Incidental Mutation 'IGL02346:Tdp2'
ID |
289282 |
Institutional Source |
Australian Phenomics Network
(link to record)
|
Gene Symbol |
Tdp2
|
Ensembl Gene |
ENSMUSG00000035958 |
Gene Name |
tyrosyl-DNA phosphodiesterase 2 |
Synonyms |
D13Ertd656e, Ttrap |
Accession Numbers |
|
Essential gene? |
Possibly essential
(E-score: 0.674)
|
Stock # |
IGL02346
|
Quality Score |
|
Status
|
|
Chromosome |
13 |
Chromosomal Location |
25015662-25026136 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 25025335 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Alanine
at position 368
(V368A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000035660
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000006893]
[ENSMUST00000038039]
[ENSMUST00000141572]
[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: ENSMUST00000006893
|
SMART Domains |
Protein: ENSMUSP00000006893 Gene: ENSMUSG00000006711
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
Blast:MANEC
|
23 |
102 |
3e-44 |
BLAST |
low complexity region
|
236 |
270 |
N/A |
INTRINSIC |
FN3
|
332 |
427 |
3.43e1 |
SMART |
PKD
|
345 |
436 |
3.96e0 |
SMART |
FN3
|
435 |
521 |
3.08e1 |
SMART |
PKD
|
444 |
533 |
7.12e-10 |
SMART |
PKD
|
539 |
629 |
1.46e-6 |
SMART |
PKD
|
630 |
723 |
6.75e-11 |
SMART |
FN3
|
634 |
711 |
5.1e1 |
SMART |
FN3
|
728 |
808 |
9.15e1 |
SMART |
PKD
|
729 |
820 |
4.38e-10 |
SMART |
transmembrane domain
|
965 |
987 |
N/A |
INTRINSIC |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000038039
AA Change: V368A
PolyPhen 2
Score 0.858 (Sensitivity: 0.83; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000035660 Gene: ENSMUSG00000035958 AA Change: V368A
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: ENSMUST00000141572
|
SMART Domains |
Protein: ENSMUSP00000116004 Gene: ENSMUSG00000006711
Domain | Start | End | E-Value | Type |
signal peptide
|
1 |
22 |
N/A |
INTRINSIC |
Blast:MANEC
|
23 |
102 |
2e-44 |
BLAST |
low complexity region
|
236 |
270 |
N/A |
INTRINSIC |
FN3
|
332 |
427 |
3.43e1 |
SMART |
PKD
|
345 |
436 |
3.96e0 |
SMART |
FN3
|
435 |
521 |
3.08e1 |
SMART |
PKD
|
444 |
533 |
7.12e-10 |
SMART |
PKD
|
539 |
629 |
1.46e-6 |
SMART |
PKD
|
630 |
723 |
6.75e-11 |
SMART |
FN3
|
634 |
711 |
5.1e1 |
SMART |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000224542
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000225138
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000225490
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000226055
|
Coding Region Coverage |
|
Validation Efficiency |
|
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: 41 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acacb |
A |
T |
5: 114,376,760 (GRCm39) |
I1948F |
probably damaging |
Het |
Adgre1 |
T |
C |
17: 57,750,919 (GRCm39) |
V531A |
probably benign |
Het |
Ano3 |
A |
T |
2: 110,601,271 (GRCm39) |
|
probably benign |
Het |
Api5 |
A |
T |
2: 94,257,875 (GRCm39) |
F125I |
possibly damaging |
Het |
Arhgap21 |
A |
G |
