210V |
possibly damaging |
Het |
| Sik3 |
C |
A |
9: 46,109,891 (GRCm39) |
N541K |
probably damaging |
Het |
| Slc26a1 |
T |
C |
5: 108,821,448 (GRCm39) |
D147G |
possibly damaging |
Het |
| Tbc1d14 |
G |
A |
5: 36,700,559 (GRCm39) |
R270* |
probably null |
Het |
| Tbc1d9 |
C |
T |
8: 83,960,161 (GRCm39) |
T138I |
probably damaging |
Het |
| Tec |
T |
C |
5: 72,939,520 (GRCm39) |
|
probably null |
Het |
| Tmf1 |
C |
A |
6: 97,153,167 (GRCm39) |
R302L |
probably damaging |
Het |
| Tnip3 |
A |
T |
6: 65,574,379 (GRCm39) |
T137S |
possibly damaging |
Het |
| Trim30d |
C |
T |
7: 104,121,728 (GRCm39) |
G339D |
probably damaging |
Het |
| Tspan32 |
T |
A |
7: 142,560,735 (GRCm39) |
M61K |
probably damaging |
Het |
| Ttc6 |
T |
C |
12: 57,744,238 (GRCm39) |
V1290A |
probably benign |
Het |
| Ttn |
A |
G |
2: 76,799,593 (GRCm39) |
V429A |
possibly damaging |
Het |
| Unc13b |
A |
G |
4: 43,256,834 (GRCm39) |
Y3962C |
probably damaging |
Het |
| Vmn2r95 |
T |
A |
17: 18,660,358 (GRCm39) |
Y257N |
possibly damaging |
Het |
| Zfp677 |
A |
G |
17: 21,618,079 (GRCm39) |
K379E |
possibly damaging |
Het |
| Zfp865 |
T |
A |
7: 5,035,013 (GRCm39) |
D999E |
probably damaging |
Het |
|
| Other mutations in Tdp2 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00775:Tdp2
|
APN |
13 |
25,024,521 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01376:Tdp2
|
APN |
13 |
25,020,932 (GRCm39) |
splice site |
probably null |
|
|
IGL02346:Tdp2
|
APN |
13 |
25,025,335 (GRCm39) |
missense |
possibly damaging |
0.86 |
|
IGL02455:Tdp2
|
APN |
13 |
25,025,245 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R0008:Tdp2
|
UTSW |
13 |
25,025,333 (GRCm39) |
splice site |
probably null |
|
|
R0008:Tdp2
|
UTSW |
13 |
25,025,333 (GRCm39) |
splice site |
probably null |
|
|
R0164:Tdp2
|
UTSW |
13 |
25,022,222 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0164:Tdp2
|
UTSW |
13 |
25,022,222 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0179:Tdp2
|
UTSW |
13 |
25,024,431 (GRCm39) |
missense |
possibly damaging |
0.46 |
|
R1939:Tdp2
|
UTSW |
13 |
25,025,260 (GRCm39) |
missense |
probably benign |
0.07 |
|
R3807:Tdp2
|
UTSW |
13 |
25,015,776 (GRCm39) |
nonsense |
probably null |
|
|
R4943:Tdp2
|
UTSW |
13 |
25,022,248 (GRCm39) |
missense |
probably benign |
0.02 |
|
R5044:Tdp2
|
UTSW |
13 |
25,015,809 (GRCm39) |
missense |
probably benign |
0.00 |
|
R5529:Tdp2
|
UTSW |
13 |
25,022,219 (GRCm39) |
nonsense |
probably null |
|
|
R5827:Tdp2
|
UTSW |
13 |
25,015,836 (GRCm39) |
missense |
probably damaging |
0.99 |
|
R6235:Tdp2
|
UTSW |
13 |
25,024,378 (GRCm39) |
nonsense |
probably null |
|
|
R6326:Tdp2
|
UTSW |
13 |
25,024,540 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7091:Tdp2
|
UTSW |
13 |
25,022,207 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7244:Tdp2
|
UTSW |
13 |
25,025,284 (GRCm39) |
missense |
probably benign |
0.02 |
|
R7341:Tdp2
|
UTSW |
13 |
25,016,059 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8010:Tdp2
|
UTSW |
13 |
25,020,010 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9203:Tdp2
|
UTSW |
13 |
25,020,916 (GRCm39) |
nonsense |
probably null |
|
|
Z1177:Tdp2
|
UTSW |
13 |
25,025,234 (GRCm39) |
missense |
probably benign |
0.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- TAAATGTGAGGGTTCTTGCCTCC -3'
(R):5'- GTGTTCCAATTCACCAAGACCC -3'
Sequencing Primer
(F):5'- ATGTGAGGGTTCTTGCCTCCATAAC -3'
(R):5'- TACTCAGAAGCTGACCTTAAAGTC -3'
|
| Posted On |
2015-04-29 |
Incidental Mutation