2: 20,884,762 (GRCm39) |
|
probably benign |
Het |
Atp13a5 |
T |
A |
16: 29,146,554 (GRCm39) |
K247* |
probably null |
Het |
Col9a1 |
C |
T |
1: 24,262,690 (GRCm39) |
A585V |
probably damaging |
Het |
Eef1akmt3 |
A |
G |
10: 126,868,805 (GRCm39) |
V223A |
probably benign |
Het |
Eml1 |
T |
C |
12: 108,503,700 (GRCm39) |
S766P |
possibly damaging |
Het |
Fam13b |
G |
T |
18: 34,595,158 (GRCm39) |
A402E |
probably benign |
Het |
Gad2 |
A |
G |
2: 22,519,951 (GRCm39) |
|
probably benign |
Het |
Gbf1 |
A |
G |
19: 46,274,369 (GRCm39) |
E1859G |
probably damaging |
Het |
Gli3 |
T |
G |
13: 15,898,278 (GRCm39) |
V786G |
probably damaging |
Het |
Gm5592 |
A |
G |
7: 40,938,889 (GRCm39) |
S724G |
probably damaging |
Het |
Hgs |
A |
G |
11: 120,373,377 (GRCm39) |
Y634C |
probably damaging |
Het |
Hoxa3 |
T |
A |
6: 52,147,579 (GRCm39) |
|
probably benign |
Het |
Id4 |
C |
A |
13: 48,415,189 (GRCm39) |
Y72* |
probably null |
Het |
Il5ra |
T |
A |
6: 106,719,619 (GRCm39) |
E71D |
probably benign |
Het |
Kcnh4 |
G |
A |
11: 100,647,768 (GRCm39) |
T168M |
possibly damaging |
Het |
Kdm3b |
A |
T |
18: 34,967,291 (GRCm39) |
I1699L |
probably damaging |
Het |
Madd |
A |
G |
2: 90,992,836 (GRCm39) |
Y1048H |
probably damaging |
Het |
Mix23 |
T |
C |
16: 35,912,205 (GRCm39) |
V87A |
probably damaging |
Het |
Nr2f1 |
C |
A |
13: 78,343,527 (GRCm39) |
V246L |
probably damaging |
Het |
Oas2 |
A |
T |
5: 120,874,153 (GRCm39) |
I560N |
probably benign |
Het |
Or1j17 |
A |
T |
2: 36,578,016 (GRCm39) |
M1L |
probably benign |
Het |
Or1m1 |
T |
C |
9: 18,666,065 (GRCm39) |
I289V |
probably damaging |
Het |
Or8g19 |
T |
C |
9: 39,055,939 (GRCm39) |
L181P |
probably damaging |
Het |
Pclo |
A |
G |
5: 14,727,552 (GRCm39) |
|
probably benign |
Het |
Pdss2 |
T |
C |
10: 43,221,639 (GRCm39) |
F184L |
possibly damaging |
Het |
Prpf39 |
C |
T |
12: 65,104,510 (GRCm39) |
T525I |
probably benign |
Het |
Ralgps1 |
A |
T |
2: 33,047,782 (GRCm39) |
|
probably null |
Het |
Rasal3 |
A |
G |
17: 32,618,323 (GRCm39) |
W161R |
probably damaging |
Het |
Sema5b |
T |
A |
16: 35,470,125 (GRCm39) |
V329D |
probably damaging |
Het |
Serpinb9g |
A |
T |
13: 33,670,514 (GRCm39) |
M1L |
probably benign |
Het |
Sptb |
C |
T |
12: 76,667,788 (GRCm39) |
D770N |
probably damaging |
Het |
Uggt1 |
A |
G |
1: 36,218,751 (GRCm39) |
S59P |
probably benign |
Het |
Vmn2r130 |
T |
C |
17: 23,280,501 (GRCm39) |
V54A |
possibly damaging |
Het |
Vmn2r9 |
T |
A |
5: 108,990,850 (GRCm39) |
N837I |
probably benign |
Het |
Wdr7 |
A |
T |
18: 63,998,407 (GRCm39) |
E1118V |
probably benign |
Het |
Wwox |
A |
G |
8: 115,438,858 (GRCm39) |
H308R |
probably benign |
Het |
Zbtb41 |
C |
A |
1: 139,374,838 (GRCm39) |
P766Q |
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 |
|
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 |
|
R3955:Tdp2
|
UTSW |
13 |
25,020,082 (GRCm39) |
missense |
probably benign |
0.00 |
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 |
|
Posted On |
2015-04-16 |